REVIEW | doi:10.20944/preprints202306.0166.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Raman, IR, spectroscopy, phytochrome, tetrapyrrole, photoswitch
Online: 2 June 2023 (09:01:39 CEST)
Phytochromes are biological photoswitches that translate light into a physiological function. Spec-troscopic techniques are essential tools in molecular research on these photoreceptors. This review is directed to summarize how resonance Raman and IR spectroscopy contributed to the under-standing of structure, dynamics, and reaction mechanism of phytochromes, outlining the substan-tial experimental and theoretical challenges and describing the strategies to master them. It is shown that the potential of the various vibrational spectroscopic techniques can be most efficient-ly exploited in integral approaches by combination with theoretical methods as well as other ex-perimental techniques.
ARTICLE | doi:10.20944/preprints202306.0032.v1
Subject: Biology And Life Sciences, Biophysics Keywords: BACE1; Alzheimer's disease; molecular dynamics simulations, SIE; MM-GBSA
Online: 1 June 2023 (04:57:06 CEST)
The β-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design toward treatment of Alzheimer's disease (AD). In this study, three separate molecular dynamics (MD) simulations and calculations of binding free energies were carried out to comparatively probe identification mechanism of BACE1 on three inhibitors 60W, 954 and 60X. The analyses on MD trajectories indicate that the presence of three inhibitors influences structural stability, flexibility and internal dynamics of BACE1. Binding free energies calculated by using solvated interaction energy (SIE) and molecular mechanics generalized Born surface area (MM-GBSA) methods reveal that the hydrophobic interactions provide decisive forces for inhibitor-BACE1 binding. The calculations of residue-based free energy decomposition suggest that the sidechains of residues L91, D93, S96, V130, Q134, W137, F169 and I179 play key roles in inhibitor-BACE1 binding, which provides a direction for future drug design toward treatment of AD.
ARTICLE | doi:10.20944/preprints202305.2030.v1
Subject: Biology And Life Sciences, Biophysics Keywords: graphene chip; surface topography; photoresist residues; low-frequency noise
Online: 30 May 2023 (03:57:20 CEST)
Graphene quality for use in biosensors was assessed in fabricated chips by a set of methods that includes atomic force microscopy (AFM), Raman spectroscopy, and low-frequency noise. It is shown that local areas of residues on the graphene surface, which arisen due to the interaction of graphene with a photoresist at the initial stage of chips development, leads to a spread of chips resistance (R) within 1-10 kΩ and to an increase in the root mean square (RMS) roughness up to 10 times that can significantly impair reproducibility of graphene parameters in biosensors chips. It was observed that the control of the photoresist residues after photolithography (PLG) by AFM and subsequent additional cleaning allow reducing the spread of R values in chips to 1–1.6 kΩ and obtaining RMS roughness similar to the roughness in pristine graphene before PLG. Monitoring of the spectral density of low-frequency voltage fluctuation (SU), which provides integral information about the defect system and quality of the material, makes it possible to identify chips with low graphene quality and with inhomogeneously distributed compressive stresses areas by the type of frequency dependence SU (f).
REVIEW | doi:10.20944/preprints202305.1930.v1
Subject: Biology And Life Sciences, Biophysics Keywords: low-frequency magnetic fields; ion parametric resonance; calcium; cryptochrome; mitochondria; biochemical oscillations
Online: 26 May 2023 (11:27:48 CEST)
The review presents the most developed by date hypotheses on the mechanisms of the influence of low-frequency magnetic fields (LFMF) on organisms. Biophysical models that explain the resonance-like responses of biological systems to LFMF with a specific frequency and amplitude are described. Two groups can be distinguished among these models: one considers ions-cofactors of proteins as the primary targets for the LFMF influence, and the other regards the magnetic moments of particles in biomolecules. Attention is paid to the dependence of resonance-like LFMF effects on the cell type. A radical-pair mechanism of the magnetic field's influence on biochemical processes is described with the example of cryptochrome. Conditions for this mechanism's applicability to explain the biological effects of LFMF are given. A model of the influence of LFMF on radical pairs in biochemical oscillators, which can explain the frequency-amplitude efficiency windows of LFMF, is proposed.
ARTICLE | doi:10.20944/preprints202305.1868.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Plasmonic magnetoliposomes; Dual hyperthermia; Bovine lactoferrin; Cytotoxicity; Biological activity
Online: 26 May 2023 (05:40:34 CEST)
Bovine lactoferrin (bLf) is a milk-derived protein that exhibits multiple biological activities and has been explored towards different therapeutic applications. Since this molecule is susceptible to degradation and some of its properties depend on its tertiary structure, the encapsulation of bLf in stimuli-responsive therapeutic formulations provides an added value to potentiate its biological activities when administered. Plasmonic magnetoliposomes emerge as promising nanosystems for dual hyperthermia (magneto-photothermia) and local therapy, since the combination of magnetic and gold nanoparticles (NPs) in a single nanosystem (multifunctional liposomes) enables the targeting and controlled release of encapsulated drugs. In this work, plasmonic magnetoliposomes (PMLs) containing manganese ferrite nanoparticles (28 nm size) and gold nanoparticles (~ 5 nm size) functionalized with 11-mercaptoundecanoic acid or octadecanethiol, were synthesized and loaded with bLf. The structural, magnetic and optical properties of the nanoparticles were measured by TEM, SQUID and UV/vis/NIR absorption spectroscopy. Specific Absorption Rate was determined to assess the capabilities for magnetic and photothermal hyperthermia. Finally, Saccharomyces cerevisiae was used as an eukaryotic cellular model to assess the biological activity and the mechanism of entry of bLf-loaded PMLs, through counting of colony forming units and fluorescence microscopy, respectively. The results demonstrate that PMLs are mainly internalized through an energy- and temperature-dependent endocytic process, though the contribution of a diffusion component cannot be discarded. Most notably, only bLf-loaded PMLs exhibit cytotoxicity with an efficiency similar to free bLf, attesting their promising potential for bLf delivery in the context of therapeutic interventions.
ARTICLE | doi:10.20944/preprints202305.1267.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Zearalenone hydrolase; Neural Relational Inference; Umbrella sampling; MMPBSA; bmDCA
Online: 18 May 2023 (04:58:23 CEST)
Zearalenone is one of the most prevalent estrogenic mycotoxins produced mainly by Fusarium family fungi, and harmed the heath of animals. Zearalenone hydrolase is an important enzyme capable of degrading zearalenone into a non-toxic compound. Although previous research has investigated the catalytic mechanism of zearalenone hydrolase, information on its dynamic interaction with zearalenone remains unknown. This study aimed to develop a pipeline for identifying the allosteric pathway of zearalenone hydrolase. Using an identity analysis, we identified hub genes whose sequences can generalize a set of sequences in a protein family. We then utilized a neural relational inference (NRI) model to identify the allosteric pathway of the protein throughout the entire molecular dynamics simulation. The production run lasted 1 microsecond, and we analyzed residues 139-222 for the allosteric pathway using the NRI model. We found that the cap domain of the protein opened up during catalysis, resembling a hemostatic tape. We used umbrella sampling to simulate the dynamic docking phase of the ligand-protein complex and found that the protein took on a square sandwich shape. Our energy analysis using both MMPBSA and PMF analysis showed discrepancies, with scores of -8.45 kcal/mol and -1.95 kcal/mol, respectively. MMPBSA, however, obtained a similar score to that of a previous report.
REVIEW | doi:10.20944/preprints202305.1045.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Nanoparticles; nanotoxicity; mechanobiology; cell cytoskeleton; rigidity sensing
Online: 15 May 2023 (12:39:53 CEST)
Nanoparticles (NPs) are commonly used in healthcare and nano therapy, but their toxicity at high concentrations is well-known. Recent research has shown that NPs can also cause toxicity at low concentrations, disrupting various cellular functions and leading to altered mechanobiological behavior. While researchers have used different methods to investigate the effects of NPs on cells, including gene expression and cell adhesion assays, the use of mechanobiological tools in this context has been underutilized. This review emphasizes the importance of further exploring the mechanobiological effects of NPs, which could reveal valuable insights into the mechanisms behind NP toxicity. Such investigations could aid in developing new strategies to mitigate NP toxicity and improve their safety for biomedical applications. Moreover, understanding how NPs affect cell cytoskeletal functions through mechanobiology could have significant implications, including the development of innovative drug delivery systems and tissue engineering techniques. In summary, this review highlights the significance of incorporating mechanobiology into the study of NP toxicity and demonstrates the potential of this interdisciplinary field to advance our knowledge and practical use of NPs.
HYPOTHESIS | doi:10.20944/preprints202305.0607.v2
Subject: Biology And Life Sciences, Biophysics Keywords: Hox gene collinearity; temporal collinearity; Noether theory; self similarity; double strand break; split Ηox cluster; limb growth
Online: 11 May 2023 (04:34:03 CEST)
Abstract: Hox gene clusters are crucial in Embryogenesis. It was observed that some Hox genes were located in order along the telomeric to centromeric direction of the DNA sequence: Hox1, Hox2, Hox3…. These genes were expressed in the same order in the ontogenetic units of the Drosophila embryo along the Anterior-Posterior axis. The two entities (genome and embryo) differ significantly in linear size and in-between distance. This strange phenomenon was named Spatial Collinearity (SP). Later, it was observed that, particularly in the Vertebrates, a Temporal Collinearity (TC) coexists: first is Hox1 expressed, later Hox2 and even later Hox3,…,. Hox clusters are irreversibly elongated along the force direction. According to a Biophysical Model (BM), pulling forces act at the anterior end of the cluster while a cluster fastening applies at the posterior end. During Evolution, the elongated Hox clusters are broken at variable lengths thus split clusters may be created. An Empirical Rule was formulated distinguishing development due to a complete Hox cluster from development due to split Hox clusters. BM can explain this Empirical Rule. In an accidental mutation where the cluster fastening is dismantled, a minimal pulling force can automatically shift the cluster inside the Hox activation domain. This cluster translocation can probably explain the absence of temporal collinearity in Drosophila.
REVIEW | doi:10.20944/preprints202305.0503.v1
Subject: Biology And Life Sciences, Biophysics Keywords: RNP assembly; ribosome assembly; protein-RNA interactions; RNA folding; assembly intermediates; in vitro reconstitutions; mass spectrometry; single-molecule fluorescence microscopy; cryo-electron microscopy; RNA structure probing
Online: 8 May 2023 (10:01:55 CEST)
Ribosome assembly is one of the most fundamental processes in gene expression and has served as a playground to investigate the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. The bacterial ribosome is composed of around 50 ribosomal proteins several of which are co-transcriptionally assembled on a ~4,500 nucleotides long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 minutes in vivo and assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades and has resulted in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs. Here we review biochemical, structural and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of this complex and intricate molecular process of assembly. We also discuss emerging cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors and the native cellular environment shape ribosome assembly and RNP assembly at large.
COMMUNICATION | doi:10.20944/preprints202305.0275.v1
Subject: Biology And Life Sciences, Biophysics Keywords: 8-hydroxyquinoline; PBT2; amyloid; copper; terdentate; ternary; antimicrobial
Online: 5 May 2023 (02:36:19 CEST)
The metal chelator PBT2 (5,7-dichloro-2-[(dimethylamino)methyl]-8-hydroxyquinoline) acts as a terdentate ligand capable of forming binary and ternary Cu2+ complexes. It was clinically trialed as an Alzheimer’s disease (AD) therapeutic but failed to progress beyond phase II. The β-amyloid (Aβ) peptide associated with AD was recently concluded to form a unique Cu(Aβ) complex that is inaccessible to PBT2. Herein, it is shown that the species ascribed to this binary Cu(Aβ) complex in fact corresponds to ternary Cu(PBT2)NIm[Aβ] complexes formed by anchoring of Cu(PBT2) on imine nitrogen (NIm) donors of His side chains. The primary site of ternary complex formation is His6, having a conditional stepwise formation constant at pH 7.4 (K [M−1] ) of log K = 6.4 ± 0.1, and a second site is supplied by His13 or His14 (log K = 4.4 ± 0.1). The stability of Cu(PBT2)NIm[H13/14] is comparable with that of the simplest ternary complexes involving free imidazole (log K = 4.22 ± 0.09) and histamine (log K = 4.00 ± 0.05). The 100-fold larger formation constant for Cu(PBT2)NIm[H6] indicates that outer-sphere ligand–peptide interactions strongly stabilize its structure. Despite the relatively high stability of Cu(PBT2)NImH6, PBT2 is a promiscuous Cu2+-binding ligand capable of forming a ternary Cu(PBT2)NIm complex with any ligand containing NIm donor. These ligands include histamine, L-His, and ubiquitous His side chains of peptides and proteins in the extracellular milieu, whose combined effect should outweigh that of a single Cu(PBT2)NIm[H6] complex regardless of its stability. We therefore conclude that PBT2 is capable of accessing Cu(Aβ) complexes with high stability but not specificity. The results have implications for future AD therapeutic strategies and understanding the role of PBT2 in the bulk transport of transition metal ions. Given the repurposing of PBT2 as a drug for breaking antibiotic resistance, ternary Cu(PBT2)NIm and analogous Zn(PBT2)NIm complexes may be relevant to its antimicrobial properties.
ARTICLE | doi:10.20944/preprints202305.0246.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Anisotropy; polarisation analysis; Stokes parameters; polarimetry
Online: 4 May 2023 (09:13:26 CEST)
In this perspective, we give an overview of several less explored structural and optical characterisation techniques useful for biomaterials. New insights into the structure of natural fibres such as spider silk can be gained with minimal sample preparation. Electromagnetic radiation (EMR) over a broad range of wavelengths (from X-ray to THz) provides information of the structure of the material at cor- respondingly different length scales (nm-to-mm). When the sample features, such as the alignment of certain fibres, cannot be characterised optically, polarisation analysis of the optical images can provide further information on feature alignment. The 3D complexity of biological samples necessitates that there be feature measure- ments and characterisation over a large range of length scales. We discuss the issue of characterising complex shapes by analysis of the link between the color and struc- ture of spider scales and silk. For example, it is shown that the green-blue color of a spider scale is dominated by the chitin slab’s Fabry-P ́erot type reflectivity rather than the surface nanostructure. The use of a chromaticity plot simplifies complex spectra and enables quantification of the apparent colors. All the experimental data presented herein are used to support the discussion on the structure-color link in the characterisation of materials.
ARTICLE | doi:10.20944/preprints202305.0170.v1
Subject: Biology And Life Sciences, Biophysics Keywords: FOF1-ATP synthase; chloroplasts; dimers; small-angle scattering; membrane proteins
Online: 4 May 2023 (03:21:52 CEST)
F-type ATP synthases play a key role in oxidative and photophosphorylation processes producing adenosine triphosphate (ATP) for most biochemical reactions in living organisms. In contrast to the mitochondrial FOF1-ATP synthases those of chloroplasts are known to be mostly monomers with approx. 15% fraction of oligomers interacting presumably non-specifically in a thylakoid membrane. To shed light to the nature of this difference we studied interactions of the chloroplast ATP synthases using small-angle X-ray scattering (SAXS) method. Here, we report evidence of I-shaped dimerization of solubilized FOF1-ATP synthases from spinach chloroplasts at different salinity. The structural data were obtained by SAXS and showed dimerization in response to changes in ionic strength. The best model describing SAXS data was two ATP-synthases connected through F1/F1’ parts, presumably via their δ-subunits, forming dimers with the “I” shape. Such I-shaped dimers might possibly connect the neighboring lamellae in thylakoid stacks assuming that the FOF1 monomers comprising such dimers are embedded in different thylakoid membranes. If this type of dimerization exists in nature, it might be one of the pathways of inhibition of chloroplast FOF1-ATP synthase for preventing of ATP hydrolysis in dark, when salinity in plant chloroplasts is rising. Together with a redox switch inserted into a γ-subunit of chloroplast FOF1 and lateral oligomerization, an I-shaped dimerization might comprise a subtle regulatory process of ATP synthesis and stabilize the structure of thylakoid stacks in chloroplasts.
ARTICLE | doi:10.20944/preprints202305.0125.v1
Subject: Biology And Life Sciences, Biophysics Keywords: trade-off; dialectic; TRIZ; Inventive Principle; wood wasp ovipositor; intracranial endoscope; Pareto curve
Online: 3 May 2023 (09:44:40 CEST)
Our knowledge of physics and chemistry is relatively well defined. Results from that knowledge are predictable as, largely, are those of their technical offspring such as electrical, chemical, me-chanical and civil engineering. By contrast biology is relatively unconstrained and unpredictable. A factor common to all areas is the trade-off, which provides a means of defining and quantifying a problem and, ideally, its solution. In order to understand the anatomy of the trade-off and how to handle it, its development (as the dialectic) is tracked from Hegel and Marx to its implementa-tion as dialectical materialism in Russian philosophy and TRIZ, the Theory of Invention. With the ready availability of mathematical techniques, such as multi-objective analysis and the Pareto set, the trade-off is well-adapted to bridging the gaps between the quantified and the unquantifiable, allowing modelling and the transfer of concepts by analogy. It is thus an ideal tool for biomimet-ics. An intracranial endoscope can be derived with little change from the egg-laying tube of a wood wasp. More complex transfers become available as the technique is developed. Most im-portant, as more trade-offs are analyzed, their results are stored to be used again in the solution of problems. There is no other system in biomimetics which can do this.
ARTICLE | doi:10.20944/preprints202304.0837.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Gastric signet ring cell carcinoma; lymph node metastases; LODDS; prognosis
Online: 24 April 2023 (09:00:47 CEST)
Background: The lymph nodes staging system can predict the prognosis of gastric signet ring cell carcinoma (SRCC), but the optimal system for early and advanced SRCC remains unknown. Methods: This study retrospectively analyzed 693 SRCC patients who underwent radical resection in the Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital. The predicted performance of three lymph node staging systems, including pN staging, lymph node metastasis rate (LNR), and log odds of positive lymph nodes (LODDS), was compared using the receiver characteristic operating curve (ROC). The kaplan⁃meier method and the log⁃rank test analyze the overall survival of patients. The Cox risk regression model identifies independent risk factors associated with patient outcomes. The nomogram was made by R studio. Results: The 693 SRCC included 165 early SRCC and 528 advanced SRCC. ROC showed that LODDS had better predictive performance than pN and LNR in predicting prognosis regardless of early or advanced SRCC. LODDS can be used to predict the prognosis of early and advanced SRCC and was an independent risk factor associated with patient outcomes (P=0.002, P<0.001). Furthermore, the nomogram constructed by LODDS and clinicopathological features had good predictive performance. Conclusion: LODDS showed a clear prognostic superiority over both pN and LNR in early and advanced SRCC.
COMMUNICATION | doi:10.20944/preprints202304.0829.v1
Subject: Biology And Life Sciences, Biophysics Keywords: atomic force microscopy; horseradish peroxidase; enzyme aggregation; enzymatic activity; tribo-electric effect; fluid flow
Online: 24 April 2023 (06:14:42 CEST)
Glycerol has found its applications as a heat-transfer fluid in heat exchangers, and as a compo-nent of functional solutions in biosensor analysis. Flowing non-aqueous fluids are known to be able to induce electromagnetic fields due to triboelectric effect. These triboelectrically generated electromagnetic fields can affect biological macromolecules. Horseradish peroxidase (HRP) is widely employed as a convenient model object for studying how external electric, magnetic, and electromagnetic fields affect enzymes. Herein, we have studied whether the flow of glycerol in a ground-shielded cylindrical coil affects the HRP enzyme incubated at a 2 cm distance near the coil’s side. Atomic force microscopy (AFM) has been employed in order to study the effect of glycerol flow on HRP at the nanoscale. Increased aggregation of HRP on mica has been observed after the incubation of the enzyme near the coil. Moreover, the enzymatic activity of HRP has also been affected. The results reported can find their application in biotechnology, food technology and life sciences application, considering the development of triboelectric generators, en-zyme-based biosensors and bioreactors with surface-immobilized enzymes. Our data can also be of interest for scientists studying triboelectric phenomena.
ARTICLE | doi:10.20944/preprints202304.0528.v1
Subject: Biology And Life Sciences, Biophysics Keywords: serial femtosecond crystallography; X-ray free electron laser; sample delivery; injector; fixed-target scanning; hybrid method
Online: 19 April 2023 (03:22:22 CEST)
Serial femtosecond crystallography (SFX) using an X-ray free-electron laser (XFEL) enables determination of room-temperature structures without causing radiation damage. Using an optical pump-probe or mix-and-injection, SFX enables the intermediate state visualization of a molecular reaction. In SFX experiments, serial and stable microcrystal delivery to the X-ray interaction point is vital for reasonable data collection and efficient beam time. The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) facility established SFX instruments at a nanocrystallography and coherent imaging (NCI) experimental station. Various sample delivery methods, including injection, fixed-target scanning, and hybrid methods, have been developed and applied to collect XFEL diffraction data. Herein, we review the currently available sample delivery methods for SFX at the NCI experimental station at the PAL-XFEL. This article will help PAL-XFEL users access the SFX system for their experiments.
COMMUNICATION | doi:10.20944/preprints202303.0042.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Structured illumination; Spatial transcriptomics; Super-resolution; Gene expression; In situ sequencing; Deconvolution microscopy
Online: 2 March 2023 (10:42:14 CET)
Spatial biology is a rapidly growing research field which focuses on the transcriptomic or proteomic profiling of single cells within tissues with preserved spatial information. Imaging-based spatial transcriptomics uses epifluorescence microscopy, which has shown remarkable results for identification of multiple targets in situ. Nonetheless, the number of genes that can be reliably visualized is limited by the diffraction of light. Here, we investigate the effect of structured illumination (SIM), a super-resolution microscopy approach, over the performance of single gene transcript detection in spatial transcriptomics experiments. We performed direct mRNA-targeted hybridization in situ sequencing for multiple genes in mouse coronal brain tissue sections. We evaluated spot detection performance in widefield and confocal images versus those with SIM in combination with 20X, 25X and 60X objectives. In general, SIM increases the detection efficiency of gene transcripts spots compared to widefield and confocal modes. For each case, the specific fold increase in localizations is dependent on gene transcripts density and the numerical aperture of the objective used, which showed to play an important role especially for densely clustered spots. Taken together, our results suggest that SIM has the capacity to improve spot detection and overall data quality in spatial transcriptomics.
REVIEW | doi:10.20944/preprints202302.0516.v1
Subject: Biology And Life Sciences, Biophysics Keywords: BOLD fMRI; HRF; resting state connectivity; aging; sex differences; confound
Online: 28 February 2023 (09:32:04 CET)
Functional magnetic resonance imaging (fMRI) is an indirect measure of neural activity with the hemodynamic response function (HRF) coupling it with unmeasured neural activity. The HRF, modulated by several non-neural factors, is variable across brain regions, individuals and populations. Yet, a majority of resting-state fMRI connectivity studies continue to assume a non-variable HRF. In this article, with supportive prior evidence, we argue that HRF variability cannot be ignored as it substantially confounds within-subject connectivity estimates and between-subjects connectivity group differences. We also discuss its clinical relevance with connectivity impairments confounded by HRF aberrations in several disorders. We present limited data on HRF differences between women and men, which resulted in a 15.4% median error in functional connectivity estimates in a group-level comparison. We also discuss the implications of HRF variability for fMRI studies in the spinal cord. There is a need for more dialogue within the community on the HRF confound, and we hope that our article is a catalyst in the process.
ARTICLE | doi:10.20944/preprints202302.0389.v1
Subject: Biology And Life Sciences, Biophysics Keywords: entropic dynamics; biosystems; Kullback Principle of Minimum Information Discrimination; biocontinuum; information geometry
Online: 22 February 2023 (15:32:36 CET)
Central to an understanding of the physical nature of biosystems is an apprehension of their ability to control entropy dynamics in their environment. To achieve ongoing stability and survival, living systems must adaptively respond to incoming information signals concerning matter and energy perturbations in their biological continuum (biocontinuum). Entropy dynamics for the living system are then determined by the natural drive for reconciliation of these information divergences in the context of the constraints formed by the geometry of the biocontinuum information space. The configuration of this information geometry is determined by the inherent biological structure, processes and adaptive controls that are necessary for the stable functioning of the organism. The trajectory of this adaptive reconciliation process can be described by an information-theoretic formulation of the living system’s procedure for actionable knowledge acquisition that incorporates the axiomatic inference of the Kullback Principle of Minimum Information Discrimination (a derivative of Jaynes’ principle of maximal entropy). Utilizing relative information for entropic inference provides for the incorporation of a background of the adaptive constraints in biosystems within the operations of Fisher biologic replicator dynamics. This mathematical expression for entropic dynamics within the biocontinuum may then serve as a theoretical framework for the general analysis of biological phenomena.
ARTICLE | doi:10.20944/preprints202302.0059.v1
Subject: Biology And Life Sciences, Biophysics Keywords: hSERT; comprehensive molecular dynamics (MD) simulation; drug design; MM/GBSA
Online: 3 February 2023 (06:16:06 CET)
The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin from the synaptic cleft, which is an essential process plays an important role in depression. In addition to substrate serotonin, hSERT is also the target of drugs of abuse like cocaine and clinically used antidepressants such as escitalopram and paroxetine. To date, few studies attempt to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of hSERT. The high-resolution X-ray structure of hSERT resolved recently enables us to theoretically study the unbinding of the above four ligands against the S1 or S2 site of hSERT, by means of molecular docking, molecular dynamics (MD) and potential of mean force (PMF) simulations. We proved that for either the S1 or S2 site, the other three ligands (cocaine, escitalopram and paroxetine) are much more favorable than the original substrate serotonin, whether in kinetics along the unbinding pathways or in thermodynamics at the equilibrium states. Furthermore, the S1 site is much more favorable than the S2 site, for each ligand. Interestingly, inspection revealed that there are ~ 3Å lengths between the allosteric site of serotonin and cocaine, and an unseen un-binding pathway for escitalopram at the S1 site except for verification of the broadest trail.
ARTICLE | doi:10.20944/preprints202301.0346.v1
Subject: Biology And Life Sciences, Biophysics Keywords: G-protein-coupled-receptors; GPCRs; Membrane protein; Protein-lipid interactions; Cholesterol; Class C GPCRs
Online: 19 January 2023 (06:32:01 CET)
G-protein coupled receptors (GPCRs), one of the largest superfamilies of cell-surface receptors, are heptahelical integral membrane proteins that play critical roles in virtually every organ system. G-protein-coupled receptors operate in membranes rich in cholesterol, with an imbalance in cholesterol level within the vicinity of GPCR transmembrane domains affecting the structure and/or function of many GPCRs, a phenomenon that has been linked to several diseases. These effects of cholesterol could result in indirect changes by altering the mechanical properties of the lipid environment or direct changes by binding to specific sites on the protein. There are a number of studies and reviews on how cholesterol modulates class A GPCRs, however, this area of study is yet to be explored for class C GPCRs, which are characterized by a large extracellular region and often form constitutive dimers. This review highlights specific sites of interaction, functions, and structural dynamics involved in the cholesterol recognition of the class C GPCRs. We summarize recent data from some typical family members to explain the effects of membrane cholesterol on the structural features and functions of Class C GPCRs and speculate on their corresponding therapeutic potential.
ARTICLE | doi:10.20944/preprints202301.0344.v1
Subject: Biology And Life Sciences, Biophysics Keywords: microtubule-severing enzyme; tubulin isotypes; tubulin code; post-translational modifications; katanin; microtubule-associated protein
Online: 19 January 2023 (03:16:41 CET)
In celIs, microtubule location, length, and dynamics are regulated by a host of microtubule-associated proteins and enzymes that read where to bind and act based on the microtubule “tubulin code,” which is predominantly encoded in the tubulin carboxy-terminal tail (CTT). Katanin is a highly conserved AAA ATPase enzyme that binds to the tubulin CTTs to remove dimers and sever microtubules. We have previously demonstrated that short CTT peptides are able to inhibit katanin severing. Here, we examine effects of CTT sequences on this inhibition activity. Specifically, we examine CTT sequences found in nature, alpha1A (TUBA1A), detyrosinated alpha1A, Δ2 alpha1A, beta5 (TUBB/TUBB5), beta2a (TUBB2A), beta3 (TUBB3), and beta4b (TUBB4b). We find that these natural CTTs have distinct abilities to inhibit, most noticeably beta3 cannot inhibit katanin. Two non-native CTT tail constructs are also unable to inhibit – despite having 94% sequence identity with alpha1 or beta5 sequences. Surprisingly, we demonstrate that poly-E and poly-D peptides are capable of inhibiting katanin significantly. An analysis of the hydrophobicity of the CTT constructs indicates that more hydrophobic polypeptides are less inhibitory than more polar polypeptides. These experiments not only demonstrate inhibition, but also likely interaction and targeting of katanin to these various CTTs when they are part of a polymerized microtubule filament.
ARTICLE | doi:10.20944/preprints202301.0259.v1
Subject: Biology And Life Sciences, Biophysics Keywords: MEG; LED; color perception
Online: 16 January 2023 (01:36:12 CET)
Color plays an important part in human activities, affects circadian cycle and decision making process. Therefore, it is important to investigate human judgment under different color of illumination, especially, because color perception is subjective. In this study, we developed required instrumentation to control the red (R), green (G), Blue (B) and Amber (A) colored light emitting diode (LED) lamp for carrying out Magneto Encephalography (MEG) brain scan. We developed a software to generate all the colors in the visual spectrum, predefined white light combinations and saturation of an illuminated objects by using RGBA color pallet. The lamp is required to control from outside of the MEG electromagnetically shielded room with the LED lamp located inside the MEG room. Hence, USB is used for the communication mode. The feasibility of using LED lamp with MEG brain scanner has been validated for bio-medical and psychological MEG experiments.
ARTICLE | doi:10.20944/preprints202301.0201.v1
Subject: Biology And Life Sciences, Biophysics Keywords: FFR, Blood Flow Simulation, coronal stenosis, Coronary Computed Tomography Angiography (CCTA), OpenFOAM
Online: 11 January 2023 (11:56:16 CET)
A novel physiologically based algorithm (PBA) for the computation of fractional flow reserve (FFR) in coronary artery trees (CATs) using computational fluid dynamics (CFD) is proposed and developed. The PBA is based on the extension of Murray's law and additional inlet conditions prescribed iteratively, and is implemented in OpenFOAM for testing and validation. 3D models of CATs are created using CT scans and computational meshes, and the results are compared to in-vasive coronary angiographic (ICA) data to validate the accuracy and effectiveness of the PBA. The discrepancy between calculated and experimental FFR is within 2.33-5.26% in steady-state and transient simulations, respectively, when convergence is reached. The PBA is a reliable and physiologically sound technique compared to the current lumped parameter model (LPM), which is based on empirical scaling correlations and requires nonlinear iterative computing for conver-gence. The accuracy of the PBA method is further confirmed using the FDA nozzle, which demonstrates good alignment with CFD-validated values.
REVIEW | doi:10.20944/preprints202301.0004.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Baroenzymology; Cryoenzymology; Intrinsic disorder; Intrinsically disordered proteins; Macromolecular crowding; Nanomaterials; Partially folded intermediate; Protein denaturation; Protein engineering; Protein flexibility; Protein folding; Protein function; Protein stability; Protein structure; Protein refolding; Protein unfolding
Online: 3 January 2023 (06:48:30 CET)
Transition between the unfolded and native states of the ordered globular proteins is accompanied by accumulation of several intermediates, such as pre-molten globule, wet molten globule, and dry molten globule. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under the conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
ARTICLE | doi:10.20944/preprints202212.0201.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Waves; Protein Synthesis; Resonance; Long Term Memory
Online: 12 December 2022 (12:11:00 CET)
Conclusive evidence that specic long-term memory formation relies on den- dritic growth and structural synaptic changes has proven elusive. Connec- tionist models of memory based on this hypothesis are confronted with the so-called plasticity stability dilemma or catastrophic interference. Other fun- damental limitations of these models are the feature binding problem, the speed of learning, the capacity of the memory, the localisation in time of an event and the problem of spatio-temporal pattern generation. This paper suggests that the generalisation and long-term memory mechanisms are not correlated. Only the development and the improvement of the feature ex- tractors in the cortex involves structural synaptic changes. We suggest the long-term memory has a separate mechanism which involves protein synthe- sis to encode the information into the structure of these proteins. A model of memory should be capable of explaining the dierence between memorisation and learning. Learning has in our approach two dierent mechanisms. The generalisation in the brain is handled by the proper development of the links between neurons via synapses. The Hebbian learning rule could be applied only for this part of learning. Storing an internal ring pattern involves, in our approach, a new mechanism which puts the information regarding this ring pattern into the structure of special proteins in such a way that it can be retrieved later. The hypotheses introduced in this article includes a physiological assumption which has not been yet verified because it is not currently experimentally accessible. Keywords: Waves, Protein Synthesis, Resonance, Long Term Memory Preprint submitted to Neural Networks
REVIEW | doi:10.20944/preprints202212.0046.v1
Subject: Biology And Life Sciences, Biophysics Keywords: oscillations, theta rhythm, gamma rhythm, coherence, temporal lobe epilepsy
Online: 2 December 2022 (10:11:23 CET)
The dentate gyrus (DG) is part of the hippocampal formation and is essential for important cognitive processes such as navigation and memory. The oscillatory activity of the DG network is believed to play a critical role in cognition. DG circuits generate three main rhythms: theta, beta, and gamma, which participate in the specific information processing performed by DG neurons. In the temporal lobe epilepsy (TLE), cognitive abilities are impaired, which may be due to drastic alterations in the DG structure and network activity during epileptogenesis. The theta rhythm and theta coherence are especially vulnerable in dentate circuits; disturbances in DG theta oscillations and their coherence may be responsible for general cognitive impairments observed during epileptogenesis. Some researchers suggested that the vulnerability of DG mossy cells is a key factor in the genesis of TLE, but others did not support this hypothesis. The aim of the review is not only to present the current state of the art in this field of research but to help pave the way for future investigations by highlighting the gaps in our knowledge to completely appreciate the role of DG rhythms in brain functions. Disturbances in oscillatory activity of the DG during TLE development are described in detail that may be a diagnostic marker in the treatment of this disease.
TECHNICAL NOTE | doi:10.20944/preprints202211.0477.v1
Subject: Biology And Life Sciences, Biophysics Keywords: cross-country skiing; temporal event detection; wearable sensors; field analysis
Online: 25 November 2022 (10:09:08 CET)
The aim of this study was to adapt a treadmill-developed method for determination of inner-cycle parameters in cross-country roller ski skating for a field application. The method is based on detecting initial and final ground-contact of poles and skis during cyclic movements. Eleven athletes skied four laps of 2.5 km at low and high endurance-intensity, using two types of skis with different rolling coefficients. Participants were equipped with inertial measurement units (IMUs) attached to their wrists and skis, while insoles with pressure sensors and poles with force measurements were used as reference systems. The method based on IMUs was able to detect more than 97% of the temporal events compared to the reference system. The inner-cycle temporal parameters had a precision ranging from 49 to 59 ms, corresponding to 3.9% to 13.7% of the corresponding inner-cycle duration. Overall, this study showed good reliability of using IMUs on athlete’s wrists and skis to determine temporal events, inner-cycle parameters and the performed sub-techniques in cross-country roller ski skating in field-conditions.
ARTICLE | doi:10.20944/preprints202211.0313.v1
Subject: Biology And Life Sciences, Biophysics Keywords: cytokine; Tumor necrosis factor; S100 protein; protein–protein interaction; inflammatory diseases
Online: 16 November 2022 (13:12:59 CET)
Tumor necrosis factor (TNF) inhibitors (anti-TNFs) represent a cornerstone of the treatment of various immune-mediated inflammatory diseases and are among the most commercially successful therapeutic agents. Knowledge of TNF binding partners is critical for identification of the factors able to affect clinical efficacy of the anti-TNFs. Here we report that among eighteen representatives of the multifunctional S100 protein family only S100A11, S100A12 and S100A13 interact with the soluble form of TNF (sTNF) in vitro. The lowest equilibrium dissociation constants (Kd) for the complexes with monomeric sTNF determined using surface plasmon resonance spectroscopy range from 2 nM to 28 nM. The apparent Kd values for the complexes of multimeric sTNF with S100A11/A12 estimated from fluorimetric titrations are 0.1-0.3 µM. S100A12/A13 suppress the cytotoxic activity of sTNF against Huh-7 cells, as evidenced by the MTT assay. Structural modeling indicates that the sTNF-S100 interactions may interfere with the sTNF recognition by the therapeutic anti-TNFs. Bioinformatic analysis reveals dysregulation of TNF and S100A11/A12/A13 in numerous disorders. Overall, we have shown a novel potential regulatory role of the extracellular forms of specific S100 proteins that may affect efficacy of anti-TNF treatment in various diseases.
ARTICLE | doi:10.20944/preprints202210.0186.v3
Subject: Biology And Life Sciences, Biophysics Keywords: neural; brain; structural intelligence; cell expression; evolution
Online: 4 November 2022 (09:43:59 CET)
This concept paper gives a narrative about intelligence from insects to the human brain, showing where evolution may have been influenced by the structures in these simpler organisms. The ideas also come from the author's own cognitive model, where a number of algorithms have been developed over time and the precursor structures should be codable to some level. Through developing and trying to implement the design, ideas like separating the data from the function have become architecturally appropriate and there have been several opportunities to make the system more orthogonal. Similarly for the human brain, neural structures may work in-sync with the neural functions, or may be slightly separate from them. Each section discusses one of the neural assemblies with a potential functional result, that cover ideas such as timing or scheduling, structural intelligence and neural binding. Another aspect of self-representation or expression is interesting and may help the brain to realise higher-level functionality based on these lower-level processes.
ARTICLE | doi:10.20944/preprints202210.0457.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Hepcidin; prohepcidin; cadmium; affinity constant; metallothionein; MT2A
Online: 28 October 2022 (13:00:05 CEST)
Hepcidin (DTHFPICIFCCGCCHRSKCGMCCKT), an iron regulatory hormone is a 25 amino acid peptide with 4 intramolecular disulfide bonds, circulating in blood. Its hormonal activity is indirect and consists of marking ferroportin-1 (an iron exporter) for degradation. Hepcidin biosynthesis involves N-terminally extended precursors prepro-hepcidin and pro-hepcidin, processed by peptidases to the final 25-peptide form. A sequence-specific formation of disulfide bonds and export of the oxidized peptide to the bloodstream follows. In this study we considered the fact that prior to export, reduced hepcidin may function as an octathiol ligand bearing some resemblance to the N-terminal part of α-domain of metallothioneins. Consequently, we studied its ability to bind Zn(II) and Cd(II) ions using the original peptide and a model for prohepcidin, extended N-terminally with a stretch of five arginine residues (5R-hepcidin). We found that both form equivalent mononuclear complexes with two Zn(II) or Cd(II) ions saturating all eight Cys residues. The average affinity at pH 7.4, determined from pH-metric spectroscopic titrations, is 1010.1 M-1 for Zn(II) ions, the Cd(II) ions bind with affinities of 1015.2 M-1 and 1014.1 M-1. Using mass spectrometry and 5R-hepcidin we demonstrated that hepcidin can compete for Cd(II) ions with metallothionein-2, a cellular cadmium target. These studied empowered us to conclude that hepcidin binds Zn(II) and Cd(II) sufficiently strongly to participate in zinc physiology and cadmium toxicity under intracellular conditions.
ARTICLE | doi:10.20944/preprints202210.0386.v1
Subject: Biology And Life Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; Pandemic; Empirical formula; Growth stoichiometry; Thermodynamic properties of biosynthesis; Multiplication rate; Enthalpy; Entropy; Gibbs energy
Online: 25 October 2022 (10:53:13 CEST)
SARS-CoV-2 belongs to the group of RNA viruses with a pronounced tendency to mutate. Omicron BA.2.75 is a subvariant believed to be able to suppress the currently dominant BA.5. Omicron BA.2.75 is characterized by a greater infectivity compared to earlier Omicron variants. However, Gibbs energy of biosynthesis of virus particles is slightly less negative compared to those of other variants. Thus, the multiplication rate of Omicron BA.2.75 is lower than that of other variants. This leads to slower accumulation of newly formed virions and less damage to host cells, indicating evolution of SARS-CoV-2 towards decreasing pathogenicity.
Subject: Biology And Life Sciences, Biophysics Keywords: biology; thermodynamics; biothermodynamics; entropy; Gibbs energy
Online: 21 October 2022 (09:58:33 CEST)
During the last 50 years, an interdisciplinary approach in research in various scientific fields has become widely spread. This process significantly deepens and widens our scientific knowledge, but on the other hand makes more difficult choosing a discipline to be used by students and young researchers. The dynamic development of science makes this choice even harder. There is a widely spread opinion that thermodynamics uses a rigorous mathematical apparatus. This paper describes that knowledge of the fundamental principles of thermodynamics is required for deep understanding of crucial biological processes. Thus the effort put into learning classical and nonequilibrium thermodynamics does not make harder, but easier gaining a better knowledge of biological processes. This essay is an attempt to convey personal experience in using thermodynamics to describe biological systems and processes they perform.
ARTICLE | doi:10.20944/preprints202210.0276.v1
Subject: Biology And Life Sciences, Biophysics Keywords: colorectal cancer; cancer stem cells; extracellular vesicles; high frequency dielectrophoresis; mi-crofluidic lab-on-a-chip
Online: 19 October 2022 (10:03:50 CEST)
Cancer stem cells remain a challenge to isolate and characterize because of their plastic phenotype. Using a microfluidic lab-on-a-chip based on ultra-high frequency dielectophoresis, we measured the electromagnetic signature of colorectal cancer cells and demonstrated that cancer stem cells show a distinct and lower electromagnetic signature than differentiated cells. The release of extracellular vesicles from tumor cells can drive tumor progression and metastasis development. As extracellular vesicles from cancer stem cells carry more aggressive content, we treated colorectal cancer cells with these vesicles to test whether the lab-on-a-chip can detect a change in phenotype. The electromagnetic signature of treated cells is modified in comparison to untreated cells and sometimes even when no biological change is observed. The lab-on-a-chip provides rapid and relevant result without prior labeling compared to conventional biological approaches. It could be useful in the clinic for early detection of cancer stem cells in the tumor mass and for monitoring the aggressive potential of extracellular vesicles in the bloodstream in order to adapt therapeutic management and prevent relapse.
ARTICLE | doi:10.20944/preprints202209.0450.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Heslington brain; intrinsically disordered protein; intrinsically disordered region; binding-induced folding; disorder-to-order transition
Online: 29 September 2022 (03:49:27 CEST)
Proteomic analysis revealed the preservation of many proteins in the “Heslington brain” (which is at least 2,600-year-old brain tissue uncovered within the skull excavated in 2008 from a pit in Heslington, Yorkshire, England). Five of these proteins (“main proteins”), heavy, medium, and light neurofilament proteins (NFH, NFM, and NFL), glial fibrillary acidic protein (GFAP), and myelin basic (MBP) protein are engaged in the formation non-amyloid protein aggregates, such as intermediate filaments and myelin sheath. We used a wide spectrum of bioinformatics tools to evaluate the prevalence of functional disorder in several related sets of proteins, such as “main proteins” and their 44 interactors, as well as all other protein identified in the Heslington brain. These analyses revealed that all five “main proteins”, half of their interactors and almost one third of the Heslington brain proteins are expected to be mostly disordered. Furthermore, most of the remaining proteins are expected to contain sizable disordered regions. This is in contrary the expected substantial (if not complete) elimination of the disordered proteins from the Heslington brain. Therefore, it seems that the intrinsic disorder of NFH, NFM, NFL, GFAP, and MBP, their interactors and many other proteins might play a crucial role in preserving the Heslington brain by forming tightly folded brain protein aggregates, in which different parts are glued together via the disorder-to-order transitions.
ARTICLE | doi:10.20944/preprints202209.0442.v1
Subject: Biology And Life Sciences, Biophysics Keywords: TDP-43; Liquid-liquid phase separation; Solution-state NMR
Online: 28 September 2022 (12:22:40 CEST)
Liquid-liquid phase separation (LLPS) of proteins has been found ubiquitously in eukaryotic cells, critical in the controlling of many biological processes through forming a temporary condensed phase with different bimolecular components. TDP-43 is recruited to stress granules in cells and is the main component of TDP-43 granules and proteinaceous amyloid inclusions in patients with amyotrophic lateral sclerosis (ALS). TDP-43 low complexity domain (LCD) is able to demix in solution forming the protein condensed droplets. The molecular interactions regulating its LLPS were investigated at the protein fusion equilibrium stage, where the droplets stopped growing. We found the molecules in the droplet were still liquid-like but with enhanced intermolecular helix-helix interaction in the LCD. The protein would start to aggregate after about 200 minutes of lag time and aggregate slower than at the condition when the protein does not phase separate or the molecules have a reduced intermolecular helical interaction. A structural transition intermediate towards protein aggregation was also discovered involving a decrease of the intermolecular helix-helix interaction and a reduction in the helicity. Therefore, LLPS and the intermolecular helical interaction could help maintain the stability of TDP-43 LCD.
ARTICLE | doi:10.20944/preprints202209.0395.v1
Subject: Biology And Life Sciences, Biophysics Keywords: chilling requirement; chlorophyll fluorescence; non-photochemical quenching; PAM; photoprotection; stress resilience; winter dormancy
Online: 26 September 2022 (11:01:44 CEST)
Dormancy is a physiological state that confers winter hardiness to and orchestrates phenological phase progression in temperate perennial plants. Weather fluctuations caused by climate change increasingly disturb dormancy onset and release in many plant species including tree crops leading to aberrant growth, flowering, and fruiting. Currently, research in this field is impeded by the lack of affordable non-invasive methods for on-line monitoring of dormancy. We report on an automatic framework for low-cost, long-term, and scalable dormancy studies in deciduous plants. The proposed method is based on continuous near-field sensing of the photosynthetic activity of shoots via pulse-amplitude modulated chlorophyll fluorescence sensors connected remotely to a data processing system. The resulting high-resolution time series of JIP-test parameters indicative of the responsiveness of the photosynthetic apparatus to environmental stimuli are subjected to frequency-domain analysis. The proposed approach allows to overcome the variance coming from diurnal changes of insolation and to derive estimations on the depth of dormancy. Our approach was validated over three seasons in an experimental apple (Malus × domestica Borkh.) orchard by collating the non-invasive estimations with the results of traditional methods (growing of the cuttings obtained from the tress at different phases of dormancy) and the output of commonly used chilling requirement models. We discuss the advantages of the proposed monitoring framework such as prompt detection of freeze damages along with its potential limitations.
ARTICLE | doi:10.20944/preprints202209.0319.v1
Subject: Biology And Life Sciences, Biophysics Keywords: cytokine; S100 protein; S100P; protein–protein interaction
Online: 21 September 2022 (09:45:39 CEST)
S100 proteins are multifunctional calcium-binding proteins of vertebrates that act intracellularly, extracellularly, or both, and are engaged in the progression of many socially significant diseases. Their extracellular action is typically mediated by the recognition of specific receptor proteins. Besides, recent studies indicate the ability of some S100 proteins to affect cytokine signaling through direct interaction with cytokines. S100P was shown to be the S100 protein most actively involved in interactions with some of four-helical cytokines. To assess selectivity of S100P protein binding to four-helical cytokines, we have probed interaction of Ca2+-bound recombinant human S100P with a panel of 32 four-helical human cytokines covering all structural families of this fold, using surface plasmon resonance spectroscopy. 22 cytokines from all families of four-helical cytokines are S100P binders with the equilibrium dissociation constants, Kd, ranging from 1 nM to 3 µM (below the Kd value for the S100P complex with the V domain of its conventional receptor, receptor for advanced glycation end products, RAGE). Molecular docking and mutagenesis studies revealed the presence in the S100P molecule of a cytokine-binding site, which overlaps with the RAGE-binding site. Since S100 binding to four-helical cytokines inhibits their signaling in some cases, the revealed ability of S100P protein to interact with ca 71% of the four-helical cytokines indicates that S100P may serve as a poorly selective inhibitor of their action.
ARTICLE | doi:10.20944/preprints202209.0119.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Suspended bilayer; Pore-forming toxin; Cytolysin A; Virus fusion; Pore formation
Online: 8 September 2022 (07:45:44 CEST)
Artificial membrane systems can serve as models to investigate molecular mechanisms of different cellular processes, including transport, pore formation, and viral fusion. However, the current simulacrums such as SUVs, GUVs, and the supported lipid bilayers suffer from issues, namely high curvature, heterogeneity, and surface artefacts, respectively. Freestanding membranes provide a facile solution to these issues, but current systems developed by various groups use silicon or aluminium oxide wafers for fabrication that involves access to a dedicated nanolithography facility and high cost while conferring poor membrane stability. Here, we report the development, characterization and applications of an easy-to-fabricate suspended lipid bilayer (SULB) membrane platform leveraging commercial track-etched porous filters (PCTE) with defined microwell size. Our SULB system offers a platform to study the lipid composition-dependent structural and functional properties of membranes with exceptional stability in a high throughput fashion. With dye entrapped in PCTE microwells by SULB, we show that sphingomyelin significantly augments the activity of pore-forming toxin, Cytolysin A (ClyA) and the pore formation induces lipid exchange between the bilayer leaflets. Further, we demonstrate high efficiency and rapid kinetics of membrane fusion by dengue virus in our SULB platform. Our suspended bilayer membrane mimetic offers a novel platform to investigate a large class of biomembrane interactions and processes.
ARTICLE | doi:10.20944/preprints202208.0327.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Fourier Transform Infrared spectroscopy; water structure; hydrogen bonds; protein solution; solvent properties
Online: 18 August 2022 (03:25:26 CEST)
This work presents the first evidence that dissolved globular proteins change the arrangement of hydrogen bonds in water, with different proteins showing quantitatively different effects. Using ATR-FTIR (Attenuated Total Reflection – Fourier Transform Infrared) spectroscopic analysis of OH-stretch bands, we obtain quantitative estimates of the relative amounts of the previously reported four subpopulations of water structures coexisting in a variety of aqueous solutions. Where solvatochromic dyes can measure the properties of solutions of non-ionic polymers, the results correlate well with ATR-FTIR measurements. In protein solutions to which solvatochromic dye probes cannot be applied, NMR (Nuclear Magnetic Resonance) spectroscopy was used for the first time to estimate the hydrogen bond donor acidity of water. We found strong correlations between the solvent acidity and arrangement of hydrogen bonds in aqueous solutions for several globular proteins. Even quite similar proteins are found to change water properties in dramatically different ways.
ARTICLE | doi:10.20944/preprints202208.0213.v1
Subject: Biology And Life Sciences, Biophysics Keywords: intermolecular binding affinity; drug target binding affinity; computer-aided drug design (CADD); artificial intelligence-integrated drug discovery (AIDD); machine learning
Online: 11 August 2022 (08:40:37 CEST)
Thanks to the continued development of experimental structural biology and the half-a-century old Protein Data Bank, 2021 saw a big step forward in the development of protein structure prediction with deep learning algorithms. Recently, DeepMinds AlphaFold has determined the structures of ∼ 200 million proteins from 1 million species. The speed of this progress raise the question of what becomes possible for computational drug discovery and design when we have a systems-wide account of the structures and motions of most proteins. Therefore, this article puts forward the concept of a general intermolecular binding affinity calculator (GIBAC): Kd = f(molA, molB, envPara), towards the acceleration of traditional computer-aided drug design (CADD) and artificial intelligence-integrated drug discovery (AIDD), for both small molecules and biologics such as therapeutic proteins.
ARTICLE | doi:10.20944/preprints202207.0182.v1
Subject: Biology And Life Sciences, Biophysics Keywords: ADAM; Adaptive response; ALK1; ALK5; Bystander effects; Hyper-radiosensitive response; Low-dose radiation; Low dose rate; MMP; TGF-β3
Online: 12 July 2022 (09:25:07 CEST)
Hyper-radiosensitivity (HRS) is the increased sensitivity to low doses of ionizing radiation observed in most cell lines. We previously demonstrated that HRS is permanently abolished in cells irradiated at a low dose rate (LDR), in a mechanism dependent on transforming growth factor β3 (TGF-β3). In this study, we aimed to elucidate the activation and receptor binding of TGF-β3 in this mechanism. T-47D cells were pre-treated with inhibitors of potential receptors and activators of TGF-β3, along with addition of small extracellular vesicles (sEVs) from LDR primed cells, before their radiosensitivity was assessed by the clonogenic assay. The protein content of sEVs from LDR primed cells was analyzed with mass spectrometry. Our results show that sEVs contain TGF-β3 regardless of priming status, but only sEVs from LDR primed cells remove HRS in reporter cells. Inhibition of the matrix metalloproteinase (MMP) family prevents removal of HRS, suggesting an MMP-dependent activation of TGF-β3 in the LDR primed cells. We demonstrate a functional interaction between TGF-β3 and activin receptor like kinase 1 (ALK1), by showing that TGF-β3 removes HRS through ALK1 binding, independent of ALK5 and TGF-βRII. These results are an important contribution to a more comprehensive understanding of the mechanism behind TGF-β3 mediated removal of HRS.
ARTICLE | doi:10.20944/preprints202207.0120.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Brain; sensitivity to EMFs; EEG; ERPs; N400; LPP; joint processing effects (JPEs)
Online: 7 July 2022 (09:19:44 CEST)
The effects of transcranial magnetic stimulations (TMS) show that the human brain is impacted by some magnetic fields (EMFs). Moreover, after a delay, it produces potentials that reveal a subsequent processing of this impact. The human brain might also be sensitive to very weak magnetic fields of extremely low frequencies (vwEMFelf). Namely, to the vwEMelf produced by the brain of other persons when they process visual stimuli. In effect, two studies report that the event-related brain potentials (ERPs) that are evoked by presenting a picture to a participant can be modulated by simultaneously presenting a picture to a partner. To confirm it here, we followed most of the methods of these studies. We recorded the ERPs evoked by presenting, at each trial, the photograph of a face. Simultaneously and, most importantly, privately, we presented a partner with the same or with a different face photograph. ERPs of participants were found to depend on that sameness (p0.001), unbeknownst to them. These joint processing effects (JPEs), confirm a sensitivity of the human brain to the vwEMFelf produced by other brains.
ARTICLE | doi:10.20944/preprints202207.0058.v1
Subject: Biology And Life Sciences, Biophysics Keywords: human interferon gamma; human interferon gamma receptor; receptor binding; heparan sulfate; co-receptor; molecular dynamics simulations; sodium chlorate; kynurenine antiproliferative assays; hIFNγ signalling
Online: 5 July 2022 (04:43:05 CEST)
The extremely controversial conclusions about the function of human interferon-gamma (hIFNγ) C-terminus as well as the lack of a consistent model explaining its role in the receptor binding prompted us to scrutinize the interaction of hIFNγ with its extracellular receptor hIFNGR1 in different scenarios by means of molecular dynamics simulations. We find that the two molecules alone fail to form a stable complex but the presence of heparan-sulfate-like oligosaccharides largely facilitates the process by both demobilizing the highly flexible C-termini of the cytokine and assisting in the proper positioning of its globule between the receptor subunits. An antiproliferative-activity essay on cells depleted from surface sulfation confirms qualitatively the simulation-based multistage complex-formation model. Our results reveal the key role of HS and its proteoglycans in all processes involving hIFNγ signalling.
REVIEW | doi:10.20944/preprints202207.0031.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Cell-state transitions; Phenotypic plasticity; Cancer Stem Cells; Intratumoral heterogeneity; Lamarckian Induction; Drug resistance
Online: 4 July 2022 (04:56:00 CEST)
Intratumoral heterogeneity can exist along multiple axes: Cancer Stem Cells (CSCs)/non-CSCs, drug-sensitive/drug-tolerant states and a spectrum of epithelial-hybrid-mesenchymal phenotypes. Further, these diverse cell-states can switch reversibly among one another, thereby posing a major challenge to therapeutic efficacy. Therefore, understanding the origins of phenotypic plasticity and heterogeneity remains an active area of investigation. While genomic components (mutations, chromosomal instability) driving heterogeneity have been well-studied, recent reports highlight the role of non-genetic mechanisms in enabling both phenotypic plasticity and heterogeneity. Here, we discuss various processes underlying phenotypic plasticity such as stochastic gene expression, chromatin reprogramming, asymmetric cell division and the presence of multiple “attractors”. These processes can facilitate a dynamically evolving cell population such that a subpopulation of (drug-tolerant) cells can survive lethal drug exposure and recapitulate population heterogeneity on drug withdrawal, leading to relapse. These drug-tolerant cells can be both pre-existing and also induced by the drug itself through cell-state reprogramming. The dynamics of cell-state transitions both in absence and presence of the drug can be quantified through mathematical models. Such a dynamical systems approach to elucidating patterns of intratumoral heterogeneity by integrating longitudinal experimental data with mathematical models can help design effective combinatorial and/or sequential therapies for better clinical outcomes.
REVIEW | doi:10.20944/preprints202206.0309.v1
Subject: Biology And Life Sciences, Biophysics Keywords: lab-on-a-chip; cell migration; microfluidics; PDMS; hydrogels; femtosecond laser microfabrication; two-photon polymerization
Online: 22 June 2022 (08:21:44 CEST)
Understanding cell migration is a key step to unravel many physiological phenomena and predict several pathologies, like cancer metastasis. In particular, mechanical confinement has been proved to be a key factor in the cellular migration strategy choice. As our insight in the field improves, new tools are needed in order to empower biologists’ analysis capabilities. In this framework, microfluidic devices have been used to engineer the mechanical stimuli and to investigate cellular migration response in a more controlled way. In this work, we will review the existing technologies employed in the realization of microfluidic cellular migration assays, namely soft lithography of PDMS and hydrogels and femtosecond laser micromachining. We will give an overview of the state of the art of these devices, focusing on the different geometrical configurations that have been exploited to study specific aspects of cellular migration. Our scope is to highlight the advantages and possibilities given by each approach and to envisage the future developments in in-vitro migration studies under mechanical confinement in microfluidic devices.
REVIEW | doi:10.20944/preprints202206.0253.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Bioinorganic chemistry; metal-binding; structural biology; zinc; iron; copper; transition metals
Online: 17 June 2022 (09:30:07 CEST)
All living organisms require some metal ions for their energy production as well as metabolic and biosynthetic processes. Within cells, metal ions are involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been a tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted also by the successful applications of neural networks and deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarize recent DL applications enhancing the functional interpretation of metalloprotein structures.
ARTICLE | doi:10.20944/preprints202206.0228.v1
Subject: Biology And Life Sciences, Biophysics Keywords: catastrophe model; multicellular organization; IPS cell
Online: 16 June 2022 (03:51:39 CEST)
Thermodynamic studies consider living entities as dissipative structures. Organisms maintain and develop an orderly structure by exchanging matter, energy, and entropy with the surrounding environment; thus, maintaining life and growth. For a single cell, the temperature, volume, content concentration, and content complexity are four control variables. For warm-blooded animals, both temperature and content concentration are assumed to be constant, and only volume and content complexity, i.e., various proteins, nucleic acids, and small molecular substances in the cell and their interactions, are considered as acting variables. Thus, the potential function of a single cell should conform to the cusp catastrophe model. As the studies on the specific mathematical models of the relationship between the volume and content complexity are not available, we could not propose specific methods for the specific variants of the potential function of this cusp catastrophe model. We could only present our approximate results based on the basic characteristics of the cusp catastrophe model. We speculated that when a single cell is in a stable state, it cannot undergo differentiation, dedifferentiation, and division. These behaviors occur only when the cell enters an unstable state. Based on this speculation, we divided somatic cells of warm-blooded animals into two types, namely stable cells and non-steady cells. If we consider a warm-blooded animal as a whole dissipative structure, its control variables should have steady-state cells, non-steady-state cells, and negative entropy input. If we assume that the negative entropy input is constant, the proportion of non-steady cells and the total number of cells can be used as the control variables of the potential function. For warm-blooded animals, their potential function also conforms to the cusp catastrophe model. Because the studies on the relationship between the proportion of non-steady-state cells and the total cell number are rare, we could not propose specific methods for the variation of the potential function of this cusp catastrophe model. We could only present our approximate results according to the basic characteristics of the cusp catastrophe model. We speculated that as individuals, animals should be in a stable state during development. Once they enter an unstable state, they will fall ill or die. For humans, the proportion of non-steady cells decreases during the growth process from a fertilized egg to old age. From the fertilized egg to adulthood, the total cell number increases; however, in old age, the total cell number begins to decrease gradually. The entire developmental curve will gradually enter an unstable state. We speculated that once the developmental curve of a human enters an unstable state, it is death for the elderly.
ARTICLE | doi:10.20944/preprints202206.0199.v1
Subject: Biology And Life Sciences, Biophysics Keywords: KCNQ1; Kv7.1; IKs; patch-clamp; inherited channelopathy; LQTS
Online: 14 June 2022 (08:42:22 CEST)
We identified a single nucleotide variation (SNV) (c.1264A>G) in the KCNQ1 gene in a 5-year-old boy who presented with a prolonged QT interval. His elder brother and mother, but not sister and father, also had this mutation. This missense mutation leads to a p.Lys422Glu (K422E) substitution in the Kv7.1 protein, never mentioned before. We inserted this substitution in an expression plasmid containing Kv7.1 cDNA and studied the electrophysiological characteristics of the mutated channel expressed in CHO-K1 using the whole-cell configuration of the patch-clamp technique. Expression of the mutant Kv7.1 channel in both homo- and heterozygous conditions, in the presence of auxiliary subunit KCNE1, results in a significant decrease in tail current densities compared to the expression of wild-type (WT) Kv7.1 and KCNE1. This study also indicates that K422E point mutation causes a dominant negative effect. The mutation was not associated with a trafficking defect, the mutant channel protein was confirmed to localize at the cell membrane. This mutation disrupts the poly-Lys strip in the proximal part of the highly conserved cytoplasmic A-B linker of Kv7.1, which was not shown before to be crucial for channel functioning.
ARTICLE | doi:10.20944/preprints202206.0138.v1
Subject: Biology And Life Sciences, Biophysics Keywords: posturography; insomnia; sleep disorders
Online: 9 June 2022 (08:11:21 CEST)
Lack of sleep is a factor that disrupts the receptors' reception of information from the environ-ment and contributes to the emergence of problems with maintaining balance. The main pur-pose of this study was to find out whether Computer Dynamic Posturography could be a useful tool in distinguishing between people who sleep well from people with insomnia. The study participants were 76 male students who were divided into groups based on the results obtained from the Pittsburgh Sleep Quality Questionnaire. In each group, postural stability had been tested using three main tests: Strategy Organization Test SOT, Motor Control Test MCT and Ad-aptation Test ADT. The results of the analysis show that the obtained results differ in the exam-ined groups under the SOT test. Among people with insomnia, higher values of the tested pa-rameters were noted, than with people who sleep well, which translates into a worse ability to maintain balance. The greatest impact is observed when using eyesight and a vestibular system to maintain a stable posture. It was confirmed that Computer Dynamic Posturography is used to differentiate between people who sleep well from people with insomnia in the group of men. Lack of sleep significantly disturbs postural stability.
ARTICLE | doi:10.20944/preprints202205.0392.v1
Subject: Biology And Life Sciences, Biophysics Keywords: atrial-fibrillation; multi-target; drug promiscuity; druggable binding site; flecainide; Nav1.5; Kv1.5; binding site comparison; polypharmacology
Online: 30 May 2022 (10:10:41 CEST)
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that combined blockade of Nav1.5 (and its current INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without effect on ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD), as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We presented a computational workflow for flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the inner cavity and consist of a hydrophobic patch and a polar region, involving residues from S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.
ARTICLE | doi:10.20944/preprints202105.0488.v6
Subject: Biology And Life Sciences, Biophysics Keywords: solar system; complete relativity; nature; mechanics
Online: 23 May 2022 (05:50:22 CEST)
Origin, mechanics and properties of the Solar System are analyzed in the framework of Complete Relativity. The analysis confirms the postulates and hypotheses of the theory with a high degree of confidence. During the analysis, some new hypotheses have emerged. These are discussed and confirmed with various degrees of confidence. To increase confidence or refute some hypotheses, experimental verification is necessary. Main hypotheses and conclusions are: - Solar System is a scaled Carbon isotope with a nucleus in a condensed (bosonic) state and components in various vertically excited states, - Earth is a living being of extremely introverted intelligence, life is common everywhere, albeit extroverted complex forms are present on planetary surfaces only during planetary neurogenesis, - anthropogenic climate change is only a part (trigger from one perspective) of bigger global changes on Earth and in the Solar System during planetary neurogenesis, - major extinction events are relative extinctions, a regular part of transformation and transfer of life in the process of planetary neurogenesis.
ARTICLE | doi:10.20944/preprints202205.0255.v1
Subject: Biology And Life Sciences, Biophysics Keywords: SILCS; hERG channel; Physicochemical properties; Multiple linear regression; FragMaps
Online: 19 May 2022 (08:46:24 CEST)
Human ether-a-go-go-related gene (hERG) potassium channel is well-known contributor to drug-induced cardiotoxicity and therefore an extremely important target when performing safety assessments of drug candidates. Ligand-based approaches in connection with quantitative structure active relationships (QSAR) analyses have been developed to predict hERG toxicity. Availability of the recent published cryogenic electron microscopy (cryo-EM) structure for the hERG channel opened the prospect for using structure-based simulation and docking approaches for hERG drug liability predictions. In recent time, the idea of combining structure- and ligand-based approaches for modeling hERG drug liability has gained momentum offering improvements in predictability when compared to ligand-based QSAR practices alone. The present article demonstrates uniting the structure-based SILCS (site-identification by ligand competitive saturation) approach in conjunction with physicochemical properties to develop predictive models for hERG blockade. This combination leads to improved model predictability based on Pearson’s R and percent correct (represents rank-ordering of ligands) metric for different validation sets of hERG blockers involving diverse chemical scaffold and wide range of pIC50 values. The inclusion of the SILCS structure-based approach allows determination of the hERG region to which compounds bind and the contribution of different chemical moieties in the compounds to blockade, thereby facilitating the rational ligand design to minimize hERG liability.
ARTICLE | doi:10.20944/preprints202205.0234.v1
Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; virions mass balance; spatial modelling of toxics concentrations; human exposure to airborne substances; Substance Flow Analysis (SFA); environmental routes of toxic viruses; primary production of SARS-2 virions
Online: 17 May 2022 (14:19:43 CEST)
Measures in the SARS-CoV-2 pandemic were based on rough ideas regarding transmission routes of pathogens. Quantified models of physical transmission routes are mostly lacking, a gap to be filled. Vaccines and medicines, important, are not studied here. We first survey main routes, from primary production in the alveoli and intestines to emissions, environmental routes, to exposure and alveolar infection. Next, specific routes are modelled, mostly at a preliminary state, open to systematic improvement. Starting from a standardized emitter, modelling results show extreme differences in potential exposure, in a range covering up to 4 orders of magnitude. The outcomes are pathogen-specific, already different between SARS-CoV-2 and influenza. Extreme exposures may result in smaller spaces; with lower ventilation rates; with a high density of emitting persons per m3; who stay there for several hours; and visitors staying more than a few minutes. In spaces where a build-up of concentrations is low, exposures are low, lowest in open air situations. A main conclusion for the next pandemic is that a quantified model can give strong guidance on where measures are primarily due. For SARS-CoV-2, ventilation can be improved short-term. Longer-term, effective ventilation rules and adaptation of buildings may reduce high exposures substantially.
ARTICLE | doi:10.20944/preprints202205.0200.v1
Subject: Biology And Life Sciences, Biophysics Keywords: membrane potential; Nernst equation; ion adsorption; surface charge; surface potential
Online: 16 May 2022 (08:12:52 CEST)
Although there is a common physiological notion that the origin of the membrane potential is attributed to transmembrane ion transport, it is theoretically possible to explain its generation by the mechanism of ion adsorption. It was previously suggested that the ion adsorption mechanism led even to the potential formulas which are even identical to either the famous Nernst equation or Goldman-Hodgkin-Katz equation. Our further analysis shown in this paper indicates that the potential formula based on the ion adsorption mechanism leads to one equation which is the function of material surface charge density and the material surface potential. Furthermore, we confirmed that the equation holds in all the different experimental systems we studied. Although we have not succeeded in elucidating why such an equation is established, the equation appears to be the key equation governing the characteristics of the membrane potential regardless of the systems in question.
REVIEW | doi:10.20944/preprints202205.0171.v1
Subject: Biology And Life Sciences, Biophysics Keywords: principal component analysis; collective variables; molecular dynamics; energy landscape; solvent effects; linear response theory; independent component analysis
Online: 12 May 2022 (10:53:37 CEST)
Principal component analysis (PCA) is used to reduce the dimensionalities of high dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods, and their applications for investigating protein dynamics.
ARTICLE | doi:10.20944/preprints202205.0006.v1
Subject: Biology And Life Sciences, Biophysics Keywords: structured illumination; fluorescence; brain; multi-camera
Online: 4 May 2022 (12:24:22 CEST)
Fluorescence microscopy provides an unparalleled tool for imaging biological samples. However, producing high-quality volumetric images quickly and without excessive complexity remains a challenge. Here, we demonstrate a simple multi-camera structured illumination microscope (SIM) capable of simultaneously imaging multiple focal planes, allowing for the capture of 3D fluorescent images without any axial movement of the sample. This simple setup allows for the acquisition of many different 3D imaging modes, including 3D time lapses, high-axial-resolution 3D images, and large 3D mosaics.
REVIEW | doi:10.20944/preprints202204.0156.v1
Subject: Biology And Life Sciences, Biophysics Keywords: nanovesicles; flow; homology; vortex; Betti number; Borsuk–Ulam theorem
Online: 18 April 2022 (06:14:33 CEST)
Mechanical properties such as shape, volume and size affect the dynamics of biological systems. Most of the current methodological approaches are inclined to remove the existence of holes and impurities from systems’ description, regarding them as routes toward mechanical failure. On the contrary, we suggest that the occurrence of holes might be of utmost functional importance, allowing reversible transformations of cellular structures. The focus here is on the widespread occurrence of intracytoplasmic holes, that deeply modifies the topology of living cells and provides researchers with novel operational tools to investigate intracellular dynamics. We take as example the prokaryotic gas vesicles, i.e., intracellular cavities filled with gases spreading from the nearby medium. The mechanical and topological cellular properties dictated by intracytoplasmic holes are investigated, focusing on the physical constraints imposed by their very existence. For instance, the presence of gas vesicles breaks the cytoplasmic homogeneity, leading to inhomogeneity in functional activities and modifications in intracellular flows. Also, a topological approach to cytoplasmic holes suggests novel physiological roles for gas vesicles. For example, the gas vesicles’ ability to increase/decrease cellular volumes provides a mechanism that counteracts the detrimental effects of the surface/volume ratio. In conclusion, a structural/methodological approach based on the occurrence of holes testifies once again how the simple biophysical structure alone can dictate the function.
TECHNICAL NOTE | doi:10.20944/preprints202203.0146.v1
Subject: Biology And Life Sciences, Biophysics Keywords: expansion microscopy; yeast; Saccharomyces cerevisiae; super-resolution
Online: 10 March 2022 (10:51:02 CET)
The unicellular eukaryote S. cerevisiae is an invaluable resource for the study of basic eukaryotic cellular and molecular processes. However, due to its small size compared to other eukaryotic organisms the study of subcellular structures is challenging. Expansion microscopy (ExM) holds great potential to study the intracellular architecture of yeast, especially when paired with pan-labelling techniques visualising the full protein content inside cells. ExM allows to increase imaging resolution by physically enlarging a fixed sample that is embedded and cross- linked to a swellable gel followed by isotropic expansion in water. The cell wall present in fungi – including yeast – and Gram-positive bacteria is a resilient structure that resists denaturation and conventional digestion processes usually used in ExM protocols, resulting in uneven expansion. Thus, the digestion of the cell wall while maintaining the structure of the resulting protoplasts are crucial steps to ensure isotropic expansion. For this reason, specific experimental strategies are needed, and only a few protocols are currently available. We have developed a modified ExM protocol for S. cerevisiae, with 4x expansion factor, which allows the visualisation of the ultrastructure of the cells. Here, we describe the experimental procedure in detail, focusing on the most critical steps required to achieve isotropic expansion for ExM of S. cerevisiae.
COMMUNICATION | doi:10.20944/preprints202203.0079.v1
Subject: Biology And Life Sciences, Biophysics Keywords: thermal neutral; acclimation; acclimatization; adaptation; health; indoor environments
Online: 4 March 2022 (11:23:44 CET)
The goal of this short communication is to analyze a published discussion that states that long-term residing at a thermoneutral indoor temperature condition hinders human thermal acclimation capacities. According to current research, human thermal acclimation and acclimatization capacities can be easily gained through repeated heat and cold exposures mixed with physical activity over a period of days (often 3–21 days). Furthermore, heat and cold adaptations are not permanent, and heat acclimation would progressively fade away if frequent heat exposures (associated with physical work/exercise) were discontinued. People who have been heat acclimatized for a long period and live in tropical places may progressively lose their physiological and perceptual benefits when they shift to temperate zones. On the other hand, the decay of cold acclimation and cold acclimatization has not been well examined, demanding future research on this area. To summarize, there is no evidence to support the claim that extended exposure to thermoneutral conditions impairs human acclimatization abilities.
ARTICLE | doi:10.20944/preprints202203.0050.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Coronary vasculature; lumped parameter model; fractional flow reserve; computational cardiology
Online: 2 March 2022 (12:34:43 CET)
Background. The treatment of coronary stenosis relies on invasive high risk surgical assessment to generate the fractional flow reserve diagnostics index, a ratio of distal to proximal pressures in respect of coronary atherosclerotic plaque causing stenosis. Non-invasive methods are therefore a need of the times. This study proposes an extensible mathematical description of the coronary vasculature that permits rapid estimation of the coronary fractional flow reserve. Methods. By adapting an existing closed loop model of human coronary blood flow, the effects of large vessel stenosis and microvascular disease on fractional flow reserve were quantified. Several simula-tions generated flow and pressure information which was used to compute fractional flow re-serve under a spectrum of conditions including focal stenosis, diffuse stenosis, and microvascular disease. Sensitivity analysis stratified the influence of model parameters on the index. The model was simulated as coupled non-linear ordinary differential equations and numerically solved us-ing an implicit higher order method. Results. Large vessel stenosis affected fractional flow re-serve. The model predicts that the presence, rather than severity, of microvascular disease affect coronary flow deleteriously. Sensitivity analysis revealed that heart rate may not affect the index. Conclusions. The model provides a computationally inexpensive instrument for future in silico coronary blood flow investigations as well as clinical-imaging decision making. A combination of focal and diffuse stenosis appears to be essential in reducing the index. In addition to pressure measurements in the large epicardial vessels, diagnosis of microvascular disease is essential. The independence of the index with respect to heart rate suggests that computationally inexpensive steady state simulations may provide sufficient information to reliably compute the index.
REVIEW | doi:10.20944/preprints201902.0122.v4
Subject: Biology And Life Sciences, Biophysics Keywords: Leishmania; leishmaniasis; Theoretical Physics and Chimistry; Molecular Dynamics
Online: 1 March 2022 (12:58:34 CET)
We report on the state of the art of research on proteins recognized as potential targets for the development of Leishmania treatments and the search of active chemical species. We have reviewed information from experimental in vitro, in vivo, or in silico sources. We classify the gathered information on: a) vector taxonomy and geographical distribution, b) parasite taxonomy, geographical distribution, c) enzymatic function of proteins related to the parasite/host in any of its development states, id. est., oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases and cytokines, and d) information on standard and non-standard treatments from bioactive chemical species. Our aim is to provide a much needed reference layout for research efforts aimed to understand the interaction mechanisms of ligand-protein activation/inactivation processes, specifically related to Leishmania, thus, we focus on enzymes known to be part of the biochemical molecular pathways initiated following a Leishmania infectious episode.
ARTICLE | doi:10.20944/preprints202201.0354.v2
Subject: Biology And Life Sciences, Biophysics Keywords: origin of life; disspative structuring; prebiotic chemistry; abiogenisis; non-equilibrium thermodynamics; thermodynamic dissipation theory
Online: 31 January 2022 (13:13:26 CET)
There is little doubt that life's origin followed from the known physical and chemical laws of Nature. The most general scientific framework incorporating the laws of Nature and applicable to most known processes to good approximation, is that of thermodynamics and its extensions to treat out-of-equilibrium phenomena. The event of the origin of life should therefore also be amenable to such an analysis. In this paper, I describe the non-equilibrium thermodynamic foundations of the origin of life for the non-expert. This ``Thermodynamic Dissipation Theory for the Origin of Life'' is founded on Classical Irreversible Thermodynamic theory developed by Lars Onsager, Ilya Prigogine, and coworkers.
HYPOTHESIS | doi:10.20944/preprints202104.0606.v2
Subject: Biology And Life Sciences, Biophysics Keywords: Parkinson’s disease; alpha-synuclein; Lewy bodies; phase transition; thermodynamics; and mitochondria
Online: 10 January 2022 (12:23:19 CET)
I wish to suggest a physiological function for alpha-synuclein (a-syn) that has the potential to explain its role in pathology. Intraneuronal proteinaceous Lewy Bodies (LBs), the pathological hallmark of Parkinson’s disease and other synucleinopathies, consist majorly of a-syn. Ample evidence suggests that LBs are not the result of simple amyloidosis of cytosolic a-syn. Benign soluble unstructured a-syn gets converted into toxic species which preferentially accumulates in LBs. But how these aberrant a-syn molecules are produced in the cytosol, is still not clear. The present hypothesis is an effort to relate a metabolic reaction specific to neuronal function, that is, phase transition, with the pathobiology of a-syn. During high frequency stimulation, which entails rapid phase transition reactions at the presynaptic compartment, aberrant interaction of a-syn with the membrane occasionally generates toxic a-syn molecules. My conjecture is that the physiological function of a-syn is to modulate membrane fluidity by a process wherein it goes through a conformation cycle driven by a flux of energy from mitochondria. It is the range of toxic a-syn produced during aberrant phase transition reaction that is responsible for pathology, not the normal a-syn that reenters the conformation cycle, thereby, resolving the paradox of the Janus-face of a-syn.
ARTICLE | doi:10.20944/preprints202201.0046.v1
Subject: Biology And Life Sciences, Biophysics Keywords: voltage-gated sodium channels; cardiac sodium channels; SCN5A; veratridine; toxins; molecular docking; Rosetta; electrophysiology; site-directed mutagenesis
Online: 5 January 2022 (18:02:52 CET)
The cardiac sodium ion channel (NaV1.5) is a protein with four domains (DI-DIV), each with six transmembrane segments. Its opening and subsequent inactivation results in the brief rapid influx of Na+ ions resulting in the depolarization of cardiomyocytes. The neurotoxin veratridine (VTD) inhibits NaV1.5 inactivation resulting in longer channel opening times, and potentially fatal action potential prolongation. VTD is predicted to bind at the channel pore, but alternative binding sites have not been ruled out. To determine the binding site of VTD on NaV1.5, we performed docking calculations and high-throughput electrophysiology experiments. The docking calculations identified two distinct binding regions. The first site was in the pore, close to the binding site of NaV1.4 and NaV1.5 blocking drugs in experimental structures. The second site was at the “mouth” of the pore at the cytosolic side, partly solvent-exposed. Mutations at this site (L409, E417, and I1466) had large effects on VTD binding, while residues deeper in the pore had no effect, consistent with VTD binding at the mouth site. Overall, our results suggest a VTD binding site close to the cytoplasmic mouth of the channel pore. Binding at this alternative site might indicate an allosteric inactivation mechanism for VTD at NaV1.5.
ARTICLE | doi:10.20944/preprints202201.0022.v1
Subject: Biology And Life Sciences, Biophysics Keywords: clay; mica; biotite; muscovite; origin of life; abiogenesis; mechanical energy; work; wet-dry cycles
Online: 4 January 2022 (20:36:31 CET)
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral, mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged.
ARTICLE | doi:10.20944/preprints202112.0500.v1
Subject: Biology And Life Sciences, Biophysics Keywords: immunoglobulin G; complement component C1; high-speed atomic force microscopy; CH1; CL
Online: 31 December 2021 (10:36:38 CET)
Immunoglobulin G (IgG) adopts a modular multidomain structure that mediates antigen recognition and effector functions, such as complement-dependent cytotoxicity. IgG molecules are self-assembled into a hexameric ring on antigen-containing membranes, recruiting the complement component, C1q. To provide deeper insights into the initial step of the complement pathway, we report a high-speed atomic force microscopy study for quantitative visualization of the interaction between IgG and the C1 complex composed of C1q, C1r, and C1s. Results showed that C1q in the C1 complex is restricted regarding internal motion and has a stronger binding affinity for on-membrane IgG assemblages than C1q alone, presumably because of smaller conformational entropy loss upon binding. Furthermore, we visualized a 1:1 stoichiometric interaction between C1/C1q and an IgG variant that lacks the entire CH1 domain in the absence of antigen. In addition to the canonical C1q-binding site on Fc, their interactions are mediated through a secondary site on the CL domain that is cryptic in the presence of the CH1 domain. Our findings offer clues for novel-modality therapeutic antibodies.
ARTICLE | doi:10.20944/preprints202112.0228.v1
Subject: Biology And Life Sciences, Biophysics Keywords: lipofuscin; retina; retinal pigment epithelium; docosahexaenoate; docosahexaenoic acid; fluorescence; photodegradation; photobleaching; cell viability; endocytic activity
Online: 14 December 2021 (11:41:14 CET)
Retinal lipofuscin accumulates with age in the retinal pigment epithelium (RPE) where its fluorescence properties are used to assess the retinal health. It was observed that there is a decrease in lipofuscin fluorescence above the age of 75 years and in early stages of age-related macular degeneration (AMD). The purpose of this study was to investigate the response of lipofuscin isolated from human RPE, and lipofuscin-laden-cells to visible light, and determine whether an abundant component of lipofuscin, docosahexaenoate (DHA) can contribute to lipofuscin fluorescence upon oxidation. Exposure of lipofuscin to visible leads to a decrease of its long-wavelength fluorescence at about 610 nm with concomitant growth of the short-wavelength fluorescence. The emission spectrum of photodegraded lipofuscin exhibits similarity with that of oxidized DHA. Exposure to light of lipofuscin-laden cells leads to loss of lipofuscin granules from cells, while retaining cell viability. The spectral changes of fluorescence in lipofuscin-laden cells resemble those seen during photodegradation of isolated lipofuscin. Our results demonstrate that fluorescence emission spectra together with quantitation of intensity of long-wavelength fluorescence can serve as a marker useful for lipofuscin quantification and for monitoring its oxidation, thereby useful for screening the retina for increased oxidative damage and early AMD-related changes.
REVIEW | doi:10.20944/preprints202112.0174.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Calcium channels; somatic exocytosis; serotonin; extrasynaptic release; leech
Online: 10 December 2021 (12:16:40 CET)
The soma, dendrites and axon of neurons may display calcium-dependent release of transmitters and peptides. Such release is named extrasynaptic for occurring in the absence of synaptic structures. This review describes cooperative actions of three calcium sources on somatic exocytosis. Emphasis is given to the release of serotonin by the classical serotonergic leech Retzius neuron, which has allowed detailed studies of each step between excitation and exoctytosis. Trains of action potentials induce transmembrane calcium entry through L-type channels. If the frequency of action potentials is above 5 Hz, summation of calcium transients upon individual action potentials increases the intracellular calcium concentration to activate calcium–induced calcium release. The amplified calcium wave activates motochondrial ATP synthesis that fuels the transport of vesicles to the plasma membrane. Serotonin that is released activates autoreceptors coupled to phospholipase C. Production of IP3 produces release of calcium that sustains the large-scale exocytosis. The swiss-clock workings of the release machinery for somatic exocytosis has a striking disadvantage. The essential calcium-releasing endoplasmic reticulum that lays between resting vesicles and the plasma membrane becomes an obstacle for the vesicle transport. Such architecture reduces drastically the thermodynamic efficiency of the vesicle transport and elevates its energy cost..
ARTICLE | doi:10.20944/preprints202111.0406.v1
Subject: Biology And Life Sciences, Biophysics Keywords: CBNs; amino acids; Molecular dynamics
Online: 22 November 2021 (14:22:59 CET)
We research the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional-graphene(Graphene33). Their curvatures decrease sequentially, and all of CNT are single-walled carbon nanotubes. We have observed that as the curvature of CBNs decreases, the adsorption effect of 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and “Benzene-like” Pro also have a strong adsorption effect with carbon-based nanoparticles.
ARTICLE | doi:10.20944/preprints202111.0098.v1
Subject: Biology And Life Sciences, Biophysics Keywords: spatiotemporal analysis; high to ultra high spatial resolution; high to very high temporal resolution; NDVI; NIR; neural network modelling, Bay of Mont-Saint-Michel
Online: 4 November 2021 (09:35:50 CET)
The salt marshes, lying at the land-sea temperate interface, furnish a plethora of ecosystems services such as biodiversity niche support, ocean-climate change regulation, ornithology recreo-tourism or plant gathering by hand. They undergo significant worldwide losses due to their conversion into crop fields and to their spatial compression between the rising sea-level and the armoring shoreline. Their monitoring however requires to use a suite of remote sensing sensors to embrace the regional scale while capturing the plant details. This research innovatively adopts a multiscale approach using a cascading spaceborne and airborne process, from the 10-m Sentinel-2, through the 3-m Dove, to the 0.03-m unmanned airborne vehicle (UAV) imageries. The high to very high temporal resolution of the Sentinel-2 and Dove enabled to cover twenties and tens of km2 over five and four years, respectively, in the form of normalized difference vegetation index (NDVI) classes, associated with microphytobenthos, low, medium and high salt marsh vegetation, including the opportunistic Elyma genus. The NDVI was then modelled at the UAV scale (a few km2) using a three-layered NN prediction, providing the final near-infrared (NIR), and the intermediate red, green and blue reflectance imageries, calibrated/validated/tested with the Dove reflectance imageries (R2NIR=0.98, R2red=0.88, R2green=0.84, and R2blue=0.90). The 100fold increase in pixel size allowed to detect the decimeter-scale objects of the tidal flats and salt marshes, to enlarge the NDVI class ranges, and hold great promise to model other spectral bands at the UAV scale for further deeply enhancing the salt marsh mapping.
ARTICLE | doi:10.20944/preprints202110.0455.v1
Subject: Biology And Life Sciences, Biophysics Keywords: connexin hemichannel; gap junction; oxidative stress; Inflammatory receptors; Fasudil; Y-27632.
Online: 29 October 2021 (13:12:44 CEST)
Connexin 43 (Cx43) is expressed in kidneys and constitutes a feedforward mechanism leading to inflammation in other tissues where they form hemichannels and gap junction channels. However, the possible functional relationship between these membrane channels and their role in damaged renal cells remains unknown. Here, analyses of ethidium uptake and thiobarbituric acid reactive species revealed that TNF-α plus IL-1β increase Cx43 hemichannel activity and oxidative stress in MES-13 cells, a cell line derived from mesangial cells. The latter also was accompanied by a reduction in gap junctional communication, whereas western blotting analysis showed a progressive increase of phosphorylated MYPT (a substrate of RhoA/ROCK) and Cx43 upon TNF-α/IL-1β treatment. Additionally, inhibition of RhoA/ROCK strongly diminished the TNF-α/IL-1β-induced activation of Cx43 hemichannels and reduction in gap junctional coupling. We propose that activation of Cx43 hemichannels and inhibition of cell coupling during pro-inflammatory conditions could contribute to oxidative stress and damage of mesangial cells via the RhoA/ROCK pathway.
ARTICLE | doi:10.20944/preprints202110.0443.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Keywords: Corneal Biomechanics; Corneal structure; Corneal Aberrations; Optical Density; Scheimpflug imaging; Ocular Response Analyzer.
Online: 28 October 2021 (15:24:20 CEST)
Optical properties of the cornea are responsible for correct vision, ultrastructure allows optical transparency and biomechanical properties governs the shape, elasticity or stiffness of the cor-nea affecting ocular integrity and intraocular pressure. Therefore, optical aberrations, corneal transparency, structure and biomechanics play a fundamental role in the optical quality of hu-man vision, ocular health and refractive surgery outcomes. However, the convergence of those properties is not yet reported at macroscopic scale within the hierarchical structure of the cornea. This work explores the relationships between biomechanics, structure and optical properties (corneal aberrations and optical density) at macrostructural level of the cornea through dual Placido-Scheimpflug imaging and air-puff tonometry systems in a healthy young adult popula-tion. Results showed convergence between optical transparency, corneal macrostructure and biomechanics.
ARTICLE | doi:10.20944/preprints202109.0403.v1
Subject: Biology And Life Sciences, Biophysics Keywords: RKIP expression regulation; Stochastic binary regulation of gene expression; Treatment targeting RKIP levels increase; Reduction of heterogeneity of treatment response
Online: 23 September 2021 (11:43:54 CEST)
In this manuscript we use an exactly solvable stochastic binary model for regulation of gene expression to analyse the dynamics of response to a treatment aiming to modulate the number of transcripts of RKIP gene. We demonstrate the usefulness of our method simulating three treatment scenarios aiming to reestablish RKIP gene expression dynamics towards pre-cancerous state: i. to increase the promoter’s ON state duration; ii. to increase the mRNAs’ synthesis rate; iii. to increase both rates. We show that the pre-treatment kinetic rates of ON and OFF promoter switching speeds and mRNA synthesis and degradation will affect the heterogeneity and time for treatment response. Hence, we present a strategy for reducing drug dosage by simultaneously targeting multiple kinetic rates. That enables a reduction of treatment response time and heterogeneity which in principle diminishes the chances of emergence of resistance to treatment. This approach may be useful for inferring kinetic constants related to expression of antimetastatic genes or oncogenes and on the design of multi-drug therapeutic strategies targeting master regulatory genes.
ARTICLE | doi:10.20944/preprints202109.0390.v1
Subject: Biology And Life Sciences, Biophysics Keywords: COVID-19; vibraimage; behavioral parameters; diagnosis accuracy; ANN; AI
Online: 22 September 2021 (16:28:12 CEST)
The Covid-19 pandemic spreads in waves for a year and a half, despite significant worldwide efforts, the development of biochemical diagnostic methods and population vaccination. One of the reasons for the infection spread is the impossibility of early disease detection through biochemical diagnostics, since biochemical processes slowly develop in a body. At the same time, well known that behavioral characteristics of a person, measured based on reflex movements, are capable for inertialess assessment of psychophysiological parameters. Vibraimage technology is the method of head micromovements video processing by inter-frame difference accumulation and converting spatial and temporal characteristics of the inter-frame difference into behavioral and psychophysiological parameters. Here we shown that behavioral parameters measured by vibraimage changed during COVID-19 infection. The identification of changes signs in behavioral parameters detected by AI trained on patients and controls. The best diagnostic accuracy (higher 94%) obtained using instantaneous values of behavioral parameters measured with the following vibraimage settings: 10Hz frequency of basic measurements; 25 inter-frame difference accumulations and averaging the diagnostic results over period of at least 5 seconds. COVID-19 diagnoses by behavioral parameters showed earlier (5-7 days) detection of the disease compared to symptoms and positive results of biochemical RT-PCR testing. Proposed method for COVID-19 diagnosis indicates infected persons within 5 seconds video processing using standard television cameras (web, IP) and computers, allows mass testing/selftesting and will stop the pandemic spread. We assume that head micromovements analysis for diagnosis of various diseases is possible not only with the help of vibraimage technology. Further research of human head micromovement analysis will help stop the COVID-19 pandemic and will contribute to the development of new contactless and environmentally friendly methods for early diagnosis of diseases.
ARTICLE | doi:10.20944/preprints202109.0333.v1
Subject: Biology And Life Sciences, Biophysics Keywords: small RNA Oxys; RNA chaperone Hfq protein; gene expression regulator; molecular dynamics simulations; binding free energy; interaction entropy
Online: 20 September 2021 (12:47:28 CEST)
Under the oxidative stress condition, the small RNA (sRNA) Oxys that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in defection of gene regulation. But, how the Hfq protein interacts with sRNA Oxys and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized Born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result is in excellent correlation with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly comes from the increased van der Waals interactions (vdW). This research explores the binding mechanism between Oxys and chaperone protein Hfq, and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights on the mechanism of gene expression regulation affected by protein mutations.
ARTICLE | doi:10.20944/preprints202109.0265.v1
Subject: Biology And Life Sciences, Biophysics Keywords: poly-PR/GR; neurodegenerative disease; LLPS; p53; intrinsically disordered domains; membraneless organelles
Online: 15 September 2021 (14:43:48 CEST)
Abstract: The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the presence of poly-PR/GR dipeptide repeats which are encoded by the C9orf72 gene. Recently, it was shown that poly-PR/GR alters chromatin accessibility which results in stabilization and enhancement of transcriptional activity of the tumor suppressor p53 in several neurodegenerative disease models. Reduction of p53 protein levels in cell and model organisms protects against neurotoxicity of poly-PR, and partially protects against neurotoxicity of poly-GR. Here, we aimed to study the detailed molecular mechanisms how p53 contributes to poly-PR/GR mediated neurodegeneration. Using a combination of biophysical techniques such as nuclear magnetic resonance (NMR) spectroscopy, fluorescence polarization, turbidity assays and differential interference contrast (DIC) microscopy, we found that p53 physically interacts with poly-PR/GR and triggers liquid-liquid phase separation of p53. We identified p53 transactivation domain 2 (TAD2) as the main binding site for PR25/GR25 and show that binding of poly-PR/GR to p53 is mediated by a network of electrostatic and/or hydrophobic interactions. Our findings might help to understand the mechanistic role of p53 in poly-PR/GR - associated neurodegeneration.
ARTICLE | doi:10.20944/preprints202109.0101.v1
Subject: Biology And Life Sciences, Biophysics Keywords: E6; variants; MAGI-1; molecular dynamic simulation; docking
Online: 6 September 2021 (13:51:17 CEST)
Oncogenic protein E6 from Human Papilloma Virus 16 (HPV-16) mediates the degradation of Membrane-associated guanylate kinase with inverted domain structure-1 (MAGI-1), throughout the interaction of its protein binding motif (PBM) with the Discs-large homologous regions 1 (PDZ1) domain of MAG1-1. Generic variation in the E6 gene that translates to changes in the protein’s amino acidic sequence modifies the interaction of E6 with the cellular protein MAGI-1. MAGI-1 is a scaffolding protein found at tight junctions of epithelial cells, where it interacts with a variety of proteins regulating signaling pathways. MAGI-1 is a multidomain protein containing two WW (rsp-domain-9), one guanylate kinase-like, and six PDZ domains. PDZ domains played an important role in the function of MAGI-1 and served as targets for several viral proteins including the HPV-16 E6. The aim of this work was to evaluate, with an in silico approach, employing molecular dynamics simulation and protein-protein docking, the interaction of the intragenic variants E-G350 (L83V), E-C188/G350 (E29Q/L83V), E-A176/G350 (D25N/L83V), E6-AAa (Q14H/H78Y/83V) y E6-AAc (Q14H/I27RH78Y/L83V) and E6-reference of HPV-16 with MAGI-1. We found that variants E-G350, E-C188/G350, E-A176/G350, AAa and AAc increase their affinity to our two models of MAGI-1 compared to E6-reference.
REVIEW | doi:10.20944/preprints202108.0453.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Hybrid epithelial/mesenchymal phenotypes; Collective cell migration; epithelial-mesenchymal heterogeneity; mathematical modeling; cell-state transition; live-cell imaging
Online: 23 August 2021 (14:32:04 CEST)
The Epithelial- Mesenchymal Transition (EMT) is a biological phenomenon associated with explicit phenotypic and molecular changes in cellular traits. Unlike the earlier-held popular belief of it being a binary process, EMT is now thought of as a landscape including diverse hybrid E/M phenotypes manifested by varying degrees of the transition. These hybrid cells can co-express both epithelial and mesenchymal markers and/or functional traits, and can possess the property of collective cell migration, enhanced tumor-initiating ability, and immune/targeted therapy-evasive features, all of which are often associated with worse patient outcomes. These characteristics of the hybrid E/M cells have led to a surge in studies that map their biophysical and biochemical hallmarks that can be helpful in exploiting their therapeutic vulnerabilities. This review discusses recent advances made in investigating hybrid E/M phenotype(s) from diverse biophysical and biochemical aspects by integrating live cell-imaging, cellular morphology quantification and mathematical modeling, and highlights a set of questions that remain unanswered about the dynamics of hybrid E/M states.
ARTICLE | doi:10.20944/preprints202107.0039.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Mixed-chain lipids; Neutron scattering; X-ray scattering; MD simulations
Online: 1 July 2021 (22:26:58 CEST)
We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, reported previously for gel phase structures also extend to the physiological more relevant fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementary performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. This suggests that hydrocarbon chain interdigitation plays only a minor role in transbilayer coupling. For both cases of adaption to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.
Subject: Biology And Life Sciences, Biophysics Keywords: consciousness 1; subjective experience 2; will 3; agency 4; self 5; psychopathology 6; treatment 7; transcranial near infrared light 8; biophotomodulation 9
Online: 25 May 2021 (08:44:47 CEST)
In this paper I will address Dr. Sonne’s questions about will, agency, choice, consciousness, relevant brain regions, impacts of disorders and their therapeutics, and I will do this by referring to my theory, Dual-brain Psychology, which posits that within most of us there exist two mental agencies with different experiences, wills, choices, and behaviors. Each of these agencies is associated as a trait with one brain hemisphere (either left or right) and its composite regions. One of these agencies is more adversely affected by past traumas and is more immature and more symptomatic while the other is more mature and healthier. The theory has extensive experimental support through 17 peer-reviewed publications with clinical and non-clinical research. I will discuss how this theory relates to the questions that Dr. Sonne presented and will discuss also my published theory on the physical nature of subjective experience and its relation to the brain and how that theory interacts with DBP, and how the 2 theories relate to subjective experience, will, behavior, psychopathology and its treatment.
ARTICLE | doi:10.20944/preprints202105.0394.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Modularity; Protein-to-protein interaction networks; Spectral characterization; Tree of life
Online: 17 May 2021 (16:56:57 CEST)
Modularity and organizational hierarchy are important concepts in understanding the structure and evolution of interactions in complex biological systems. In this work, we introduce and use a spectral characterization measure (Spectral Entropy) to quantify modularity in protein-to-protein interaction (PPI) networks in species across the tree of life. We evaluated the relation between the size of a PPI network and its (Spectral Entropy-based) modularity, and found a sigmoidal response between the two. We also found significant differences in the distribution of Spectral Entropy values among the three domains of life (Bacteria, Archaea, Eukaryotes). To explore further correlations with biological traits, we focused solely on bacterial PPI networks, which are the most numerous among the three domains and had associated trait metadata, and investigated how modularity impacts or is impacted by growth, aerobicity, selection and location on the tree of life. We found no relation between maximal growth rate and Spectral Entropy, but a strong dependence between G-C content (a proxy for selection) and Spectral Entropy. We also discovered that Spectral Entropy is negatively affected by phylogenetic placement (evolutionary distance from the last universal common ancestor). The general nature of the Spectral Entropy measure of hierarchical modularity in networks suggests that it will be useful in other settings where structural properties of real-world networks are being compared.
ARTICLE | doi:10.20944/preprints202105.0042.v1
Subject: Biology And Life Sciences, Biophysics Keywords: viral particles; radiobiology; RNA detection; microbiology; matter identification; particle physics; physical modelling; particle accelerators in environmental studies
Online: 10 May 2021 (15:35:15 CEST)
This study presents a methodology to reveal traces of viral particles, as aerosol with known chemical and molecular structure, in a sample by means of photon and electron interactions. The method is based on Monte Carlo simulations and on the analysis of photon-electron fluxes-spectra through energy channels counts as a function of different aerosol viral concentrations in the air sample and looking at the peculiar photon/electron interactions with the potential abnormal atomic hydrogen (H), oxygen (O), carbon (C), and phosphorus (P) compositions present in the air sample as a function of living and nonliving matter with PO4 group RNA/DNA strands in a cluster configuration.
ARTICLE | doi:10.20944/preprints202104.0681.v1
Subject: Biology And Life Sciences, Biophysics Keywords: non-classical logic; Richard Avenarius; Nicholas of Autrecourt; aganglionosis; Paolo and Francesca; Scholastics; Mohammed Ali.
Online: 26 April 2021 (15:12:32 CEST)
Set theory faces two difficulties: formal definitions of sets/subsets are incapable of assessing biophysical issues; formal axiomatic systems are complete/inconsistent or incomplete/consistent. To overtake these problems reminiscent of the old-fashioned principle of individuation, we provide formal treatment/validation/operationalization of a methodological weapon termed “outer approach” (OA). The observer’s attention shifts from the system under evaluation to its surroundings, so that objects are investigated from outside. Subsets become just “holes” devoid of information inside larger sets. Sets are no longer passive containers, rather active structures enabling their content’s examination. Consequences/applications of OA include: a) operationalization of paraconsistent logics, anticipated by unexpected forerunners, in terms of advanced truth theories of natural language, anthropic principle and quantum dynamics; b) assessment of embryonic craniocaudal migration in terms of Turing’s spots; c) evaluation of hominids’ social behaviors in terms of evolutionary modifications of facial expression’s musculature; d) treatment of cortical action potentials in terms of collective movements of extracellular currents, leaving apart what happens inside the neurons; e) a critique of Shannon’s information in terms of the Arabic thinkers’ active/potential intellects. Also, OA provides an outer view of a) humanistic issues such as the enigmatic Celestino of Verona’s letter, Dante Alighieri’s “Hell” and the puzzling Voynich manuscript; b) historical issues such as Aldo Moro’s death and the Liston/Clay boxing fight. Summarizing, the safest methodology to quantify phenomena is to remove them from our observation and tackle an outer view, since mathematical/logical issues such as selective information deletion and set complement rescue incompleteness/inconsistency of biophysical systems.
REVIEW | doi:10.20944/preprints202103.0111.v1
Subject: Biology And Life Sciences, Biophysics Keywords: soft matter; liquid crystals; braid group; anyon; brain; microcolumn
Online: 2 March 2021 (16:56:14 CET)
The dynamical processes of living systems are characterized by the cooperative interaction of many units. This claim enables us to portray the embryo-fetal development of the central and peripheral nervous systems in terms of assemblies of building blocks. We describe how the structure and arrangement of nervous fibers is - at least partially - dictated by biophysical and topological constraints. The far-flung field of soft-matter polymers/nematic colloids sheds new light on the neurulation in mammalian embryos, suggesting an intriguing testable hypothesis: the development of the central and peripheral nervous systems might be correlated with the occurrence of local thermal changes in embryo-fetal tissues. Further, we show a correlation between the fullerene-like arrangement of the cortical microcolumns and the Frank-Kasper phases of artificial quasicrystals assemblies. The last, but not the least, we explain how and why the multisynaptic ascending nervous fibers connecting the peripheral receptors to the neocortical areas can be viewed as the real counterpart of mathematical tools such as knot theory and braid groups. Their group structure and generator operations point towards a novel approach to long-standing questions concerning human sensation and perception, leading to the suggestion that the very arrangement and intermingling of the peripheral nervous fibers contributes to the cortical brain activity. In touch with the old claims of D’Arcy Thompson, we conclude that the arrangement and the pattern make the function in a variety of biological instances, leading to countless testable hypotheses.
ARTICLE | doi:10.20944/preprints202102.0173.v1
Subject: Biology And Life Sciences, Biophysics Keywords: MINFLUX, STED, SMLM, localisation precision, image resolution, super-resolution imaging
Online: 8 February 2021 (07:50:16 CET)
Gwosch et al. (2020) and Balzarotti et al. (2017) purport MINFLUX as the next revolutionary fluorescence microscopy technique claiming a spatial resolution in the range of 1-3 nm in fixed and living cells. Though the claim of molecular resolution is attractive, I am concerned whether true 1 nm resolution has been attained. Here, I compare the performance with other super-resolution methods focussing particularly on spatial resolution claims, atypical image rendering, visualisation enhancement, subjective filtering of localizations, detection vs labelling efficiency and the possible limitations when imaging biological samples containing densely labelled structures. I hope the analysis and evaluation parameters presented here are not only useful for future research directions but also microscope users, developers and core facility managers when deciding on an investment for the next 'state-of-the-art' instrument.
ARTICLE | doi:10.20944/preprints202102.0038.v1
Subject: Biology And Life Sciences, Biophysics Keywords: chymotrypsin; β-casein; nanoparticles; UV-Vis spectroscopy; dynamic light scattering; quartz crystal microbalance.
Online: 1 February 2021 (13:59:40 CET)
Chymotrypsin is an important proteolytic enzyme in human digestion system that cleaves milk proteins, through hydrolysis reaction, which makes it interesting subject to study activity of milk proteases. In this work, we compared detection of chymotrypsin by spectrophotometric, dynamic light scattering (DLS) and quartz crystal microbalance (QCM) methods and determined the limit of chymotrypsin detection (LOD), 0.15 ± 0.01 nM for spectrophotometric, 0.67 ± 0.05 nM for DLS and 1.40 ± 0.30 nM for QCM methods, respectively. We discuss peculiarities and give perspective for implementation of detection methods and note that while the optical detection methods are simple to implement, the QCM method is more robust for sample preparation. We give an overview on methods and instruments for detection of chymotrypsin and other milk proteases.
ARTICLE | doi:10.20944/preprints202011.0032.v2
Subject: Biology And Life Sciences, Biophysics Keywords: Non-ionizing Radiation; Millimeter waves; Novel biomedical applications; Yeast; Non-invasive devices
Online: 22 January 2021 (14:31:18 CET)
Nonionizing millimeter-waves (MMW) interact with cells in a variety of ways. Here the inhibited cell division effect was investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. We irradiated using radiation with a power density of about 1.0 mW/cm2 over 5-6 hours on 50 cells/μl samples of Saccharomyces cerevisiae model organism. This resulted in 62% growth rate reduction compared to the control (sham). The effect was specific for 85-105 GHz range, and was energy and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deleted cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause permanent genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. Combinations of MMW mediated Structure Resonant Energy Transfer (SRET), membrane modulations eliciting signaling effects, and energetic resonance with biomolecules are conjectured to be responsible for the observations reported. Our results suggest innovative applications of nonionizing radiation procedures for yeast related diseases and other targeted biomedical outcomes.
Subject: Biology And Life Sciences, Biophysics Keywords: double-stranded DNA; DNA dynamical models; correlated oscillations in macromolecules; epigenetic changes
Online: 4 January 2021 (16:35:40 CET)
A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment which considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard-Dauxois-Bishop model we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables when going from the bp local scale to the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.
ARTICLE | doi:10.20944/preprints202011.0731.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Anthelmintic; EPG; Strongyle; Coccidia; Epidemiology; ODE
Online: 30 November 2020 (14:15:33 CET)
Identifying the correct dosage and time are key factors to successful implementation of anthelmintic. Comparing differential evolution of infection between anthelmintic treated animals against untreated ones, we present a mathematical model that first calibrates data collected and analyzed over an extended period of 10 years (2011-2019), and then predicts the dynamical evolution of gastrointestinal parasites in livestock, focusing specifically on Stronglye \& Coccidia oocysts, the two prime negative contributors to cattle health, measured using the standard Eggs-Per-Gram (EPG) index. The model incorporates information about all three critical regimes of infection - low infection regime ($< 50$ EPG), medium infection regime ($50-100$ EPG) and high infection regime ($>100$ EPG), including fatally large doses of infection ($> 500$), and probabilistically estimates the variation in animal weight due to infection propagation. A key success of our model is its ability to accurately predict the appropriate anthelmintic treatment times for cattle from a numerical solution of the model presented. The generic model can be applied to other agroclimatic conditions and can serve as a major diagnostic tool for anthelmintic strategizing.
ARTICLE | doi:10.20944/preprints202011.0199.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Gene Regulatory Networks; Non-Linear Variable Order Fractional System; Gene Expression; Epigenetic Memory
Online: 4 November 2020 (15:35:24 CET)
Complex diseases such as cancer are caused by changes in the Gene Regulatory Networks. Systems that model the complex dynamics of these networks along with adapting to real gene expression data are closer to reality and can help understand the creation and treatment of cancer. In this paper, for the first time, modelling of gene regulatory networks is performed using delayed nonlinear variable order fractional systems in the state space by a new tool called GENAVOS. This tool uses gene expression time series data to identify and optimize system parameters. This software has several tools for analyzing system dynamics. The results show that the nonlinear variable order fractional systems have very good flexibility in adapting to real data. We found that regulatory networks in cancer cells actually have a larger delay parameter than in normal cells. It is also possible to create chaos, periodic and quasi-periodic oscillations by changing the delay, degradation and synthesis rates. Our findings indicate a profound effect of time-varying order on these networks, which may be related to a type of cellular memory due to epigenetic and environmental factors. We showed that by changing the delay parameter and the variable order function for a normal cell system, its behavior changes and becomes quite similar to the behavior of a cancer cell. This work also confirms the effective role of the miR-17-92 cluster in the cancer cell cycle. GENAVOS is available at https://github.com/hanif-y/GENAVOS with its user guide and MATLAB codes.
Subject: Biology And Life Sciences, Biophysics Keywords: non-ionizing radiation; millimeter waves; novel biomedical applications; yeast; non-invasive devices
Online: 17 September 2020 (07:08:47 CEST)
Nonionizing millimeter-waves (MMW) are reported to interact with cells in a variety of ways. Possible mechanisms of the inhibited cell division effect were investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. ~1.0 mW/cm2 exposure over 5-6 hours treatment on 50 cells/μl samples of Saccharomyces cerevisiae model organism, resulted in 62% growth rate reduction compared to control (sham). The effect was specific for 85-105 GHz range and energy dose and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deletion cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. Combinations of MMW mediated Structure Resonant Energy Transfer (SRET), membrane modulations eliciting signaling effects, and energetic resonance with biomolecules were indicated to be responsible for the observations reported. Our results provide novel mechanistic insights enabling innovative applications of nonionizing radiation procedures for eliciting targeted biomedical outcomes.
COMMUNICATION | doi:10.20944/preprints202009.0343.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Poincaré–Weyl gauge theory; super-early Universe; effective cosmological constant
Online: 16 September 2020 (03:27:49 CEST)
The stage of a super-early scale-invariant Universe is considered on the basis of the Poincaré–Weyl gauge theory of gravity in a Cartan–Weyl space-time. An approximate solution has been found that demonstrates an inflationary behavior of the scale factor and, at the same time, a sharp exponential decrease in the effective cosmological constant from a huge value at the beginning of the Big Bang to an extremely small (but not zero) value in the modern era, which solves the well-known “cosmological constant problem”.
ARTICLE | doi:10.20944/preprints202008.0529.v2
Subject: Biology And Life Sciences, Biophysics Keywords: membrane potential; Nernst; Bernstein; action potential; propagation; theory
Online: 9 September 2020 (09:24:15 CEST)
Man has always been interested in animal electricity, which seems to be measured in every living cell. He has been fascinated by trying to elucidate the mechanisms by which this potential is created and maintained. Biology is the science that seeks to explain this mystery. Biology is based on basic sciences such as physics or chemistry. The latter, in turn, make systematic use of mathematics to measure, evaluate and predict certain phenomena and to develop "laws" and models that are as general as possible while respecting, as closely as possible, observations and facts. The Nernst equation was one of the pillars of electrochemistry. Biology also uses this same equation as one of the indispensable bases for the computation of membrane potential. Man has established a cellular model that highlights this equation in several forms. However, we are going to show by various means that this model is inadequate or even inapplicable.
Subject: Biology And Life Sciences, Biophysics Keywords: axon; neuron; saltatory conduction; action potential; impulse propagation; HH model
Online: 30 August 2020 (18:39:44 CEST)
For more than 70 years, biologists and biophysicists have been trying to unravel the mystery that exists regarding the saltatory conduction of so-called myelinated neurons. Albert Einstein used the train metaphor to explain the theory of relativity. It is possible to use a similar metaphor to better understand this transient functioning of the neuron: the action potential. We will, once again, use a train to demonstrate unequivocally that the action potential does not jump from node of Ranvier to node of Ranvier (noR) as we thought it would. It is possible to describe that the neuron uses an elegant method to increase the speed of transmission of the neural message. It is also important to conclude that this increase in speed, contrary to the common idea, has a certain energy cost that is proportional to speed and in accordance with thermodynamics.
ARTICLE | doi:10.20944/preprints202008.0548.v1
Subject: Biology And Life Sciences, Biophysics Keywords: promoter sequences; repetitive sequences; pausing; abortive initiation; RNA polymerase; dsDNA rigidity
Online: 25 August 2020 (11:28:21 CEST)
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences enriched with thymine bases represent the signal inducing abortive transcription. On the other hand, certain repetitive sequence elements broadly embedded in promoter regions constitute the signal inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we also suggest that repetitive sequence elements of promoter DNA modulate the rigidity of its double-stranded form, which profoundly influences the reaction coordinates of the productive initiation via pausing.
Subject: Biology And Life Sciences, Biophysics Keywords: computational molecular biology, biochemistry, quantum computing, hybrid quantum-classical algorithms
Online: 24 August 2020 (09:37:44 CEST)
Chemistry has been viewed as one of the most fruitful near-term applications to science of quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Much less effort has been placed on how one finishes these calculations by using the results from the quantum computer (on the active region of the molecule) and embeds them back into the remainder of the molecule in order to determine the properties of the entire molecule. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with classical algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.
ARTICLE | doi:10.20944/preprints202008.0425.v1
Subject: Biology And Life Sciences, Biophysics Keywords: TSPO; Martini Force-Field; cholesterol
Online: 20 August 2020 (05:13:23 CEST)
The translocator protein (TSPO) is a transmembrane protein present in the three domains of life. Its functional quaternary structure consists of one or more subunits. In mouse, the dimer-to-monomer equilibrium is shifted in vitro towards the monomer by adding cholesterol, a natural component of mammalian membranes. Here, we present a coarse-grained molecular dynamics study on the mouse protein in the presence of a physiological content and of an excess of cholesterol. The latter turns out to weaken the interfaces of the dimer by clusterizing mostly at the inter-monomeric space and pushing the contact residues apart. It also increases the compactness and the rigidity of the monomer. These two factors might play a role for the experimentally observed incremented stability of the monomeric form with increased content of cholesterol. Comparison with simulations on bacterial proteins suggests that the effect of cholesterol is much less pronounced for the latter than for the mouse protein.
ARTICLE | doi:10.20944/preprints202008.0318.v1
Subject: Biology And Life Sciences, Biophysics Keywords: nicotinic acetylcholine receptors; three-finger toxins; acetylcholine binding protein; protein – protein docking; computational modeling
Online: 14 August 2020 (09:57:35 CEST)
Three finger toxins (3FTX) are a group of peptides that affect multiple receptor types. One group of proteins affected by 3FTX are nicotinic acetylcholine receptors (nAChR). Structural information on how neurotoxins interact with nAChR is limited and are confined to a small group of neurotoxins. Therefore, in silico methods are valuable in understanding the interactions between 3FTX and different nAChR subtypes, but there are no established protocols to model 3FTX – nAChR interactions. We developed a homology modeling and protein docking protocol to address this issue and tested its success on three different systems. First, neurotoxin peptides co-crystallized with acetylcholine binding protein (AChBP) were re-docked to assess whether Rosetta protein – protein docking can reproduce the native poses. Second, experimental data on peptide binding to AChBP was used to test whether the docking protocol can qualitatively distinguish AChBP-binders from non-binders. Finally, we docked eight peptides with known α7 and muscle-type nAChR binding properties to test whether the protocol can explain the differential activities of the peptides at the two receptor subtypes. Overall, our docking protocol succeeded in predicting both qualitative and specific aspects of 3FTX binding to nAChR and shed light on some unknown aspects of 3FTX binding to different receptor subtypes.
COMMUNICATION | doi:10.20944/preprints202005.0423.v2
Subject: Biology And Life Sciences, Biophysics Keywords: Sars-CoV2; Zn Finger; orf7a/orf8 and Theterin
Online: 9 August 2020 (22:08:56 CEST)
Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins. A conceivable hypothesis is that lack of cellular zinc, or substitution thereof, might lead to a significant slowing down of viral maturation.