REVIEW | doi:10.20944/preprints202110.0344.v1
Subject: Life Sciences, Molecular Biology Keywords: Glycoprotein; gp120; HIV-1; conformation; immunity
Online: 25 October 2021 (11:50:08 CEST)
Infection by human immunodeficiency virus type I (HIV-1) requires virus particle binding to host cell-surface receptor CD4 via the viral envelope glycoprotein gp120. HIV-1 therapy and prevention efforts involve development of mimetic or recombinant gp120 vaccines or deployment of antiviral agents that target specific epitopes of gp120. The unliganded conformational state of gp120 is closed, whereas the CD4-bound state is open. However, in between, there exist dynamic conformational states, indicating intrinsically flexible region(s) of structural dynamics, imposing a structural challenge for developing drug or antibody targets. Known conformational states of gp120 were determined by X-ray crystallographic and cryo-electron microscopy, and neither method captures the population of gp120 species arising from conformational plasticity, motions, and transitions. gp120 plasticity brings up several important questions. How will differences in conformation affect receptor binding, antibody recognition, and neutralization? Which regions are crucial for gp120 structural plasticity? How could structural dynamics influence HIV-1 evasiveness against host immunity and drugs or vaccines, and facilitate the viral entry into its host? This review explores the structural constraints presented by conformational states of the glycoprotein to antibodies or drugs and how these conformational states provide structural avenues for the virus to escape neutralizing agents and evade host immunity.
Subject: Keywords: molecular engineering; natural conformation; polymeric biomaterials; biocompatibility
Online: 17 March 2020 (03:53:20 CET)
Molecular engineering research is the fundamental way and the only way for the development of biomaterials. Based on molecular engineering, the biocompatibility of natural conformation and polymer biomaterials was studied. In this paper, we discuss that natural conformation is the basis of protein biological function, and that the synergistic action of peptide chain and side group is the motive force for protein to construct natural conformation and complete biological function. On the basis of the influence of the adsorption of polymer biomaterials on the natural conformation of proteins, the relationship between biocompatibility of biomaterials and protein conformation is further explained. Studies have shown that bismuth molecular materials can only be applied in the market and have their functionality if they have good biocompatibility. Therefore, the biocompatibility evaluation of new materials has important practical significance.
Subject: Chemistry, Physical Chemistry Keywords: diperoxides; monomolecular layers; quantum-chemical calculation; conformation
Online: 28 March 2019 (09:33:41 CET)
The monomolecular films of diacylic diperoxides on the water/air interface were studied. Their general formula: CH3-(CH2)m-C(O)-O-O-C(O)-(CH2)n-C(O)-O-O-C(O)-(CH2)m-CH3. The behavior of monomolecular films of diperoxides are affected by the structure of their molecule. The numerical values of the areas of molecules that are extrapolated to zero pressure are different. This indicates a different conformation of the molecules in the monolayer. The optimal geometric structure of the molecule of diperoxide, the total area (S), the volume (V), the heat of formation (∆fH298), the energy of higher occupied (EHOMO) and the lower vacant (ELUMO) molecular orbitals were obtain in the calculations. The optimal geometric structures of peroxides and their electronic properties were calculated by the quantum-chemical method. Calculations of conformational states of the molecule of diperoxides are carried out. Experimental data and quantum-chemical calculations are consistent with each other.
Subject: Physical Sciences, Other Keywords: conformation of protein; albumin protein; non-gaussian chain
Online: 7 August 2019 (09:59:10 CEST)
We study a conformation of an albumin protein in the temperature range of 300K-315K, i.e. in the physiological range of temperature. Using simulations we calculate values of two backbone angles, that carry most of information about positioning of the protein chain in a conformational space. Given these, we calculate energy components of such protein. Further, using the Flory theory we determine the temperature in which investigated albumin chain model is closest to the free joined chain model. Near the Flory temperature, we study energy components and the conformational entropy, both derived from two angles that reflect most of the chain dynamics in a conformational space. We show that the conformational entropy is an oscillating function of time in considered range of temperature. Our finding is that, the only regular oscillation pattern appears near the Flory temperature.
ARTICLE | doi:10.20944/preprints202208.0029.v1
Subject: Life Sciences, Biochemistry Keywords: heme distortion; pocket conformation; convolutional neural network; machine learning
Online: 2 August 2022 (03:20:13 CEST)
Heme proteins serve diverse and pivotal biological functions. Therefore, clarifying the mechanisms of these diverse functions of heme is a crucial scientific topic. Distortion of heme porphyrin is one of the key factors regulating the chemical properties of heme. Here, we constructed convolutional neural network models for predicting heme distortion from the tertiary structure of the heme-binding pocket to examine their correlation. For saddling, ruffling, doming, and waving distortions, the experimental structure and predicted values were closely correlated. Furthermore, we assessed the correlation between the cavity shape and molecular structure of heme and demonstrated that hemes in protein pockets with similar structures exhibit near-identical structures, indicating the regulation of heme distortion through the protein environment. These findings indicate that the tertiary structure of the heme-binding pocket regulates the distortion of heme porphyrin, thereby controlling the chemical properties of heme relevant to the protein function; this implies a structure–function correlation in heme proteins.
ARTICLE | doi:10.20944/preprints202205.0364.v1
Subject: Life Sciences, Molecular Biology Keywords: Hemoglobin switch; BGLT3-lncRNA expression; chromatin conformation; LRF/ZBTB7A overexpression
Online: 26 May 2022 (10:39:49 CEST)
Hemoglobin switch from fetal (HbF) to adult (HbA) has been studied intensively as an essential model for gene’s expression regulation, but also as a beneficial therapeutic approach for β-hemoglobinopathies, towards the objective of reactivating HbF. Transcription factor LRF (Leukemia/lymphoma-related), encoded from ZBTB7A gene has been implicated in fetal hemoglobin silencing, though has a wide range of functions that have not been fully clarified. We thus established LRF/ZBTB7A-overexpressing and ZBTB7A-knockdown K562 (human erythroleukemia cell line) clones and hemoglobin production was evaluated pre- and post-induction. Related effects on the process of hemoglobin switch from fetal to adult were also assessed. Transgenic K562 clones were further developed and studied under the influence of epigenetic chromatin regulators, such as DNA methyl transferase 3 (DNMT3) and Histone Deacetylase 1 (HDAC1), to evaluate LRF’s potential disturbance upon aberrant epigenetic background and provide valuable information of the preferable epigenetic frame, in which LRF unfolds its action on the β-type globin’s expression. ChIP-seq analysis demonstrated that LRF binds το γ-globin genes (HBG2/1) and apparently associates BCL11A for their silencing, but also, during erythropoiesis induction LRF binds BGLT3 gene promoting BGLT3-lncRNA production through the γ-δ intergenic region of β-type globin’s locus, triggering the transcriptional events from γ- to β-globin switch.
ARTICLE | doi:10.20944/preprints201808.0284.v1
Subject: Life Sciences, Biophysics Keywords: adsorbed vaccines, identity, protein conformation, particle sizing, FTIR, SEM, Fluorescence
Online: 16 August 2018 (12:54:59 CEST)
1) Background: Traditionally, complex biological products such as vaccines presented unique challenges to implementation of even rudimentary characterization packages; thus, the product was defined almost exclusively by its manufacturing process. The advances in technology and analytical tools allowed the application of more comprehensive characterization packages for products such as adsorbed combination vaccines, which contain several antigens in a single formulation to protect against more than one disease, and may contain adjuvants and excipients. Aluminum phosphate (AlPO4) is a well-established adjuvant for enhancing the uptake of vaccines and to induce robust immunity against pathogens. During manufacturing, adjuvant is mixed with protein antigens which may in turn impact their higher order structure and stability. 2) Methods: To study the structural changes of protein antigens after adsorption several analytical tools including DLS, FTIR, Fluorescence, LD, and SEM were used. 3) Results: the AlPO4 adjuvant suspension consists of small submicron particles that form a continuous porous surface. Secondary structure alpha-helix and beta-sheet content of DT and TT increased after adsorption to AlPO4 adjuvant, whereas no significant changes were noted for other protein antigens. Interactions were noted between AlPO4 adjuvant and DT, TT, and FHA. 4) Conclusions: here we report for the first time the use of SEM for the visualization of adsorbed multivalent vaccine components. A unique signature profile detected for each multivalent vaccine by FTIR can be used as a lean in-process test to verify vaccine product composition and identity prior to filling.
ARTICLE | doi:10.20944/preprints202212.0010.v1
Subject: Life Sciences, Biochemistry Keywords: structure–function correlation; active site conformation; convolutional neural network; machine learning
Online: 1 December 2022 (04:11:37 CET)
Structure–function relationships in proteins have been one of the crucial scientific topics. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure–function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure–function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB–OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with very different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure–function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
COMMUNICATION | doi:10.20944/preprints202003.0125.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: 2019-nCoV; Darunavir; ACE-2; Receptor Binding Domain; Metastable Conformation; FDA database
Online: 7 March 2020 (16:28:05 CET)
The transnational spread of coronavirus (2019-nCoV) first detected in Wuhan is causing global panic; thus, accelerated research into clinical intervention is of high necessity. The spike glycoprotein structure has been resolved, and its affinity to human angiotensin-converting enzyme 2 (ACE-2) has been experimentally validated. Here, using computational methods, a metastable conformation of 2019-nCoV-RBD/ACE-2 complex has been revealed and FDA-database of approved drugs have been docked into the interface. Darunavir has been discovered as high ligand affinity candidate capable of disrupting communication between 2019-nCoV-RBD and ACE-2. Darunavir, in addition to its previously known anti-HIV protease inhibitor is now repurposeable for the treatment 2019-nCoV disease acting via disruption of cellular recognition, binding and invasion.
ARTICLE | doi:10.20944/preprints201911.0271.v1
Subject: Life Sciences, Genetics Keywords: breast cancer risk; GWAS; candidate causal variant; chromatin conformation capture; reporter gene activity; enhancer; promoter
Online: 24 November 2019 (05:12:07 CET)
Genome-wide association studies have revealed a locus at 8p12 that is associated with breast cancer risk. Fine-mapping of this locus identified 16 candidate causal variants (CCVs). However, as these variants are intergenic, their function is unclear. To map chromatin looping from this risk locus to a previously identified candidate target gene, DUSP4, we performed chromatin conformation capture analyses in normal and tumoral breast cell lines. We identified putative regulatory elements, containing CCVs, that loop to the DUSP4 promoter region. Using reporter gene assays, we found that the risk allele of CCV rs7461885 reduced the activity of a DUSP4 enhancer element, consistent with the function of DUSP4 as a tumor suppressor gene. Furthermore, the risk allele of CCV rs12155535, located in another DUSP4 enhancer element, was negatively correlated with looping of this element to the DUSP4 promoter region, suggesting that this allele would be associated with reduced expression. These findings provide the first evidence that CCV risk alleles downregulate DUSP4 expression, suggesting that this gene is a regulatory target of the 8p12 breast cancer risk locus.
ARTICLE | doi:10.20944/preprints202210.0164.v1
Subject: Chemistry, Physical Chemistry Keywords: conformation; steroid skeleton; surfactants; mixed micelles; bile salts; regular solution theory; thermodynamic stabilization; first neighbor intermolecular interactions
Online: 12 October 2022 (07:11:07 CEST)
Binary mixtures of surfactants build a binary mixed micelle in which the ratio of surfactants usually differs from the initial ratio of surfactants in their binary mixture. The thermodynamic stabilization of the binary mixed micellar pseudophase about the hypothetical ideal state (intermolecular interactions between the different particles and the conformational states of the particles are identical to those of monocomponent states) is described by the molar excess Gibbs free energy (gE). The dependence of gE on the molar fraction of surfactant i (xi) from the binary mixed micelle can be described by a symmetric function (symmetry is described to the line parallel to the y-axis and passes through xi = 0.5) or by an asymmetric function. Theoretical analysis (canonical partition function, conformational analysis) examines how the presence of different polar functional groups, some of which are sterically shielded from the steroid skeleton of bile salt (surfactant), affect the symmetry of the function gE of the binary mixed micelle of the cholic acid anion (bile salt) and classical cationic surfactant (hydrophobic tail and polar head). Suppose the steroid skeleton of the bile salt contains non-sterically shielded polar groups (or the temperature is relatively high). In that case, gE is a symmetric function. At the same time, if the steroid skeleton also contains sterically shielded polar groups, then the gE function is asymmetric.
ARTICLE | doi:10.20944/preprints202209.0184.v1
Subject: Materials Science, Polymers & Plastics Keywords: unentangled systems; constitutive modeling; materials functions; non-affine parameter; slip parameter; conformation tensor; NEMD simulations; atomistic simulations; polyethylene
Online: 14 September 2022 (02:54:18 CEST)
Since its introduction, back in the late 1970s, the non-affine or slip parameter, ξ, has been routinely employed by numerous constitutive models as a constant parameter. However, the evidence seems to imply that it should be a function of polymer deformation. In the present work, we phenomenologically modify a constitutive model for the rheology of unentangled polymer melts [P. S. Stephanou et al. J. Rheol. 53, 309 (2009)] to account for a non-constant slip parameter. The revised model predictions are compared against newly accumulated rheological data for a C48 polyethylene melt obtained via direct non-equilibrium molecular dynamics simulations in shear. We find that the conformation tensor data are very well predicted; however, the predictions of the material functions are noted to deviate from the NEMD data, especially at large shear rates.
ARTICLE | doi:10.20944/preprints202210.0152.v1
Subject: Life Sciences, Other Keywords: immobilization of DNA molecules on the surface of dielectrics; interaction of nanopowders with nucleotides; molecular electronics; nanotechnology; molecular dynamics modeling; DNA conformation in an electric field; genotoxic effects
Online: 11 October 2022 (10:39:29 CEST)
A variational analysis of dispersion medium (electrolytes and surfactants) was carried out for the best nucleotide interactions with the presence of nanoparticles and the ability to formation of homogeneous coatings upon drying / lyophilization. Using UV-spectroscopy and transmission electron microscopy, the processes of immobilization of nucleotides on the surface of nanoparti-cles of the composition ZrO2-3mol% Y2O3 (YSZ) in the presence of various dispersing agents were investigated. Promising dispersing agents were established, the optimal composition of suspen-sions based on DNA nucleotides and YSZ nanoparticles, which is potentially suitable for adaptive technologies of bionanoelectronics, was selected. The aim of the work is to obtain and study functional media for molecular electronics based on heterojunctions biological molecule – wide-gap dielectric.