Version 1
: Received: 31 January 2022 / Approved: 8 February 2022 / Online: 8 February 2022 (14:53:06 CET)
How to cite:
D'Amelio, N.; Tanielian, B.; Sadqi, M.; Lopez-Navajas, P.; Victor Muñoz, V. Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. Preprints2022, 2022020118. https://doi.org/10.20944/preprints202202.0118.v1
D'Amelio, N.; Tanielian, B.; Sadqi, M.; Lopez-Navajas, P.; Victor Muñoz, V. Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. Preprints 2022, 2022020118. https://doi.org/10.20944/preprints202202.0118.v1
D'Amelio, N.; Tanielian, B.; Sadqi, M.; Lopez-Navajas, P.; Victor Muñoz, V. Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. Preprints2022, 2022020118. https://doi.org/10.20944/preprints202202.0118.v1
APA Style
D'Amelio, N., Tanielian, B., Sadqi, M., Lopez-Navajas, P., & Victor Muñoz, V. (2022). Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. Preprints. https://doi.org/10.20944/preprints202202.0118.v1
Chicago/Turabian Style
D'Amelio, N., Pilar Lopez-Navajas and Victor Victor Muñoz. 2022 "Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch" Preprints. https://doi.org/10.20944/preprints202202.0118.v1
Abstract
Transcription factors must scan genomic DNA, recognize the cognate sequence of their control element(s), and bind tightly to them. The DNA recognition process is primarily carried out by their DNA binding domains (DBD), which interact with the cognate site with high affinity and more weakly with any other DNA sequence. DBDs are generally thought to bind to their cognate DNA without changing conformation (lock-and-key). Here we used nuclear magnetic resonance and circular dichroism to investigate the interplay between DNA recognition and DBD conformation in the Engrailed homeodomain (EnHD), as model case for the homeodomain family of eukaryotic DBDs. We found that the conformational ensemble of EnHD is rather flexible and becomes more structured as ionic strength increases following a Debye-Hückel’s dependence. Our analysis indicates that EnHD’s response to ionic strength is mediated by a built-in electrostatic spring-loaded latch that operates as conformational transducer. We also found that, at moderate ionic strengths, EnHD changes conformation upon binding to cognate DNA. This change is of larger amplitude and somewhat orthogonal to the response to ionic strength. As a consequence, very high ionic strengths (e.g. 700 mM) block the electrostatic-spring-loaded latch and binding to cognate DNA becomes lock-and-key. However, the interplay between EnHD conformation and cognate DNA binding is robust across a range of ionic strengths (i.e. 45 to 300 mM) that covers the most physiologically-relevant conditions. Therefore, our results demonstrate the presence of a mechanism for the conformational control of cognate DNA recognition on a eukaryotic DBD. This mechanism can function as a signal transducer that immediately locks the DBD in place upon encountering the cognate site during active DNA scanning. The electrostatic-spring-loaded latch of EnHD can also enable the fine control of DNA recognition in response to local/temporal changes in ionic strength induced by variate physiological processes.
Keywords
protein-DNA interactions; DNA recognition; transcription factors; DNA binding domains; con-formational change; nuclear magnetic resonance; circular dichroism; control of gene expression; homeodomains.
Subject
Chemistry and Materials Science, Analytical Chemistry
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
