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Understanding Allosteric Control of Enzymatic and Cellular Activities with Integrated Computational and Experimental Approaches

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 2013

Special Issue Editors


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Guest Editor
École Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France
Interests: modeling; structure; dynamics; normal mode analysis; conformational sampling and pathways; allostery

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Guest Editor
UPMC-Sorbonne Université, CNRS, IRD and MNHN. 4, place Jussieu, 75005 Paris, France
Interests: cryoelectron microscopy; molecular model; electron tomography; Fanconi anemia; DNA; chromosome fragility; bacteriophages; phycodnaviridae; microorganisms

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Guest Editor
Institut Pasteur, 75015 Paris, France
Interests: channel-receptors; neuropharmacology; structural biology; electrophysiology; fluorescence

Special Issue Information

Dear Colleagues, 

In biology, allostery plays an essential role in controlling complex biochemical processes. Computational approaches combined with experiments are essential in unveiling its multiple characteristics from a physicochemical point of view and its deep involvement in the complexity of living systems. Many models based on mechanical, thermodynamical, vibrational, and chemical characteristics; interaction networks; and others have been proposed in the literature. They tend to show allostery as having a multifaceted property. However, the intimate connection with the environment, such as water molecules, membrane, partner molecules, pH, and other factors, still needs to be thoroughly investigated at the atomic level to obtain a more unified theory and a deeper understanding of allostery in biological systems. Such an in-depth understanding is also needed to better intervene in the allosteric behavior of biological systems.

This Special Topic intends to bring together articles addressing the physicochemical bases of allostery and its significance in biology through theoretical and experimental studies. The involvement of allostery in different fields of biology can also be addressed. The themes listed below, though not exhaustive, can be addressed:

  • Allosteric networks;
  • Structural and dynamical changes;
  • Evolutionary approaches;
  • Design of allosteric proteins;
  • Design of allosteric drugs;
  • Prediction of allosteric sites;
  • Signal transduction;
  • Building molecular switches;
  • Control of the enzymatic activity;
  • Conformational changes and pathways;
  • Free energy landscapes;
  • Protein membrane interactions;
  • Control of protein stability;
  • Molecular motors;
  • Assembly of macromolecular complexes

Prof. Dr. David Pérahia
Prof. Dr. Catherine Vénien-Bryan
Prof. Dr. Pierre-Jean Corringer
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Allostery;
  • Molecular Dynamics;
  • Normal Modes;
  • Thermodynamics;
  • Modeling;
  • Enhanced Sampling;
  • NMR;
  • Cryo-EM;
  • SAXS;
  • X-Ray;
  • AFM;
  • FRET

Published Papers (1 paper)

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Research

16 pages, 9485 KiB  
Article
The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS
by Maham Hamid, Muhammad Farhan Khalid, Safee Ullah Chaudhary and Shahid Khan
Int. J. Mol. Sci. 2022, 23(21), 12771; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232112771 - 23 Oct 2022
Viewed by 1568
Abstract
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS [...] Read more.
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction. Full article
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