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Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics.
Bondar, Ana-Nicoleta.
  • Bondar AN; University of Bucharest, Faculty of Physics, Str. Atomistilor 405, 077125 Bucharest-Magurele, Romania.
J Phys Chem B ; 126(22): 3973-3984, 2022 06 09.
Article in English | MEDLINE | ID: covidwho-1873396
ABSTRACT
Dynamic hydrogen bonds and hydrogen-bond networks are ubiquitous in proteins and protein complexes. Functional roles that have been assigned to hydrogen-bond networks include structural plasticity for protein function, allosteric conformational coupling, long-distance proton transfers, and transient storage of protons. Advances in structural biology provide invaluable insights into architectures of large proteins and protein complexes of direct interest to human physiology and disease, including G Protein Coupled Receptors (GPCRs) and the SARS-Covid-19 spike protein S, and give rise to the challenge of how to identify those interactions that are more likely to govern protein dynamics. This Perspective discusses applications of graph-based algorithms to dissect dynamical hydrogen-bond networks of protein complexes, with illustrations for GPCRs and spike protein S. H-bond graphs provide an overview of sites in GPCR structures where hydrogen-bond dynamics would be required to assemble longer-distance networks between functionally important motifs. In the case of spike protein S, graphs identify regions of the protein where hydrogen bonds rearrange during the reaction cycle and where local hydrogen-bond networks likely change in a virus variant of concern.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / COVID-19 Topics: Variants Limits: Humans Language: English Journal: J Phys Chem B Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: Acs.jpcb.2c00200

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / COVID-19 Topics: Variants Limits: Humans Language: English Journal: J Phys Chem B Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: Acs.jpcb.2c00200