Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery

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dc.contributor.author Sikorska, Celina
dc.contributor.author Liwo, Adam
dc.coverage.spatial United States
dc.date.accessioned 2024-04-03T01:01:34Z
dc.date.available 2024-04-03T01:01:34Z
dc.date.issued 2022-11
dc.identifier.citation (2022). Journal of Physical Chemistry B, 126(46), 9493-9505.
dc.identifier.issn 1520-6106
dc.identifier.uri https://hdl.handle.net/2292/67889
dc.description.abstract By analyzing the Kubo-cluster-cumulant expansion of the potential of mean force of polypeptide chains corresponding to backbone-local interactions averaged over the rotation of the peptide groups about the C<sup>α</sup>···C<sup>α</sup> virtual bonds, we identified two important kinds of "along-chain" correlations that pertain to extended chain segments bordered by turns (usually the β-strands) and to the folded spring-like segments (usually α-helices), respectively, and are expressed as multitorsional potentials. These terms affect the positioning of structural elements with respect to each other and, consequently, contribute to determining their packing. Additionally, for extended chain segments, the correlation terms contribute to propagating the conformational change at one end to the other end, which is characteristic of allosteric interactions. We confirmed both findings by statistical analysis of the virtual-bond geometry of 77 950 proteins. Augmenting coarse-grained and, possibly, all-atom force fields with these correlation terms could improve their capacity to model protein structure and dynamics.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartofseries The journal of physical chemistry. B
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject Amino Acids
dc.subject Peptides
dc.subject Proteins
dc.subject Protein Conformation
dc.subject 34 Chemical Sciences
dc.subject Science & Technology
dc.subject Physical Sciences
dc.subject Chemistry, Physical
dc.subject Chemistry
dc.subject FORCE-FIELD
dc.subject DYNAMICS
dc.subject MODELS
dc.subject POTENTIALS
dc.subject TERMS
dc.subject 02 Physical Sciences
dc.subject 03 Chemical Sciences
dc.subject 09 Engineering
dc.subject 40 Engineering
dc.subject 51 Physical sciences
dc.title Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery
dc.type Journal Article
dc.identifier.doi 10.1021/acs.jpcb.2c04610
pubs.issue 46
pubs.begin-page 9493
pubs.volume 126
dc.date.updated 2024-03-18T11:44:29Z
dc.rights.holder Copyright: The authors en
dc.identifier.pmid 36367920 (pubmed)
pubs.author-url https://pubs.acs.org/doi/10.1021/acs.jpcb.2c04610
pubs.end-page 9505
pubs.publication-status Published
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Research Support, Non-U.S. Gov't
pubs.subtype research-article
pubs.subtype Journal Article
pubs.elements-id 928200
pubs.org-id Science
pubs.org-id Physics
dc.identifier.eissn 1520-5207
pubs.record-created-at-source-date 2024-03-19
pubs.online-publication-date 2022-11-11

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