Mean-Field Coupling Between Local Interactions in Proteins in Relation to Chirality, Secondary, and Supersecondary Structure Formation, and Allostery.

Adam Liwo, Celina Sikorska, Agnieszka G Lipska, Adam K Sieradzan, Sümeyye Atmaca, Cezary Czaplewski

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Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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Authors and funding

6 authors.

Adam LiwoFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland. adam.liwo@ug.edu.pl.ORCID 0000-0001-6942-2226

Celina SikorskaFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.ORCID 0000-0002-8288-166X

Agnieszka G LipskaCentre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.ORCID 0000-0002-8390-8473

Adam K SieradzanFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.ORCID 0000-0002-2426-3644

Sümeyye AtmacaFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.

Cezary CzaplewskiFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.ORCID 0000-0002-0294-3403

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Coarse graining is usually considered as a tool to extend the time and size scale of simulations. However, leaving out the atomistic details to keep their fingerprints in a coarse-grained model also enables us to understand better structure formation and dynamics. In this chapter, by using our scale-consistent theory of coarse graining, we demonstrate that the coarse-grained terms corresponding to the coupling between local conformational states of amino-acid residues explain secondary-structure propagation along polypeptide backbone to stabilize

Indexed as

ProteinsAllosteric RegulationModels, MolecularMolecular Dynamics SimulationProtein ConformationProtein Structure, SecondaryProteinsCoarse grainingCoupling termsKubo cluster cumulantsLocal interactionsPotential of mean forceUNRES model of polypeptide chains

Identifiers

PMID39543040

DOI10.1016/j.preteyeres.2019.100802

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