Formation of secondary and supersecondary structure of proteins as a result of coupling between local and backbone-electrostatic interactions: a view through cluster-cumulant scope

Józef Adam Liwo , Adam Sieradzan , Cezary Czaplewski

Abstract

The secondary structure of proteins results from both local and long-range interactions, the latter being primarily backbone hydrogen bonding. In this chapter, based on our recent work, we suggest that the striking regularity of secondary structure can be described, in a semi-analytical manner, in terms of Kubo cluster cumulants (corresponding to the expansion of the protein’s potential of mean force) that originate from the coupling between the backbone-local and backbone-electrostatic interactions. This finding is illustrated by the analysis of the Protein Data Bank statistics. Examples demonstrating the importance of the coupling terms in coarse-grained treatment of proteins are also presented.
Author Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
, Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Cezary Czaplewski (FCh / DTCh / LSP)
Cezary Czaplewski,,
- Laboratory of Simulation of Polymers
Journal seriesMethods in molecular biology (Clifton, N.J.), ISSN 1064-3745, (N/A 70 pkt)
Issue year2019
Vol1958
Pages133-146
Publication size in sheets0.65
Keywords in EnglishCoarse graining, potential of mean force, Kubo cluster cumulants, local and electrostatic interactions, coupling terms, UNRES force field
ASJC Classification1311 Genetics; 1312 Molecular Biology
DOIDOI:10.1007/978-1-4939-9161-7_7
Languageen angielski
Score (nominal)70
Score sourcejournalList
ScoreMinisterial score = 70.0, 29-05-2020, ArticleFromJournal
Publication indicators Scopus Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2018 = 0.404
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