NDLI: A unified coarse-grained model of biological macromolecules based on mean-field multipole

Content Provider	Springer Nature Link
Author	Liwo, Adam Barawski, Maciej Czaplewski, Cezary Gołaś, Ewa He, Yi Jagieła, Dawid Krupa, Paweł Maciejczyk, Maciej Makowski, Mariusz Mozolewska, Magdalena A. Niadzvedtski, Andrei Ołdziej, Stanisław Scheraga, Harold A. Sieradzan, Adam K. Ślusarz, Rafał Wirecki, Tomasz Yin, Yanping Zaborowski, Bartłomiej
Copyright Year	2014
Abstract	A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point multipoles. The model is an extension of the united residue (UNRES) coarse-grained model of proteins developed previously in our laboratory. The respective force fields are defined as the potentials of mean force of biomacromolecules immersed in water, where all degrees of freedom not considered in the model have been averaged out. Reducing the representation to one center per polar interaction site leads to the representation of average site–site interactions as mean-field dipole–dipole interactions. Further expansion of the potentials of mean force of biopolymer chains into Kubo’s cluster-cumulant series leads to the appearance of mean-field dipole–dipole interactions, averaged in the context of local interactions within a biopolymer unit. These mean-field interactions account for the formation of regular structures encountered in biomacromolecules, e.g., α-helices and β-sheets in proteins, double helices in nucleic acids, and helicoidally packed structures in polysaccharides, which enables us to use a greatly reduced number of interacting sites without sacrificing the ability to reproduce the correct architecture. This reduction results in an extension of the simulation timescale by more than four orders of magnitude compared to the all-atom representation. Examples of the performance of the model are presented. Figure Components of the Unified Coarse Grained Model (UCGM) of biological macromolecules
Starting Page	1
Ending Page	15
Page Count	15
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	20
Issue Number	8
e-ISSN	09485023
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2014-07-15
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Coarse-graining Mean-field approach Multipole–multipole interactions Proteins Nucleic acids Polysaccharides Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Characterization and Evaluation of Materials Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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