Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to re...

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Main Authors:	Dasgupta, Bhaskar, Kasahara, Kota, Kamiya, Narutoshi, Nakamura, Haruki, Kinjo, Akira R.
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953337/

id	pubmed-3953337
recordtype	oai_dc
spelling	pubmed-39533372014-03-18 Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics Dasgupta, Bhaskar Kasahara, Kota Kamiya, Narutoshi Nakamura, Haruki Kinjo, Akira R. Research Article The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. Public Library of Science 2014-03-13 /pmc/articles/PMC3953337/ /pubmed/24625758 http://dx.doi.org/10.1371/journal.pone.0091347 Text en © 2014 Dasgupta et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Dasgupta, Bhaskar Kasahara, Kota Kamiya, Narutoshi Nakamura, Haruki Kinjo, Akira R.
spellingShingle	Dasgupta, Bhaskar Kasahara, Kota Kamiya, Narutoshi Nakamura, Haruki Kinjo, Akira R. Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
author_facet	Dasgupta, Bhaskar Kasahara, Kota Kamiya, Narutoshi Nakamura, Haruki Kinjo, Akira R.
author_sort	Dasgupta, Bhaskar
title	Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
title_short	Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
title_full	Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
title_fullStr	Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
title_full_unstemmed	Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
title_sort	specific non-local interactions are not necessary for recovering native protein dynamics
description	The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953337/
_version_	1612067508520484864

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

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