Dynamical persistence of active sites identified in maltose-binding protein

From National Research Council Canada

DOIResolve DOI: https://doi.org/10.1007/s00894-017-3344-6
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Name affiliation
  1. National Research Council of Canada. Nanotechnology
FormatText, Article
Journal titleJournal of Molecular Modeling
ISSN1610-2940
0948-5023
Volume23
Issue5
Subjectanisotropic elastic network model; pairwise correlations; dynamical distances; maltose-binding protein; ligand; allosteric pathway
Abstract
This study identifies dynamical properties of maltose-binding protein (MBP) useful in unveiling active site residues susceptible to ligand binding. The described methodology has been previously used in support of novel topological techniques of persistent homology and statistical inference in complex, multi-scale, high-dimensional data often encountered in computational biophysics. Here we outline a computational protocol that is based on the anisotropic elastic network models of 14 all-atom three-dimensional protein structures. We introduce the notion of dynamical distance matrices as a measure of correlated interactions among 370 amino acid residues that constitute a single protein. The dynamical distance matrices serve as an input for a persistent homology suite of codes to further distinguish a small subset of residues with high affinity for ligand binding and allosteric activity. In addition, we show that ligand-free closed MBP structures require lower deformation energies than open MBP structures, which may be used in categorization of time-evolving molecular dynamics structures. Analysis of the most probable allosteric coupling pathways between active site residues and the protein exterior is also presented.
Publication date
PublisherSpringer
LanguageEnglish
Peer reviewedYes
NPARC number23003034
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