Prediction of protein motions from amino acid sequence and its application to protein-protein interaction.

BMC Structural Biology
Shuichi HiroseTamotsu Noguchi

Abstract

Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predi...Continue Reading

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Citations

Jun 13, 2012·Nucleic Acids Research·Alexandre G de BrevernJean-Christophe Gelly
Dec 18, 2013·Bioinformatics·Hua Zhang, Lukasz Kurgan
Nov 16, 2010·Biophysical Chemistry·Alessandro SiglioccoloStefano Pascarella
Jun 16, 2015·Frontiers in Molecular Biosciences·Pierrick CraveurAlexandre G de Brevern
Sep 11, 2020·Journal of Biomolecular Structure & Dynamics·Ahmed L Alaofi

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Methods Mentioned

BETA
NMR
X-ray
GTPase

Software Mentioned

POODLE
ASP
Wiggle
FlexPred
ProMode
HingeProt
DynDom
PROFbval
psipred
Rigid Substructure Topography ( FIRST )

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