All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins

Structural changes of proteins are closely related with their molecular function. We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. Here, we have extended MT to incorporate all heavy atoms to analy...

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Main Authors: Ryotaro Koike, Motonori Ota
Format: Article
Language:English
Published: The Biophysical Society of Japan 2019-11-01
Series:Biophysics and Physicobiology
Subjects:
Online Access:https://doi.org/10.2142/biophysico.16.0_280
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author Ryotaro Koike
Motonori Ota
author_facet Ryotaro Koike
Motonori Ota
author_sort Ryotaro Koike
collection DOAJ
description Structural changes of proteins are closely related with their molecular function. We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. Here, we have extended MT to incorporate all heavy atoms to analyze side chain-related (SCR) motions. All Atom Motion Tree (AAMT) was applied to 76 proteins that exhibited a simple domain motion identified by MT. AAMT also detected 921 SCR motions. We examined the coupling of domain and SCR motions and classified the structural changes in terms of coupling. The statistical results indicated that it is common for coupled SCR motions to also couple with the domain motion. The classification correlates properties of domain motions and SCR motions. The AAMT results suggest that a large domain motion with a sizable domain boundary is accompanied by SCR motions composed of more than a single residue, which induces further couplings of SCR motions.
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spelling doaj.art-15149bce0e6e43f7966fe7420a84ed062022-12-21T19:30:25ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792019-11-011610.2142/biophysico.16.0_280All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteinsRyotaro Koike0Motonori Ota1Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, JapanGraduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, JapanStructural changes of proteins are closely related with their molecular function. We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. Here, we have extended MT to incorporate all heavy atoms to analyze side chain-related (SCR) motions. All Atom Motion Tree (AAMT) was applied to 76 proteins that exhibited a simple domain motion identified by MT. AAMT also detected 921 SCR motions. We examined the coupling of domain and SCR motions and classified the structural changes in terms of coupling. The statistical results indicated that it is common for coupled SCR motions to also couple with the domain motion. The classification correlates properties of domain motions and SCR motions. The AAMT results suggest that a large domain motion with a sizable domain boundary is accompanied by SCR motions composed of more than a single residue, which induces further couplings of SCR motions.https://doi.org/10.2142/biophysico.16.0_280rigid-body motionstructural changeconformational change
spellingShingle Ryotaro Koike
Motonori Ota
All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
Biophysics and Physicobiology
rigid-body motion
structural change
conformational change
title All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
title_full All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
title_fullStr All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
title_full_unstemmed All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
title_short All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
title_sort all atom motion tree detects side chain related motions and their coupling with domain motion in proteins
topic rigid-body motion
structural change
conformational change
url https://doi.org/10.2142/biophysico.16.0_280
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AT motonoriota allatommotiontreedetectssidechainrelatedmotionsandtheircouplingwithdomainmotioninproteins