Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Research Abstract Details 

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Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Abstract Text:

Haibo Yu,Liang Ma,Yang Yang,Qiang Cui,

An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with previous experimental and computational studies in a critical manner. The behavior of the widely used reporter residue, Trp501, in the simulations confirms the concern that its fluorescence does not simply reflect the relay loop conformation or active-site open/close but depends subtly on its microenvironment. The findings in the targeted molecular dynamics and a previous minimum energy path analysis of the recovery stroke have been compared and analyzed, which emphasized the difference and complementarity of the two approaches. In conjunction with our previous studies, the current set of investigations suggest that the modulation of structural flexibility at both the local (e.g., active-site) and domain scales with strategically placed "hotspot" residues and phosphate chemistry is likely the general feature for mechanochemical coupling in many molecular motors. The fundamental strategies of examining both collective and local changes and combining physically motivated methods and informatics-driven techniques are expected to be valuable to the study of other molecular motors and allosteric systems in general.

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Publishing Authors By Initials

H Yu,L Ma,Y Yang,Q Cui,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: structure-activity relationship research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: structure-activity relationship research

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Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: PLoS computational biology

VOLUME: 3

Page Numbers: e23

Journal Abbreviation: PLoS Comput. Biol.

ISSN: 1553-7358

DAY: 22

MONTH: 12

YEAR: 2006

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101238922

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Keywords Mesh Terms:

KEYWORDS: Structure-Activity Relationship

MESH TERMS: physiology

Chemical & Substance for Abstract: Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Information

Substance Name: Myosins

Registry Number: EC 3.6.1.4

Grant and Affiliation Information for Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.

AFFILIATION: Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America.

Country: United States

AGENCY: United States NIGMS

GRANT: R01-GM071428–02

ACRONYM: GM

MEDLINETA: PLoS Comput Biol

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