Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling.

Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Research Abstract Details 

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Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Abstract Text:

Kim Sharp,John J Skinner,

A new method for analyzing the dynamics of proteins is developed and tested. The method, pump-probe molecular dynamics, excites selected atoms or residues with a set of oscillating forces, and the transmission of the impulse to other parts of the protein is probed using Fourier transform of the atomic motions. From this analysis, a coupling profile can be determined which quantifies the degree of interaction between pump and probe residues. Various physical properties of the method such as reciprocity and speed of transmission are examined to establish the soundness of the method. The coupling strength can be used to address questions such as the degree of interaction between different residues at the level of dynamics, and identify propagation of influence of one part of the protein on another via "pathways" through the protein. The method is illustrated by analysis of coupling between different secondary structure elements in the allosteric protein calmodulin, and by analysis of pathways of residue-residue interaction in the PDZ domain protein previously elucidated by genomics and mutational studies.

Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Publishing Authors By Initials

K Sharp,JJ Skinner,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary research

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Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Proteins

VOLUME: 65

Page Numbers: 347-61

Journal Abbreviation: Proteins

ISSN: 1097-0134

DAY: 1

MONTH: Nov

YEAR: 2006

Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 8700181

Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Keywords Mesh Terms:

KEYWORDS: Protein Structure, Tertiary

MESH TERMS: genetics

Chemical & Substance for Abstract: Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Information

Substance Name: Calmodulin

Registry Number: 0

Grant and Affiliation Information for Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling.

AFFILIATION: Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA. sharpk@mail.med.upenn.edu

Country: United States

AGENCY: United States NIGMS

GRANT: GM48130

ACRONYM: GM

MEDLINETA: Proteins

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