Premium
Pump‐probe molecular dynamics as a tool for studying protein motion and long range coupling
Author(s) -
Sharp Kim,
Skinner John J.
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21146
Subject(s) - pdz domain , molecular dynamics , calmodulin , biological system , allosteric regulation , chemistry , protein dynamics , protein structure , coupling (piping) , biophysics , chemical physics , computational chemistry , materials science , biochemistry , biology , metallurgy , enzyme
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. Proteins 2006. © 2006 Wiley‐Liss, Inc.