Realistic Extension Algorithm via Covariance Hessian
Abstract
Coarsegraining of protein interactions provides a means of simulating large biological systems. Here, a coarsegraining method, REACH, is introduced, in which the force constants of a residuescale elastic network model are calculated from the variancecovariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the Catoms variancecovariance matrices are calculated from the ensembles of 1ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarsegrained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distancedependence of the interresidue force constants allows rapid calculation of the REACH normal modes. The model force constants from monomeric and dimeric myoglobin are found to be similar in magnitude to each other. The MD intra and intermolecular meansquare fluctuations and the vibrational density of states are well reproduced by the residuescale REACH normal modes without requiring rescaling of the force constant parameters. The temperaturedependence of the myoglobin REACH force constants reveals that the dynamical transition in protein internal fluctuations arises principally from softening of the elasticity in the nonlocal interactions. The REACH method is found to be a reliable way of determining spatiotemporal protein motion without the need for expensive computations of long atomisticmore »
 Authors:
 University of Heidelberg
 ORNL
 Publication Date:
 Research Org.:
 Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
 Sponsoring Org.:
 USDOE Laboratory Directed Research and Development (LDRD) Program
 OSTI Identifier:
 932204
 DOE Contract Number:
 DEAC0500OR22725
 Resource Type:
 Journal Article
 Resource Relation:
 Journal Name: Biophysical Journal; Journal Volume: 93; Journal Issue: 10
 Country of Publication:
 United States
 Language:
 English
 Subject:
 59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; CONSTRUCTION; ELASTICITY; FLUCTUATIONS; MATRICES; MYOGLOBIN; PROTEINS; SIMULATION; TRAJECTORIES
Citation Formats
Moritsugu, K, and Smith, Jeremy C. Realistic Extension Algorithm via Covariance Hessian. United States: N. p., 2007.
Web. doi:10.1529/biophysj.107.111898.
Moritsugu, K, & Smith, Jeremy C. Realistic Extension Algorithm via Covariance Hessian. United States. doi:10.1529/biophysj.107.111898.
Moritsugu, K, and Smith, Jeremy C. Mon .
"Realistic Extension Algorithm via Covariance Hessian". United States.
doi:10.1529/biophysj.107.111898.
@article{osti_932204,
title = {Realistic Extension Algorithm via Covariance Hessian},
author = {Moritsugu, K and Smith, Jeremy C},
abstractNote = {Coarsegraining of protein interactions provides a means of simulating large biological systems. Here, a coarsegraining method, REACH, is introduced, in which the force constants of a residuescale elastic network model are calculated from the variancecovariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the Catoms variancecovariance matrices are calculated from the ensembles of 1ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarsegrained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distancedependence of the interresidue force constants allows rapid calculation of the REACH normal modes. The model force constants from monomeric and dimeric myoglobin are found to be similar in magnitude to each other. The MD intra and intermolecular meansquare fluctuations and the vibrational density of states are well reproduced by the residuescale REACH normal modes without requiring rescaling of the force constant parameters. The temperaturedependence of the myoglobin REACH force constants reveals that the dynamical transition in protein internal fluctuations arises principally from softening of the elasticity in the nonlocal interactions. The REACH method is found to be a reliable way of determining spatiotemporal protein motion without the need for expensive computations of long atomistic MD simulations.},
doi = {10.1529/biophysj.107.111898},
journal = {Biophysical Journal},
number = 10,
volume = 93,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}

Coarsegraining of protein interactions provides a means of simulating large biological systems. Here, a coarsegraining method, REACH, is introduced, in which the force constants of a residuescale elastic network model are calculated from the variancecovariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the Catoms variancecovariance matrices are calculated from the ensembles of 1ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarsegrained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distancedependence of the interresidue force constants allows rapid calculation of the REACH normal modes. Themore »

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In order to improve the sampling of restricted microstates in our previous work [C. Nie, J. Geng, and W. H. Marlow, J. Chem. Phys. 127, 154505 (2007); 128, 234310 (2008)] and quantitatively predict thermal properties of supersaturated vapors, an extension is made to the Corti and Debenedetti subcell constraint algorithm [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)], which restricts the maximum allowed local density at any point in a simulation box. The maximum allowed local density at a point in a simulation box is defined by the maximum number of particles N{sub m} allowed tomore » 
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