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Fast Simulation Protocol for Protein Structural Transitions: Modeling of the Relationship of Structure and Function

Published online by Cambridge University Press:  15 March 2011

Arun K. Setty and
D. M. Zuckerman
Arun K. Setty
Affiliation:
Center for Computational Biology and Bioinformatics and Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh
D. M. Zuckerman
Affiliation:
Center for Computational Biology and Bioinformatics and Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh
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Abstract

An approach is developed to study the dynamics of protein conformational transitions in depth. A computational (Monte Carlo) approach based on a united residue model is used. Unbiased transitions between the Apo and Holo conformations/states of calmodulin are observed at the rate of 1 per day per processor. A series of models of increasing complexity is studied, accounting for hydrophobic interactions and calcium binding. Details of the transitional region and structural information about intermediate states are obtained. Statistically converged ensembles of transitions are obtained in a reasonable real time period.

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Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 826: Symposium V – Proteins as Materials , 2004, V3.5
Copyright
Copyright © Materials Research Society 2004

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