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

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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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Acknowledgment

Funding provided by the UP-GSPH Department of Environmental Occupational Health AND NIH.

Thanks to Marty Ytreberg for useful discussions.

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Authors and Affiliations

  1. Center for Computational Biology and Bioinformatics and Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, USA

    Arun K. Setty & D. M. Zuckerman

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  1. Arun K. Setty
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  2. D. M. Zuckerman
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Setty, A.K., Zuckerman, D.M. Fast Simulation Protocol for Protein Structural Transitions: Modeling of the Relationship of Structure and Function. MRS Online Proceedings Library 826, 351–363 (2004). https://doi.org/10.1557/PROC-826-V3.5

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  • DOI: https://doi.org/10.1557/PROC-826-V3.5

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