Fast simulation protocol for protein structural transitions: Modeling of the relationship of structure and function

Arun K. Setty, D. M. Zuckerman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationProteins as Materials
Pages33-45
Number of pages13
StatePublished - Dec 1 2004
Event2004 MRS Spring Meeting - San Francisco, CA, United States
Duration: Apr 12 2004Apr 16 2004

Publication series

NameMaterials Research Society Symposium Proceedings
Volume826
ISSN (Print)0272-9172

Conference

Conference2004 MRS Spring Meeting
CountryUnited States
CitySan Francisco, CA
Period4/12/044/16/04

ASJC Scopus subject areas

  • Materials Science(all)
  • Condensed Matter Physics
  • Mechanics of Materials
  • Mechanical Engineering

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    Setty, A. K., & Zuckerman, D. M. (2004). Fast simulation protocol for protein structural transitions: Modeling of the relationship of structure and function. In Proteins as Materials (pp. 33-45). (Materials Research Society Symposium Proceedings; Vol. 826).