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  Diffusion of a protein in configuration space

Garcia, A. E., Blumenfeld, R., Hummer, G., & Sobehart, J.(1995). Diffusion of a protein in configuration space (LA-UR-95-2962; CONF-9506267-1). Los Alalmos: Los Alamos National Laboratory.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0009-205D-B Version Permalink: https://hdl.handle.net/21.11116/0000-000B-91FC-5
Genre: Report

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 Creators:
Garcia, Angel E.1, Author
Blumenfeld, Raphael1, Author
Hummer, Gerhard2, Author                 
Sobehart, Jorge1, Author
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1External Organizations, ou_persistent22              
2Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, ou_persistent22              

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 Abstract: Simulations of biomolecular dynamics are commonly interpreted in terms of harmonic or quasi-harmonic models for the dynamics of the system. These models assume that biomolecules exhibit oscillations around a single energy minimum. However, spectroscopic data on myoglobin suggest that proteins sample multiple minima. Transitions between minima reveal a broad distribution of energy barriers. This behavior has been observed in other biomolecular systems. To elucidate the nature of protein dynamics the authors have studied a 1.2ns molecular dynamics trajectory of crambin in aqueous solution. This trajectory samples multiple local energy minima. Transitions between minima involve collective motions of amino acids over long distances. The authors show that nonlinear motions are responsible for most of the atomic fluctuations of the protein. These atomic fluctuations are not well described by large motions of individual atoms or a small group of atoms, but rather by concerted motions of many atoms. These nonlinear motions describe transitions between different basins of attraction. The signature of these motions manifests in local and global structural variables. A method for extracting Molecule Optimal Dynamic Coordinates (MODC) is presented.

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Language(s): eng - English
 Dates: 1995-09
 Publication Status: Issued
 Pages: 29
 Publishing info: Los Alalmos : Los Alamos National Laboratory
 Table of Contents: -
 Rev. Type: -
 Identifiers: Report Nr.: LA-UR-95-2962; CONF-9506267-1
DOI: 10.2172/113927
BibTex Citekey: garcia_diffusion_1995
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Title: Proceedings of the 9th Conversation in Biomolecular Stereodynamics
Place of Event: Albany, NY
Start-/End Date: 1995-06-20 - 1995-06-24

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