Diffusion of a protein in configuration space

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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 ... continued below

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27 p.

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Garcia, A.E.; Blumenfeld, R.; Hummer, G. & Sobehart, J. September 1, 1995.

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Description

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.

Physical Description

27 p.

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OSTI as DE96000024

Source

  • 9. conversation in biomolecular stereodynamics, Albany, NY (United States), 20-24 Jun 1995

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  • Other: DE96000024
  • Report No.: LA-UR--95-2962
  • Report No.: CONF-9506267--1
  • Grant Number: W-7405-ENG-36
  • DOI: 10.2172/113927 | External Link
  • Office of Scientific & Technical Information Report Number: 113927
  • Archival Resource Key: ark:/67531/metadc623683

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  • September 1, 1995

Added to The UNT Digital Library

  • June 16, 2015, 7:43 a.m.

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  • Feb. 25, 2016, 4 p.m.

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Garcia, A.E.; Blumenfeld, R.; Hummer, G. & Sobehart, J. Diffusion of a protein in configuration space, report, September 1, 1995; New Mexico. (digital.library.unt.edu/ark:/67531/metadc623683/: accessed October 17, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.