Conformational Dynamics of Proteins

  Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

  Bahar, I; Atilgan, A R; Erman, B

  Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey; e-mail bahar@pitt.edu

  Abstract

BACKGROUND: An elastic network model is proposed for the interactions between closely (< or = 7.0 A) located alpha-carbon pairs in folded proteins. A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure. The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space. The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations. RESULTS: The temperature factors of the C alpha atoms of 12 X-ray structures, ranging from a 41 residue subunit to a 633 residue dimer, are accurately predicted. Cross-correlations are also efficiently characterized, in close agreement with results obtained with a normal mode analysis coupled with energy minimization. CONCLUSIONS: The simple model and method proposed here provide a satisfactory description of the correlations between atomic fluctuations. Furthermore, this is achieved within computation times at least one order of magnitude shorter than commonly used molecular approaches. [Journal Article; In English; England]

  CAS Registry Numbers: Proteins

  Citation Subset Indicators: Index Medicus

MeSH Terms: Comparative Study; Crystallography, X-Ray; Models, Chemical; Molecular Structure; Protein Conformation; * Protein Folding; Proteins, * chemistry (CH); Support, Non-U.S. Gov't; Thermodynamics
 

Folding & Design
Volume 2, Issue 3, 1997, Pages 173-181
ISSN: 1359-0278