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. |
