DIRECT EVALUATION OF THERMAL FLUCTUATIONS IN PROTEINS USING A SINGLE-PARAMETER HARMONIC POTENTIAL

Background: An elastic network model is proposed for the interactions between closely (less than or equal to 7.0 Angstrom) located alpha-car bon pairs in folded proteins, A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions i n the crystal structure, The model is based on writing the Kirchhoff a djacency matrix for a protein defining the proximity of residues in sp ace, The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations. R esults: The temperature factors of the C-alpha atoms of 12 X-ray struc tures, ranging from a 41 residue subunit to a 633 residue dimer, are a ccurately predicted. Cross-correlations are also efficiently character ized, in close agreement with results obtained with a normal mode anal ysis coupled with energy minimization. Conclusions: The simple model a nd method proposed here provide a satisfactory description of the corr elations between atomic fluctuations. Furthermore, this is achieved wi thin computation times at least one order of magnitude shorter than co mmonly used molecular approaches.