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 (< 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.
Bahar
I
I
Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey. bahar@prc.bme.boun.edu.tr
Atilgan
A R
AR
Erman
B
B
D018360:Crystallography, X-Ray; D008956:Models, Chemical; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins