Protein Engineering vol. 4 no. 8 pp. 871-875, 1991
© 1991 Oxford University Press
RESEARCH-ARTICLE |
Molecular dynamics simulation of trp-aporepressor in a solvent
Department of Biology, Faculty of Science, University of Tokyo 7-3-1 Hongo, Tokyo 113, Japan 1Fermentation Research Institute, Agency of Industrial Science and Technology, Ministry of International Trade and Industry 1-1-3 Higashi, Tsukuba-shi, Ibaraki 305, Japan 2Department of Biological Science and Technology, Science University of Tokyo 2641 Yamazaki, Noda-shi, Chiba 278, Japan
3To whom correspondence should be addressed
Molecular dynamics simulations of Escherichia coli trp-aporepressor were carried out in the absence and presence of explicit water molecules. The vacuum simulations resulted in significant deformation of the initial X-ray structure. A solvated simulation with a nonbonded cut-off radius of 9 Å gave a better result, and the most satisfactory result was obtained when electrostatic interactions within a cut-off radius of 18 Å were considered by a twin-range method. The trajectory from the last simulation was used to analyze the dynamical properties of the aporepressor. The root-mean-square fluctuations of the residues showed the rigidity of the central core and the flexibility of the DNA-binding sites, consistent with the X-ray temperature factors. The dynamical cross-correlation map indicated a significant negative correlation betewen the central core and the two DNA-binding sites, and thus reproduced the three-domain format (a central core and two DNA-binding heads) from a dynamical point of view. The core region showed weak, but many, intra- and inter-molecular correlations, while the helix-turn-helix DNA-binding motifs were free from correlations with other regions.
Keywords: dynamical cross-correlation map/electrostatic interaction/molecular dynamics/solvent/trp-aporepressor
Received July 2, 1991; accepted August 26, 1991.