Molecular dynamics simulation of trp-aporepressor in a solvent.
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 A gave a better result, and the most satisfactory result was obtained when electrostatic interactions within a cut-off radius of 18 A 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 between 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.
Komeiji
Y
Y
Department of Biology, Faculty of Science, University of Tokyo, Japan.
Uebayasi
M
M
Someya
J
J
Yamato
I
I
D001059:Apoproteins / Q000737:chemistry*; D001426:Bacterial Proteins; D003198:Computer Simulation; D003461:Crystallography; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins; D008956:Models, Chemical; D008968:Molecular Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D001059:Apoproteins; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C027190:TRPR protein, E coli; D014867:Water