Computational Chemistry and Molecular Modeling
Wiley InterScience Backfile Collection 1832-2000
Chemistry and Pharmacology
The three-dimensional structure of the carboxyl-terminal region of the human ras oncogenic protein (called p21) has been determined using the HDMC (High-directional Monte Carlo) method combined with MD (molecular dynamics) simulation. A truncated p21 containing residues 1-171 without the carboxyl-terminal end was analyzed using X-ray crystallography by Kim et al. It has been well documented that the carboxyl-terminal region of p21 is flexible and plays an important role in transmitting a signal from the membrane-attached domain. We have carried out the theoretical calculation for 18 undefined residues, which correspond to residues 172-189 of intact p21, in addition to seven residues (165-171) from X-ray coordinates of the C-terminal end of human C—Ha—ras protein. In this calculation, the main-chain atoms of residues 165-169 have been fitted to X-ray structure, and the remaining region has been allowed to move during the conformational analysis. We have confirmed that revised HDMC can easily alter the local minima of the polypeptide chains as the internal vibrations of molecules are allowed by MD simulation. Throughout this study, we suggest that the C-terminal end of human C—Ha—ras p21 protein has structures in the forms of an α helix for 165-172, a loop for 173-180, and an α helix for 181-187 regions, like the helical hairpin. © 1995 by John Wiley & Sons, Inc.
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