The structure of water in human ras oncogene proteins
Jeong Yun Yu
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorJae Kwang Shin
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorMu Shik Jhon
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorJeong Yun Yu
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorJae Kwang Shin
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorMu Shik Jhon
Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea
Search for more papers by this authorAbstract
High-directional Monte Carlo (HDMC) simulations are performed to investigate the behavior of water molecules in the catalytic sites of human ras p21 proteins and the results are compared among three types of hydrated ras p21 proteins: the normal ras complexed with GDP (normal-p21/GDP), the mutant ras complexed with GDP (mutant-p21/GDP), and the normal ras complexed with GTP (normal-p21/GTP). Also, the original Metropolis Monte Carlo (MMC) simulation is performed on the normal-p21/GDP system. Comparison between HDMC and MMC shows the improved efficeincy of HDMC on this complicated system. Interaction between water molecules is represented by the TIP3P potential function. The solute–water interaction is represented by the Coulomb and van der Waals interactions from the CHARMM force field spliced with TIP3P. The mean-square displacements and dipole correlation functions are reported. We specifically examined the hydrogen-bond interactions existing near the catalytic sites, by the distribution of small water clusters connected by the hydrogen bond and by the average lengths and fluctations of hydrogen bonds between water molecules and solute atoms. Water molecules form different local structures in different types of the p21/GDP(GTP) complexes. The structure and motion of water molecules near the catalytic sites of the proteins are discussed in detail. © 1994 John Wiley & Sons, Inc.
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