Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar
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ORIGINAL PAPER
Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation Xue Tian & Lin Jiang & Yuan Yuan & Minqi Wang & Yanzhi Guo & Xiaojun Zeng & Menglong Li & Xuemei Pu
Received: 1 January 2013 / Accepted: 12 February 2013 / Published online: 1 March 2013 # Springer-Verlag Berlin Heidelberg 2013
Abstract The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 %v/v) on the tetrahedral intermediate of chymotrypsin trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution and Hbonding are analyzed in the two organic media. Our results show that the changes in overall structure of the protein almost display a clear correlation with the water content in hexane media while to some extent U-shaped/bell-shaped dependence on the water content is observed in acetonitrile media with a minimum/maximum at 10–20 % water content. In contrast, the water content change in the two organic solvents does not play an observable role in the stability of catalytic hydrogen-bond network, which still exhibits high stability in all hydration levels, different from observations on the free enzyme system [Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M (2012) J Phys Chem B 116(10):3292– 3304]. In low hydration levels, most water molecules mainly distribute near the protein surface and an increase in the water content could not fully exclude the organic solvent from the protein surface. However, the acetonitrile solvent displays a stronger ability to strip off water molecules from the protein than the hexane. In a summary, the difference in X. Tian : L. Jiang : M. Wang : Y. Guo : X. Zeng : M. Li : X. Pu (*) Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China e-mail: [email protected] Y. Yuan College of Management, Southwest University for Nationalities, Chengdu 610041, People’s Republic of China
the calculated properties between the two organic solvents is almost significant in low water content (3 % water content levels. On the other hand, we also analyze the H-bonding between the organic solvent molecule and these active residues. The result shows that there is no H-bonding (data is not shown), different from the observation derived from the previous free chymotrypsin in the acetonitrile solvent with 3 % water content [48], which showed that the acetonitrile molecule penetrating into the active site could form H-bond with the active residues. In order to gain insight into this phenomenon, we calculate the number of solvent molecules in the active region (listed in Table 5), defined by 5 Å distance from the OG@Ser195 atom. The result shows that there is nearly no organic solvent penetrating into the active site, especially in hexane medium with more than 10 % water content. Whereas there is at least one water molecule penetrating into the ac
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