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Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation

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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 H-bonding 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 the calculated properties between the two organic solvents is almost significant in low water content (<10 %) and become to be small with increasing water content. In addition, some structural properties at 10 ~ 20 % v/v hydration zone, to large extent, approach to those in aqueous solution.

The work uses MD simulation to study effects of five water contents 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 H-bonding was discussed in the two organic media

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Acknowledgments

This project is supported by the National Science Foundation of China (Grant No. 20973115, 21273154, U1230121) and the International Science and Technology Cooperation Foundation of Sichuan province (Grant No. 2011H0003).

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Authors and Affiliations

  1. Faculty of Chemistry, Sichuan University, Chengdu, 610064, People’s Republic of China

    Xue Tian, Lin Jiang, Minqi Wang, Yanzhi Guo, Xiaojun Zeng, Menglong Li & Xuemei Pu

  2. College of Management, Southwest University for Nationalities, Chengdu, 610041, People’s Republic of China

    Yuan Yuan

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Correspondence to Xuemei Pu.

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Tian, X., Jiang, L., Yuan, Y. et al. Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation. J Mol Model 19, 2525–2538 (2013). https://doi.org/10.1007/s00894-013-1807-y

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