Effects of organic solvent and crystal water on γ-chymotrypsin in acetonitrile media: observations from molecular dynamics simulation and DFT calculation.
The use of enzymes in nonaqueous solvent has been one of the most exciting facets of enzymology in recent times; however, the mechanism of how organic solvent and essential water influence on structure and function of enzyme has been not satisfactorily explained in experiments, which limit its further application. Herein, we used molecular dynamics (MD) simulation to study γ-chymotrypsin in two types of media (viz., acetonitrile media with inclusion of 151 crystal water molecules and aqueous solution). On the basis of the MD result, the truncated active site modes containing two specific solvent molecules are furthered studied at the B3LYP/6-31+G(d,p) level of theory within the framework of PCM model. The results show that the acetontrile solvent gives rise to an extent deviation of enzyme structure from the native one, a drop in the flexibility and the total SASA of enzyme. The QM study further reveals that the structure variation of the active pocket caused by acetonitrile would lead to a weakened strength in the catalytic H-bond network, a drop in the pK(a) value of His57, and an increase in the proton transfer barriers from the Ser195 to the His57 residue, which may contribute to the drop in the enzymatic activity in acetontrile media. In addition, the crystal waters play an importance role in retaining the catalytic H-bond network and weakening the acetonitrile-induced variations above, which may be associated with the fact that the enzyme could retain catalytic activity in microhydration acetonitrile media.
Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China.
Lijuan
L
Zhu
Wei
W
Yang
Yan Yan
YY
Meng
Xiuchan
X
Xiao
Yanzhi
Y
Guo
Xuemei
X
Pu
Menglong
M
Li
D000097:Acetonitriles / Q000737:chemistry*; D020134:Catalytic Domain; D002918:Chymotrypsin / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D000097:Acetonitriles; D012997:Solvents; D014867:Water; D002918:Chymotrypsin; C117605:gamma-chymotrypsin; C032159:acetonitrile