Lu D, Voth G A
Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City 84112, USA.
Proteins. 1998 Oct 1;33(1):119-34.
In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism.
在本文中，利用从头算计算和分子动力学模拟对碳酸酐酶II（CA II）的酶活性位点进行建模，以研究该酶功能的一些重要问题。研究发现，Zn2+离子主要呈四面体配位，这与X射线晶体学研究结果一致。然而，也发现了与一个额外水分子的瞬态五重配位。对与锌结合的水和His64残基质子化状态变化时His64构象的研究也证实了X射线研究的结果，即His64构象相当灵活。然而，发现水合程度会影响这种行为。锌结合水与His64残基之间形成水桥涉及2-3千卡/摩尔的自由能垒和几皮秒的平均寿命，这支持了通过这种桥进行质子转移机制的概念。活性位点周围各种残基的突变进一步深入了解了相应的实验结果，事实上，这表明溶剂水分子在CA II催化机制中起着重要作用。
