Dong Geng, Ryde Ulf
Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00, Lund, Sweden.
J Biol Inorg Chem. 2016 Jun;21(3):383-94. doi: 10.1007/s00775-016-1348-9. Epub 2016 Mar 3.
The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.
[NiFe]氢化酶催化氢气与质子和电子的可逆转化。活性位点由一个带有一个一氧化碳、两个氰化物和两个半胱氨酸（Cys）配体的铁离子组成。后两者与一个镍离子桥连，该镍离子还有另外两个末端半胱氨酸配体。有人提出在反应机制中其中一个半胱氨酸残基会发生质子化。我们使用了量子力学和分子力学相结合（QM/MM）的几何优化方法、含817个原子的大型QM计算以及QM/MM自由能模拟，采用TPSS和B3LYP方法并将基组外推至四重ζ水平，以确定在反应机制的四个假定状态Ni-SIa、Ni-R、Ni-C和Ni-L中，四个半胱氨酸残基中的哪一个更有利于质子化。计算结果表明，对于所有状态，末端半胱氨酸-546残基最容易质子化，比其他残基容易14 - 51 kJ/mol，这是由于该残基周围在蛋白质中具有更有利的氢键模式。
