Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

作者：Hu, LiHong; Soderhjelm, Par; Ryde, Ulf^*

来源：Journal of Chemical Theory and Computation, 2013, 9(1): 640-649.

DOI：10.1021/ct3005003

• AUXILIARY BASIS-SETS
• ENZYMATIC-REACTIONS
• REORGANIZATION ENERGY
• NUMERICAL-INTEGRATION
• MOLECULAR-DYNAMICS
• QUANTUM
• APPROXIMATION
• BINDING
• SYSTEM
• LIGAND

We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimization on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a second-sphere histidine residue in the active site of [Ni,Fe] hydrogenase, which has been shown to be very sensitive to the surroundings. We include in the QM calculations all residues within 4.5 angstrom of the active site, two capped residues on each side of the active-site residues, and all charged groups that are buried inside the protein, which for this enzyme includes three iron-sulfur clusters, in total, 930 atoms. These calculations are performed at the BP86/def2-SV(P) level, but the energies are then extrapolated to the B3LYP/def2-TZVP level with a smaller QM system, and zero-point energy, entropy, and thermal effects are added. We test three approaches to model the remaining atoms of the protein solvent, viz., by standard QM/MM approaches using either mechanical or electrostatic embedding or by using a continuum solvation model for the large QM systems. Quite encouragingly, the three approaches give the same results within 14 kJ/mol, and variations in the size of the QM system do not change the energies by more than 8 kJ/mol, provided that the QM/MM junctions are not moved closer to the QM system. The statistical precision for the average over 10 snapshots is 1-3 kJ/mol.

• 出版日期2013-1
• 单位东北师范大学