Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

摘要: Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details proton transfers coupled to cleavage is one key challenges QM/MM calculations these and other enzyme catalyzed reactions. lack experimental information offers both an opportunity for computations as well often unresolved controversies. We example small GTPases including important human Ras protein. high dimensionality chemical complexity demand carefully chosen computational techniques terms underlying quantum theory sampling conformational ensemble. also point out role Mg2+ ions, recent advances their transient involvement catalytic mechanisms.