Paper Citing NAMD - Abstract
Rommel, Judith B.; Kaestner, Johannes
The Fragmentation-Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:10195-10203, JUL 6 2011
The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 (Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.
