TY - JOUR
T1 - Role of Protein Motions in Catalysis by Formate Dehydrogenase
AU - Antoniou, Dimitri
AU - Schwartz, Steven D.
N1 - Funding Information:
We happily acknowledge useful conversations with Dr Ioanna Zoi. All computer simulations were performed at the University of Arizona High Performance Computing Center, on a SGI Altix ICE 8400 supercomputer and a Lenovo NeXtScale nx360 M5 supercomputer. This research was supported through the NIH program project grant GM068036.
Publisher Copyright:
© 2020 American Chemical Society.
PY - 2020/10/29
Y1 - 2020/10/29
N2 - We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step. We found that the residue Val123 that lies behind the nicotinamide ring occasionally comes into van der Waals contact with the acceptor and that in all reactive trajectories, the barrier-crossing event is preceded by this contact, meaning that the motion of Val123 is part of the reaction coordinate. Experimental results have been interpreted with a two-dimensional formula for the chemical rate, which cannot capture effects such as the one we describe.
AB - We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step. We found that the residue Val123 that lies behind the nicotinamide ring occasionally comes into van der Waals contact with the acceptor and that in all reactive trajectories, the barrier-crossing event is preceded by this contact, meaning that the motion of Val123 is part of the reaction coordinate. Experimental results have been interpreted with a two-dimensional formula for the chemical rate, which cannot capture effects such as the one we describe.
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U2 - 10.1021/acs.jpcb.0c05725
DO - 10.1021/acs.jpcb.0c05725
M3 - Article
C2 - 33064490
AN - SCOPUS:85094931443
VL - 124
SP - 9483
EP - 9489
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
SN - 1520-6106
IS - 43
ER -