DOI: 10.1073/pnas.0704304104. Reaction coordinate of an enzymatic reaction revealed by transition path sampling

Reaction coordinate of an enzymatic reaction revealed by transition path sampling

10.1073/pnas.0704304104

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The transition path sampling method previously applied in our group to the reaction catalyzed by lactate dehydrogenase was used to generate a transition path ensemble for this reaction. Based on analysis of the reactive trajectories generated, important residues behind the active site were implicated in a compressional motion that brought the donor–acceptor atoms of the hydride closer together. In addition, residues behind the active site were implicated in a relaxational motion, locking the substrate in product formation. Although this suggested that the compression-relaxation motions of these residues were important to catalysis, it remained unproven. In this work, we used committor distribution analysis to show that these motions are integral components of the reaction coordinate.

Bibliography

Quaytman, S. L., & Schwartz, S. D. (2007). Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proceedings of the National Academy of Sciences, 104(30), 12253â12258.

Authors 2

Sara L. Quaytman (first)
Steven D. Schwartz (additional)

References 20 Referenced 109

10.1126/science.1088172
10.1021/bi0267137
10.1021/bi034824f
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L. Phillip, CD Geissler, D Chandler J Phys Chem B 103, 3706–3710 (1999). / J Phys Chem B by Phillip L. (1999)
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10.1529/biophysj.105.075689
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10.1039/a801266k

Dates

Type	When
Created	18 years, 1 month ago (July 17, 2007, 8:41 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 3:58 p.m.)
Indexed	1 month, 1 week ago (July 24, 2025, 6:55 a.m.)
Issued	18 years, 1 month ago (July 24, 2007)
Published	18 years, 1 month ago (July 24, 2007)
Published Online	18 years, 1 month ago (July 24, 2007)
Published Print	18 years, 1 month ago (July 24, 2007)

Funders 0

None

BibTeX

@article{Quaytman_2007, title={Reaction coordinate of an enzymatic reaction revealed by transition path sampling}, volume={104}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0704304104}, DOI={10.1073/pnas.0704304104}, number={30}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Quaytman, Sara L. and Schwartz, Steven D.}, year={2007}, month=jul, pages={12253–12258} }

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