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Dynamical theory of activated processes in globular proteins.
Open accessAbstract
A method is described for calculating the reaction rate in globular proteins of activated processes such as ligand binding or enzymatic catalysis. The method is based on the determination of the probability that the system is in the transition state and of the magnitude of the reactive flux for transition-state systems. An "umbrella sampling" simulation procedure is outlined for evaluating the transition-state probability. The reactive flux is obtained from an approach described previously for calculating the dynamics of transition-state trajectories. An application to the rotational isomerization of an aromatic ring in the bovine pancreatic trypsin inhibitor is presented. The results demonstrate the feasibility of calculating rate constants for reactions in proteins and point to the importance of solvent effects for reactions that occur near the protein surface.
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Cited by
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130812 · Cited by 6,808
Q UANTUM M ECHANICAL M ETHODS FOR E NZYME K INETICS
Gao, J., & Truhlar, D. G. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.091301.150114 · Cited by 733
Fischer, S., & Karplus, M. (1992) · Chemical Physics Letters · doi:10.1016/0009-2614(92)85543-j · Cited by 490
Self-citationReaction coordinates of biomolecular isomerization
Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426
Automatic Method for Identifying Reaction Coordinates in Complex Systems
Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400
Metadata
- Authors
- Northrup, S. H., Pear, M. R., Lee, C. Y., McCammon, J. A., & Karplus, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1982-07
- Volume
- 79
- Issue
- 13
- Pages
- 4035-4039
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1999270898
- Cited by
- 195
- References
- 0
- FWCI
- 2.29
- Type
- journal article
- Language
- en
- Open access
- green
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- Northrup, S. H., Pear, M. R., Lee, C. Y., McCammon, J. A., & Karplus, M. (1982). Dynamical theory of activated processes in globular proteins. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.79.13.4035
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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