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On the transition coordinate for protein folding
Abstract
To understand the kinetics of protein folding, we introduce the concept of a “transition coordinate” which is defined to be the coordinate along which the system progresses most slowly. As a practical implementation of this concept, we define the transmission coefficient for any conformation to be the probability for a chain with the given conformation to fold before it unfolds. Since the transmission coefficient can serve as the best possible measure of kinetic distance for a system, we present two methods by which we can determine how closely any parameter of the system approximates the transmission coefficient. As we determine that the transmission coefficient for a short-chain heteropolymer system is dominated by entropic factors, we have chosen to illustrate the methods mentioned by applying them to geometrical properties of the system such as the number of native contacts and the looplength distribution. We find that these coordinates are not good approximations of the transmission coefficient and therefore, cannot adequately describe the kinetics of protein folding.
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Cited by
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
Scherer, M. K., Trendelkamp-Schroer, B., Paul, F., Pérez-Hernández, G., Hoffmann, M., Plattner, N., Wehmeyer, C., Prinz, J.-H., & Noé, F. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00743 · Cited by 1,163
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Noé, F., Schütte, C., Vanden-Eijnden, E., Reich, L., & Weikl, T. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905466106 · Cited by 820
Native contacts determine protein folding mechanisms in atomistic simulations
Best, R. B., Hummer, G., & Eaton, W. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311599110 · Cited by 594
Metadata
- Authors
- Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T., & Shakhnovich, E. S.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1998-01-01
- Volume
- 108
- Issue
- 1
- Pages
- 334-350
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W1970440715
- Cited by
- 486
- References
- 0
- FWCI
- 5.29
- Type
- journal article
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: On the transition coordinate for protein folding. https://app.cochat.ai/papers/10.1063/1.475393
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- Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T., & Shakhnovich, E. S. (1998). On the transition coordinate for protein folding. The Journal of Chemical Physics. https://doi.org/10.1063/1.475393
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