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The free energy landscape for β hairpin folding in explicit water
Open accessAbstract
The folding free energy landscape of the C-terminal β hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and oplsaa force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the β strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.
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Cites
Folding funnels and energy landscapes of larger proteins within the capillarity approximation
Wolynes, P. G. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.12.6170 · Cited by 218
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Horn, H. W., Swope, W. C., Pitera, J. W., Madura, J. D., Dick, T. J., Hura, G. L., & Head-Gordon, T. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1683075 · Cited by 2,121
Parallel tempering: Theory, applications, and new perspectives
Earl, D. J., & Deem, M. W. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b509983h · Cited by 1,313
Biomolecular Modeling: Goals, Problems, Perspectives
van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., et al. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502655 · Cited by 561
How Water’s Properties Are Encoded in Its Molecular Structure and Energies
Brini, E., Fennell, C. J., Fernandez-Serra, M., Hribar-Lee, B., Lukšič, M., & Dill, K. A. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00259 · Cited by 518
The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery
Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F. L., & Nussinov, R. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00623 · Cited by 431
Metadata
- Authors
- Zhou, R., Berne, B. J., & Germain, R.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2001-12-18
- Volume
- 98
- Issue
- 26
- Pages
- 14931-14936
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2104414143
- Cited by
- 478
- References
- 1
- FWCI
- 7.93
- Type
- journal article
- Language
- en
- Open access
- green
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