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Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation
Abstract
For the structure and function of proteins, the pH of the solution is one of the determining parameters. Current molecular dynamics (MD) simulations account for the solution pH only in a limited way by keeping each titratable site in a chosen protonation state. We present an algorithm that generates trajectories at a Boltzmann distributed ensemble of protonation states by a combination of MD and Monte Carlo (MC) simulation. The algorithm is useful for pH‐dependent structural studies and to investigate in detail the titration behavior of proteins. The method is tested on the acidic residues of the protein hen egg white lysozyme. It is shown that small structural changes may have a big effect on the pK A values of titratable residues. Proteins 2002;47:469–480. © 2002 Wiley‐Liss, Inc.
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Cited by
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Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 788
Constant‐pH molecular dynamics using continuous titration coordinates
Lee, M. S., Salsbury, F. R., & Brooks, C. L. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20128 · Cited by 364
Swails, J. M., York, D. M., & Roitberg, A. E. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct401042b · Cited by 268
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136
Protein p K a Prediction by Tree-Based Machine Learning
Chen, A. Y., Lee, J., Damjanovic, A., & Brooks, B. R. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c01257 · Cited by 37
Metadata
- Authors
- Bürgi, R., Kollman, P. A., & van Gunsteren, W. F.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2002-04-19
- Volume
- 47
- Issue
- 4
- Pages
- 469-480
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2003516919
- Cited by
- 180
- References
- 0
- FWCI
- 1.94
- Type
- journal article
- Language
- en
- Open access
- closed
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- Bürgi, R., Kollman, P. A., & van Gunsteren, W. F. (2002). Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.10046
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