The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations
Abstract
Using over 75 mus of molecular dynamics simulation, we have generated several thousand folding simulations of the 20-residue Trp cage at experimental temperature and solvent viscosity. A total of 116 independent folding simulations reach RMSDcalpha values below 3 A RMSDcalpha, some as close as 1.4 A RMSDcalpha. We estimate a folding time of 5.5+/-3.5 mus, a rate that is in reasonable agreement with experimental kinetics. Finally, we characterize both the folded and unfolded ensemble under native conditions and note that the average topology of the unfolded ensemble is very similar to the topology of the native state.
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Citations
Cites
Designing a 20-residue protein
Neidigh, J. W., Fesinmeyer, R. M., & Andersen, N. H. (2002) · Nature Structural Biology · doi:10.1038/nsb798 · Cited by 793
Cited by
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., et al. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10349 · Cited by 4,441
The protein folding ‘speed limit’
Kubelka, J., Hofrichter, J., & Eaton, W. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.01.013 · Cited by 830
To milliseconds and beyond: challenges in the simulation of protein folding
Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409
Self-citationTrp-cage: Folding free energy landscape in explicit water
Zhou, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2233312100 · Cited by 363
Protein oligomerization: How and why
Ali, M. H., & Imperiali, B. (2005) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2005.05.037 · Cited by 356
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
Pitera, J. W., & Swope, W. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1330954100 · Cited by 344
Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
Ding, F., Tsao, D., Nie, H., & Dokholyan, N. V. (2008) · Structure · doi:10.1016/j.str.2008.03.013 · Cited by 326
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
Zhou, R. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10483 · Cited by 300
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
Marinelli, F., Pietrucci, F., Laio, A., & Piana, S. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000452 · Cited by 274
Metadata
- Authors
- Snow, C. D., Zagrovic, B., & Pande, V. S.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-11-16
- Volume
- 124
- Issue
- 49
- Pages
- 14548-14549
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W1992422451
- Cited by
- 237
- References
- 1
- FWCI
- 4.21
- Type
- journal article
- Language
- en
- Open access
- closed
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