The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
Open accessAbstract
Replica-exchange molecular dynamics simulations in implicit solvent have been carried out to study the folding thermodynamics of a designed 20-residue peptide, or ``miniprotein.'' The simulations in this study used the amber (parm94) force field along with the generalized Born/solvent-accessible surface area implicit solvent model, and they spanned a range of temperatures from 273 to 630 K. Starting from a completely extended initial conformation, simulations of one peptide sequence sample conformations that are <1.0 Å C α rms positional deviation from structures in the corresponding NMR ensemble. These folded states are thermodynamically stable with a simulated melting temperature of ≈400 K, and they satisfy the majority of experimentally observed NMR restraints. Simulations of a related mutant peptide show a degenerate ensemble of states at low temperature, in agreement with experimental results.
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Molecular dynamics with coupling to an external bath
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984) · The Journal of Chemical Physics · doi:10.1063/1.448118 · Cited by 30,700
Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,239
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,311
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,103
Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp003919d · Cited by 4,060
Wang, J., Cieplak, P., & Kollman, P. A. (2000) · Journal of Computational Chemistry · doi:10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-f · Cited by 4,015
Stability of Proteins Small Globular Proteins
Privalov, P. L. (1979) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(08)60460-x · Cited by 2,159
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
Sitkoff, D., Sharp, K. A., & Honig, B. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100058a043 · Cited by 2,131
Parallel tempering algorithm for conformational studies of biological molecules
Hansmann, U. H. E. (1997) · Chemical Physics Letters · doi:10.1016/s0009-2614(97)01198-6 · Cited by 1,008
Cited by
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
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
Self-citationDill, 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
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
Voelz, V. A., Bowman, G. R., Beauchamp, K., & Pande, V. S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja9090353 · Cited by 503
Trp-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
Metadata
- Authors
- Pitera, J. W., & Swope, W.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2003-06-13
- Volume
- 100
- Issue
- 13
- Pages
- 7587-7592
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2046379303
- Cited by
- 344
- References
- 35
- FWCI
- 8.79
- Type
- journal article
- Language
- en
- Open access
- green
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