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α-Helical stabilization by side chain shielding of backbone hydrogen bonds
Open accessAbstract
We study atomic models of the thermodynamics of the structural transition of peptides that form α-helices. The effect of sequence variation on α-helix formation for alanine-rich peptides, Ac-Ala 21 - methyl amide (A21) and Ac-A 5 (AAARA) 3 A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the amber force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.
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Cites
Elucidating the folding problem of helical peptides using empirical parameters
Muñoz, V., & Serrano, L. (1994) · Nature Structural & Molecular Biology · doi:10.1038/nsb0694-399 · Cited by 721
Cited by
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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
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
Coarse master equations for peptide folding dynamics
Buchete, N.-V., & Hummer, G. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp0761665 · Cited by 477
K+/Na+ Selectivity in K Channels and Valinomycin: Over-coordination Versus Cavity-size constraints
Varma, S., Sabo, D., & Rempe, S. B. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.11.059 · Cited by 150
Peptide folding kinetics from replica exchange molecular dynamics
Buchete, N.-V., & Hummer, G. (2008) · Physical Review E · doi:10.1103/physreve.77.030902 · Cited by 121
Metadata
- Authors
- García, A. E., & Sanbonmatsu, K. Y.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2002-02-26
- Volume
- 99
- Issue
- 5
- Pages
- 2782-2787
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2031273789
- Cited by
- 442
- References
- 1
- FWCI
- 10.80
- Type
- journal article
- Language
- en
- Open access
- green
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- García, A. E., & Sanbonmatsu, K. Y. (2002). α-Helical stabilization by side chain shielding of backbone hydrogen bonds. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.042496899
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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