期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 115, 期 44, 页码 12984-12992出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp2053508
关键词
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资金
- National Center of Competence in Research (NCCR) in Structural Biology
- Swiss National Science Foundation [200020-121913]
- European Research Council (ERC) [228076]
- Sino-Swiss Science and Technology Cooperation [IZLCZ2-123884]
The ability to design well-folding beta-peptides with a specific biological activity requires detailed insight into the relationship between the beta-amino acid sequence and the dominant three-dimensional structure of such a peptide. To this end, secondary structure preferences of two sets of 16 beta-peptides were investigated by means of one-step perturbation using molecular dynamics (MD) simulations. For each set of peptides, two reference-state simulations and one perturbed-state simulation were carried out to predict the secondary structure preferences for the other 15 peptides. The results show that the substitution of a methyl group in the third or fourth residue stabilizes the left-handed 3(14)-helix over the right-handed 2.7(10/12)-helix for the set of hexapeptides A; for the set of heptapeptides B, having methyl substitutions at both beta- and alpha-carbon positions of the fourth or fifth residue stabilizes the left-handed 3(14)-helix over the right-handed 2.5(12)-helix. Not only the side-chain substitution pattern but also the side-chain composition affects the relative stability of different secondary structures. The approach described here may be of use in peptide design with an eye to obtaining peptides with particular folds and biological activities.
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