Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing
© 2022 Wiley Periodicals LLC.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 43(2022), 18 vom: 05. Juli, Seite 1229-1236 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2022
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, Non-U.S. Gov't conformational sampling peptoids replica exchange Amides Peptides Peptoids |
| Zusammenfassung: | © 2022 Wiley Periodicals LLC. Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. The results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model |
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| Beschreibung: | Date Completed 30.05.2022 Date Revised 07.09.2022 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.26887 |