Stability issues of covalently and noncovalently bonded peptide subunits
Copyright 2004 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 25(2004), 8 vom: 27. Juni, Seite 1084-100 |
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| Weitere Verfasser: | , , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2004
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Peptides Alanine OF5P57N2ZX |
| Zusammenfassung: | Copyright 2004 Wiley Periodicals, Inc. The present study focuses on important questions associated with modeling of peptide and protein stability. Computing at different levels of theory (RHF, B3LYP) for a representative ensemble of conformers of di- and tripeptides of alanine, we found that the Gibbs Free Energy values correlate significantly with the total electronic energy of the molecules (0.922 < or = R2). For noncovalently attached but interacting peptide subunits, such as [For-NH2]2 or [For-L-Ala-NH2]2, we have found, as expected, that the basis set superimposition error (BSSE) is large in magnitude for small basis set but significantly smaller when larger basis sets [e.g., B3LYP/6-311++G(d,p)] are used. Stability of the two hydrogen bonds of antiparallel beta-pleated sheets were quantitatively determined as a function of the molecular structure, S10 and S14, computed as 4.0 +/- 0.5 and 8.1 +/- 1.1 kcal/mol, respectively. Finally, a suitable thermoneutral isodesmic reaction was introduced to scale both covalently and noncovalently attached peptide units onto a common stability scale. We found that a suitable isodesmic reaction can result in the total electronic energy as well as the Gibbs free energy of a molecule, from its "noninteracting" fragments, as accurate as a few tenths of a kcal per mol. The latter observation seems to hold for peptides regardless of their length (1 < or = n < or = 8) or the level of theory applied |
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| Beschreibung: | Date Completed 09.06.2004 Date Revised 21.11.2013 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |