Name
Abstract | ||
|---|---|---|
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 less than or equal to R(2)). For noncovalently attached but interacting peptide subunits, such as [For-NH(2)](2) or [For-L-Ala-NH(2)](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 P-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 inol. The latter observation seems to hold for peptides regardless of their length (1 less than or equal to n less than or equal to 8) or the level of theory applied. (C) 2004 Wiley Periodicals, Inc. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1002/jcc.20028 | JOURNAL OF COMPUTATIONAL CHEMISTRY |
Keywords | Field | DocType |
peptides,protein fragments,ab initio computation,thermodynamic functions,structure and stability,intermolecular complexes,thermoneutral isodesmic reaction | Isodesmic reaction,Antiparallel (biochemistry),Crystallography,Conformational isomerism,Molecule,Computational chemistry,Peptide,Chemistry,Tripeptide,Hydrogen bond,Gibbs free energy | Journal |
Volume | Issue | ISSN |
25 | 8 | 0192-8651 |
Citations | PageRank | References |
1 | 0.40 | 3 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| András Perczel | 1 | 39 | 16.63 |
| Péter Hudáky | 2 | 9 | 2.13 |
| Anna K Füzéry | 3 | 3 | 0.89 |
| Imre G. Csizmadia | 4 | 24 | 10.22 |