Published March 23, 2000 | Supplemental Material
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Solvent Effects on the Secondary Structures of Proteins

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Abstract

We examined the effect of solvation on the conformational preferences (e.g., α-helix versus β-sheet) of tripeptides using ab initio quantum mechanics (Hartree−Fock 6-31G**) with solvation in the Poisson−Boltzmann continuum solvent approximation. We find that aqueous solvent preferentially stabilizes the α-helix conformation over β-sheet conformations by 3.5 kcal/mol for Ala, 2.4 kcal/mol for Gly, and 2.0 kcal/mol for Pro. We determined the torsional potential surfaces of the tripeptides, Gly-Ala-Gly, Gly-Gly-Gly, and Gly-Pro-Gly using both aqueous solvent and nonpolar solvent conditions. These results were used to determine force-field torsional parameters for the protein main chains.

Additional Information

© 2000 American Chemical Society. Received: April 1, 1999; In Final Form: August 27, 1999. Publication Date (Web): November 6, 1999. This research was initiated under a grant from the Biological Chemical Technologies Research (BCTR) program of the Department of Energy and completed with funding from NSF (ASC 92-17368 and CHE 95-22179). The facilities of the MSC are also supported by grants from, BP Chemical, Chevron Corp., NASA, Beckman Institute, Army Research Office, Seiko-Epson, Exxon, Saudi Aramco, Owens-Corning, Asahi Chemical, ONR, and Avery-Dennison Corp. Some of these calculations were carried out at the NSF Supercomputer Centers in San Diego and Illinois, and on the JPL Cray.

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