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Published August 3, 1999 | Published
Journal Article Open

Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone


The intrinsic secondary structure-forming propensities of the naturally occurring amino acids have been measured both experimentally in host-guest studies and statistically by examination of the protein structure databank. There has been significant progress in understanding the origins of intrinsic alpha -helical propensities, but a unifying theme for understanding intrinsic beta -sheet propensities has remained elusive. To this end, we modeled dipeptides by using a van der Waals energy function and derived Ramachandran plots for each of the amino acids. These data were used to determine the entropy and Helmholtz free energy of placing each amino acid in the beta -sheet region of phi ---psi space. We quantitatively establish that the dominant cause of intrinsic beta -sheet propensity is the avoidance of steric clashes between an amino acid side chain and its local backbone. Standard implementations of coulombic and solvation effects are seen to be less important.

Additional Information

© 1999 by The National Academy of Sciences Communicated by William A. Goddard, III, California Institute of Technology, Pasadena, CA, May 27, 1999 (received for review January 12, 1999) We thank D. B. Gordon, B. I. Dahiyat, and D. W. Vernooy for helpful discussions. This work was supported by the Rita Allen Foundation and the David and Lucile Packard Foundation. A.G.S. was partially supported by a grant from the National Institutes of Health. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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