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

Abstract

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.

Figure 1

Correlation between calculated and average normalized experimental β-sheet propensities (J.-Y. Luo, R. Langen, B. D. Olafson, J. H. Richards, and S.L.M., unpublished work). All amino acids except Gly and Pro are shown. Asn, represented by the open circle, is discussed in the text. (A) The negative of the entropy calculated by using Eq. 1. (B) Helmholtz free energy calculated by using Eq. 2, Eq. 3, and 1/β = 9 kcal⋅mol⁻¹. R, correlation coefficient.