Thermodynamic β -sheet propensities measured using a zinc-finger host peptide

Abstract

The three-dimensional structures of proteins reveal that the distribution of amino acids within the major classes of secondary structure is not random but that each amino acid has its own preferred secondary structural arrangements. Propensity scales for residues in alpha-helices have been generated through the use of various host-guest systems. Here we measure the thermodynamic beta-sheet propensities of each of the twenty commonly occurring amino acids. A previously studied zinc-finger peptide was used as the host system in which amino acids were substituted into a guest site, a solvent-exposed position in an antiparallel beta-sheet. As these peptides are unfolded in the absence of bound metal but are folded in their presence, it is assumed that the thermodynamics of metal binding fully reflect peptide-folding energy. A competitive cobalt(II)-binding assay was used to determine these energies with high precision. The relative free energies correlate well with previously derived potential values based on statistical analysis of protein structures. We are therefore able to present a thermodynamic beta-sheet propensity scale for all the commonly occurring amino acids in aqueous solution.