The Influence of the Surrounding Media on the Structural Propensities of Amino Acid Residues in Proteins

Abstract

We have shown [1] that the intrinsic (Φ,Ψ) conformational propensities of amino acid residues in a coil state, and the corresponding structural propensities of the same type of residues to form the equivalent secondary structures, strongly depend on the residue type and their solvent accessibility. For residues in the interior and exterior of proteins, very strong correlations (>0.9) between these propensities were found. It suggests that non-covalent intraresidual interactions, in particular, electrostatic interactions, could make a crucial contribution to amino acid conformational propensities and predetermine propensities of the residue to be involved in the formation of secondary structures. To test this hypothesis, the pair wise electrostatic interactions (PEI) of the charges in a system that models the interface between a protein and aqueous solvent, containing mobile free ions, were calculated. The concept of non-local (NL) electrostatics for interfacial electrochemical systems [2,3] were used to investigate the contribution of the solvent orientational polarization, correlated by the network of hydrogen bonds, and the effect of the ionic strength on the PEI in proteins.