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Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study B

Meral, Derya, Toal, Siobhan, Schweitzer-Stenner, Reinhard, Urbanc, Brigita
The Journal of physical chemistry 2015 v.119 no.42 pp. 13237-13251
amino acids, hydrogen bonding, molecular dynamics, peptides, population growth, solvents, surface area
Amino acid residues of unfolded peptides in water sample only a few basins in the Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics of guest residues, X, in GXG peptides in water were recently reported to be dominated by pPII and β-strand-like (β) conformations, resulting in an enthalpy–entropy compensation at ∼300 K. Using molecular dynamics (MD) in explicit solvent, we here examine pPII and β conformational ensembles of 15 guest residues in GXG peptides, quantify local orientation of water around their side chains through novel water orientation plots, and study their hydration and hydrogen bonding properties. We show that pPII and β ensembles are characterized by distinct water orientations: pPII ensembles are associated with an increased population of water oriented in parallel to the side chain surface whereas β ensembles exhibit more heterogeneous water orientations. The backbone hydration is significantly higher in pPII than in β ensembles. Importantly, pPII to β hydration differences and the solvent accessible surface area of Cᵦ hydrogens both correlate with experimental pPII propensities. We propose that pPII conformations are stabilized by a local, hydrogen-bonded clathrate-like water structure and that residue-specific intrinsic pPII propensities reflect distinct abilities of side chains to template this water structure.