title: Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study.
abstract: 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.
authors.affiliation: Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States.
authors.forename: Derya
authors.initials: D
authors.lastname: Meral
authors.affiliation: Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States.
authors.forename: Siobhan
authors.initials: S
authors.lastname: Toal
authors.affiliation: Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schweitzer-Stenner
authors.affiliation: Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States.|Faculty of Mathematics and Physics, University of Ljubljana , 1000 Ljubljana, Slovenia.
authors.forename: Brigita
authors.initials: B
authors.lastname: Urbanc
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D066298:In Vitro Techniques; D056004:Molecular Dynamics Simulation; D014867:Water / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D014867:Water