Exploring Peptide–Solvent Interactions: A Computational Study
2018
Nadia Elghobashi-Meinhardt
The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called &ldquo:reconciliation problem&rdquo:. Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide&ndash:solvent interface, but the peptide&ndash:solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water: some results indicate that XAO adopts a polyproline II (P II ) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations.
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