Exploring Peptide–Solvent Interactions: A Computational Study
Theoretical Molecular Biophysics, Department of Physical and Theoretical Chemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, 14169 Berlin, Germany
Received: 20 August 2018 / Revised: 6 September 2018 / Accepted: 10 September 2018 / Published: 14 September 2018
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The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called “reconciliation problem”. Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide–solvent interface, but the peptide–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
(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
) 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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MDPI and ACS Style
Elghobashi-Meinhardt, N. Exploring Peptide–Solvent Interactions: A Computational Study. Molecules 2018, 23, 2355.
Elghobashi-Meinhardt N. Exploring Peptide–Solvent Interactions: A Computational Study. Molecules. 2018; 23(9):2355.
Elghobashi-Meinhardt, Nadia. 2018. "Exploring Peptide–Solvent Interactions: A Computational Study." Molecules 23, no. 9: 2355.
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