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Molecules 2018, 23(9), 2355; https://doi.org/10.3390/molecules23092355

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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Abstract

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 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. View Full-Text
Keywords: peptides; aqueous solvent; XAO peptide; molecular dynamics (MD); quantum mechanics/molecular mechanics (QM/MM); polyproline II peptides; aqueous solvent; XAO peptide; molecular dynamics (MD); quantum mechanics/molecular mechanics (QM/MM); polyproline II
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Elghobashi-Meinhardt, N. Exploring Peptide–Solvent Interactions: A Computational Study. Molecules 2018, 23, 2355.

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