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dc.contributor.authorIoannou, F.en
dc.contributor.authorArchontis, Georgios Z.en
dc.contributor.authorLeontidis, Epameinondasen
dc.creatorIoannou, F.en
dc.creatorArchontis, Georgios Z.en
dc.creatorLeontidis, Epameinondasen
dc.description.abstractWe examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space is achieved by the replica exchange method. In agreement with other works, we observe preferential sodium interactions with the peptide carbonyl groups, which are enhanced in the NaI solutions due to the increased affinity of the less hydrophilic iodide anion for the peptide methyl side-chains and terminal blocking groups. These interactions have been associated with a decrease in the helicities of more complex peptides. In our simulations, both salts have a small effect on the dipeptide, but consistently stabilize the intramolecular hydrogen-bonding interactions and "α-helical" conformations of the tetrapeptide. This behavior, and an analysis of the intermolecular interaction energies show that ion-peptide interactions, or changes in the peptide hydration due to salts, are not sufficient determining factors of the peptide conformational preferences. Additional simulations suggest that the observed stabilizing effect is not due to the employed force-field, and that it is maintained in short peptides but is reversed in longer peptides. Thus, the peptide conformational preferences are determined by an interplay of energetic and entropic factors, arising from the peptide sequence and length and the composition of the solution. © 2011 American Chemical Society.en
dc.sourceJournal of Physical Chemistry Ben
dc.subjectMolecular dynamicsen
dc.subjectHydrogen bondsen
dc.subjectSodium chlorideen
dc.subjectPure wateren
dc.subjectSodium salten
dc.subjectAlanine dipeptidesen
dc.subjectAmino acidsen
dc.subjectCarbonyl groupsen
dc.subjectConfiguration spaceen
dc.subjectConformational preferencesen
dc.subjectHydrogen bonding interactionsen
dc.subjectIntermolecular interaction energiesen
dc.subjectIodide anionsen
dc.subjectPeptide sequencesen
dc.subjectReplica exchange methoden
dc.subjectSalt concentrationen
dc.subjectSpecific interactionen
dc.subjectStabilizing effectsen
dc.titleSpecific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamicsAAAen
dc.description.endingpage13400Σχολή Θετικών και Εφαρμοσμένων Επιστημών / Faculty of Pure and Applied SciencesΤμήμα Φυσικής / Department of Physics
dc.description.notes<p>Cited By :16</p>en
dc.source.abbreviationJ Phys Chem Ben
dc.contributor.orcidLeontidis, Epameinondas [0000-0003-4427-0398]
dc.contributor.orcidArchontis, Georgios Z. [0000-0002-7750-8641]

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