dc.contributor.author | Ioannou, F. | en |
dc.contributor.author | Archontis, Georgios Z. | en |
dc.contributor.author | Leontidis, Epameinondas | en |
dc.creator | Ioannou, F. | en |
dc.creator | Archontis, Georgios Z. | en |
dc.creator | Leontidis, Epameinondas | en |
dc.date.accessioned | 2019-11-21T06:19:28Z | |
dc.date.available | 2019-11-21T06:19:28Z | |
dc.date.issued | 2011 | |
dc.identifier.issn | 1520-6106 | |
dc.identifier.uri | http://gnosis.library.ucy.ac.cy/handle/7/55575 | |
dc.description.abstract | We 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.source | Journal of Physical Chemistry B | en |
dc.source.uri | https://www.scopus.com/inward/record.uri?eid=2-s2.0-80855128934&doi=10.1021%2fjp207068m&partnerID=40&md5=84de743f5aed41601b9cee2b2c4aa7c1 | |
dc.subject | Peptides | en |
dc.subject | Molecular dynamics | en |
dc.subject | Hydrogen bonds | en |
dc.subject | Sodium chloride | en |
dc.subject | Pure water | en |
dc.subject | Sodium salt | en |
dc.subject | Alanine dipeptides | en |
dc.subject | Amino acids | en |
dc.subject | Carbonyl groups | en |
dc.subject | Configuration space | en |
dc.subject | Conformational preferences | en |
dc.subject | Dipeptide | en |
dc.subject | Helicities | en |
dc.subject | Hydrogen bonding interactions | en |
dc.subject | Intermolecular interaction energies | en |
dc.subject | Iodide anions | en |
dc.subject | Peptide sequences | en |
dc.subject | Replica exchange method | en |
dc.subject | Salt concentration | en |
dc.subject | Side-chains | en |
dc.subject | Specific interaction | en |
dc.subject | Stabilizing effects | en |
dc.subject | Tetrapeptide | en |
dc.title | Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamics | en |
dc.type | info:eu-repo/semantics/article | |
dc.identifier.doi | 10.1021/jp207068m | |
dc.description.volume | 115 | |
dc.description.issue | 45 | |
dc.description.startingpage | 13389 | |
dc.description.endingpage | 13400 | |
dc.author.faculty | 002 Σχολή Θετικών και Εφαρμοσμένων Επιστημών / Faculty of Pure and Applied Sciences | |
dc.author.department | Τμήμα Χημείας / Department of Chemistry | |
dc.type.uhtype | Article | en |
dc.description.notes | <p>Cited By :16</p> | en |
dc.source.abbreviation | J Phys Chem B | en |
dc.contributor.orcid | Leontidis, Epameinondas [0000-0003-4427-0398] | |
dc.contributor.orcid | Archontis, Georgios Z. [0000-0002-7750-8641] | |
dc.gnosis.orcid | 0000-0003-4427-0398 | |
dc.gnosis.orcid | 0000-0002-7750-8641 | |