Conformational changes of trialanine in sodium halide solutions: An in silico study

Specific Interactions of Sodium Salts with Alanine Dipeptide and Tetrapeptide in Water: Insights from Molecular Dynamics

“…This behavior of iodide has been observed in other simulations of oligopeptide electrolyte solutions; − it is partly due to the larger radius of the iodide first hydration shell, which facilitates the loss of hydration water around iodide, relative to chloride. Overall, the dipeptide results show that ions affect to a small extent the intrinsic conformation tendencies of the backbone, and that larger anions interact more strongly with the hydrophobic regions of the chain, in accordance with previous investigations of similar systems. − …”

“…In the case of the tetrapeptide, the enhanced interactions are accompanied by an increase in the α-helix population. An intermediate Ala oligopeptide with charged terminal ends (NH 3 + -Ala 3 -COO – ) was studied in aqueous solutions of sodium halide salts by Fedorov et al, , using the OPLSAA-2001 force field in Gromacs and a TIP5P-EW water model; the observed conformations depended on salt concentration and type, with high electrolyte concentrations usually favoring extended conformations. Thus, the above-mentioned ion–peptide interactions alone cannot determine the conformational preferences of these model peptides.…”

“…Two other recent papers examined the interactions between ions and n-methyl acetamide (NMA), the simplest model compound of the peptide bond. , Finally, question (c) is also fundamental since many researchers currently believe that ionic specificity at interfaces stems from the competition between water and ions for interfacial sites or from the competition of ions and the surface for water of hydration. ,− Does a similar balance exist in salt solutions of oligopeptides, which also compete with ions for water of hydration? This is an issue, which, in our opinion, has not been closely examined in the recent simulation works, which focus mostly on ion–peptide interactions. − …”

“…Question (a) examines the impact of solvent on short- and long-range interactions, which are present in oligopeptide chains (and proteins), and ultimately determine the thermodynamically important conformations. Numerous theoretical studies have focused on short oligoalanine peptides, which serve as models of peptide conformation dynamics and helix formation. ,,,− A detailed mapping of interactions is sought here, examining not only radial distribution functions (rdf's) at the pair-interaction level, − but also the ensemble of possible conformations, and the nature of those that are enhanced or “destroyed” by the presence of electrolytes. In this respect, our analysis is related to the recent work of Dzubiella on alanine-based peptides , or that of Fedorov at el., , but we carry out a detailed analysis of all intermolecular interactions to identify potential driving forces for the observed conformational changes in the presence of salts.…”

“…Numerous theoretical studies have focused on short oligoalanine peptides, which serve as models of peptide conformation dynamics and helix formation. ,,,− A detailed mapping of interactions is sought here, examining not only radial distribution functions (rdf's) at the pair-interaction level, − but also the ensemble of possible conformations, and the nature of those that are enhanced or “destroyed” by the presence of electrolytes. In this respect, our analysis is related to the recent work of Dzubiella on alanine-based peptides , or that of Fedorov at el., , but we carry out a detailed analysis of all intermolecular interactions to identify potential driving forces for the observed conformational changes in the presence of salts. The discussion about specific ionic interactions with various groups on peptides and protein surfaces has been going on for a long time. − ,,,− It is not clear, however, how these binding interactions may affect the overall conformation of an oligopeptide.…”