Paper Citing NAMD - Abstract
Asciutto, Eliana K.; Gaborek, Timothy; Madura, Jeffry D.
Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 13 Art. No. 1440004, MAY 2014
Equilibrium peptide conformations in solution, especially in the presence of salts, has been of interest for several decades. The fundamental interactions that determine the dominant peptide conformations in solution have been experimentally and computationally probed; however, a unified understanding has not yet emerged. In a previous study, we performed metadynamics simulations on the heptapeptide AEAAAEA in Sodium Chloride (NaCl) and Potassium Chloride (KCl) solutions at concentrations ranging from 0.5-2.0 M. Using a three-dimensional collective variable coordinate system, we computed the free energy landscapes in each saline environment as well as in pure water. We found that the presence of Na+ and K+ ions induces some changes in the stability of the conformers that define the state space, but does not alter the overall energetics between conformers and does not favor helical conformations. We investigate here, how the presence of salts (NaCl and KCl) affects the glutamic-glutamic interaction and its consequences on the stability of each equilibrium conformation. We perform this study through fixed backbone simulations for the most populated conformations identified in our previous work: the alpha-helix, 3(10)-helix, pi-helix, the extended polyproline II (PPII) and 2.5(1)-helix conformations. It was found that for each conformation, there exists stable substates determined by the glutamic acid side-chains distance and orientation, and that Na+ and K+ cations (de) stabilize preferentially each conformation. It was also found that intramolecular single water mediated hydrogen bonds play a crucial role in the observed (de) stabilization of each equilibrium conformation.
