Paper Citing NAMD - Abstract
Karandur, Deepti; Wong, Ka-Yiu; Pettitt, B. Montgomery
Solubility and Aggregation of Gly5 in Water
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9565-9572, AUG 14 2014
Experimentally, the solubility of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1-5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concentrations in explicit solvent to consider the mechanism of aggregation. The solubility limit of Gly(5) for the force field used was calculated and compared with experimental values. We find that intermolecular interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide associations, liquid liquid phase separation, are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters.
