Paper Citing NAMD - Abstract
Zanuy, David; Aleman, Carlos
Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammonium
BIOMACROMOLECULES, 8:663-671, FEB 2007
The supramolecular organization of self-assembled stoichiometric complexes formed by dodecyltrimethylammonium cations and ionized poly(gamma-glutamic) acid has been investigated in chloroform solution. Atomistic molecular dynamics simulations have been performed considering three different starting conformations for the polyelectrolyte chain, two sets of electrostatic parameters, and two methods for evaluating the electrostatic interactions. Results indicate that the polypeptide chain tends to adopt an alpha-like helix conformation similar to that obtained in aqueous solution for the un-ionized poly(gamma-glutamic) acid. On the other hand, both surfactant center dot center dot center dot amide and surfactant center dot center dot center dot carboxylate interactions were identified in the complex, this multiple pattern being previously observed in other surfactant center dot center dot center dot polypeptide complexes. Although the influence of the force-field in the results has been found to be negligible, the method used to evaluate the electrostatic interactions affects significantly the dynamics of the system. The more important differences between the results obtained using the spherical cutoff and Particle Mesh Ewald methods are discussed.
