Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.

ABSTRACT: A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consi

SUBMITTER: Fadrna E 

PROVIDER: S-EPMC1304345 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature