Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study.

Abstract

A nonequilibrium molecular dynamics (MD) study of the temperature-induced energy flow in a RNA-ligand complex is presented, which employs extensive all-atom explicit solvent MD simulations of the aptamer domain of the guanine-sensing riboswitch (GRA). Since the few existing MD investigations of biomolecular energy flow have used quite different computational approaches, the applicability and performance of the various methods are compared first. In particular, a nonequilibrium correlation function C(ij)(tau) is introduced that describes the cumulative response of residue j at delay time tau to the energy source at residue i. Employing this analysis, the anisotropic energy flow and long-range correlations in GRA are studied, which can be monitored over distances up to approximately 4 nm. To test whether these long-range correlations are relevant for molecular function, the unbinding-induced conformational changes of GRA are calculated using the linear-response theory, assuming that the unbinding of the guanine ligand represents the first step responsible for the function of GRA. Interestingly, it is found that the same residues that are of functional importance are also prominently involved in the energy transfer. In particular, significant correlations between the guanine ligand and the distant "kissing" loops of GRA are found. This finding is in line with recent experiments which indicate that these long-range interactions may be important for the induced-fit binding of the ligand.