Classical molecular dynamics (MD) simulations were used to study the relative stability among several known human G- quadruplex structures, find the equilibrium structure of Carboxyl Terminus (CT) of Bacteriorhodopsin (bR) and observe the interactions of CT in equilibrium with bR.

In the case of quadruplex DNA, recent experimental results indicate that the (TTAGGG) ₄ quadruplex undergoes isomerization to an intermediate state upon melting in potassium solution. To help establish the likely structural state of this intermediate, we have undertook MD simulations to determine the relative stability of several candidate isomers which differ in the secondary folding structure. Total energy, solvent accessible surface area, heat capacity and root-mean-square-displacements of the nucleic acid portion of the simulation ensemble indicate that the proposed initial state suggested in previously published experimental results is correct and that an intermediate state might exist.

Bacteriorhodopsin (bR) exists as a 7-helix trans-membrane protein with a 23-residue sequence C-terminus (CT) exposed to the aqueous intracellular environment. The presence of the CT has been shown to contribute to the overall stability and function of bR; however, to date XRD crystal data indicate that the CT lacks a well-defined equilibrium structure. All-atom MD simulations of the CT in aqueous ionic solution have been undertaken to help establish the likely structure of the CT as a function of solvent salt concentration. High temperature simulated annealing was used to mitigate initial state effects as well as to promote sampling of a broader space. All MD simulations included explicit water, a host lipid membrane matrix and solvent ions. The solvent accessibility and root- mean- square -deviations of the CT in equilibrium are presented, which show that the overall stability of the transmembrane portion of bR is enhanced by interactions with the CT. The investigations include a comparison of CT-bR interactions with the CT bound and unbound to bR.