Analyzing Molecular Interactions of Membrane Proteins by Computational Methods

Protein interactions with the environment are crucial for proper function, butinteraction mechanisms are not always understood. In G protein-coupled receptors (GPCRs), cholesterol modulates the function in some, but not all, GPCRs. Coarse grained molecular dynamics was used to determine a set of contact events for each residue and fit to a biexponential to determine the time scale of the long contacts observed in simulation. Several residues of interest were indicated in CCK1 R near Y140, which is known to render CCK1 R insensitive to cholesterol when mutated to alanine. A difference in the overall residence time between CCK1 R and its cholesterol insensitive homologue CCK2 R was also observed, indicating the ability to predict relative cholesterol binding for homologous proteins. Occasionally large errors and poor fits to the data were observed, so several improvements were made, including generalizing the model to include K exponential components. The sets of residence times in the improved method were analyzed using Bayesian nonparametrics, which allowed for error estimations and the classification of contact events to the individual components. Ten residues in three GPCRs bound to cholesterol in experimental structures had large tau. Slightly longer overall interaction time for the cholesterol sensitive CB1 R over its insensitive homologue CB2 R was also observed. The interactions between the cystic fibrosis transmembrane conductance regulator (CFTR) and GlyH-101, an open-channel blocker, were analyzed using molecular dynamics. The results showed the bromine in GlyH-101 was in constant contact with F337, which is just inside the extracellular gate. The simulations also showed an insertion of GlyH-101 between TM1 and TM6 deeper than the starting binding pose. Once inserted deeper between TMs 1 and 6, the number of persistent contacts also increased. This proposed binding pose may help in future investigations of CFTR and help determine an open-channel structure for the protein, which in turn may help in the development of treatments for various medical conditions. Overall, the use of molecular dynamics and state of the art analysis tools can be useful in the study of membrane proteins and eventuallyin the development of treatments for ailments stemming from their atypical function.