Application of mixed coarse-grained elastic network model to protein-ligand interactions

Abstract

Ligand binding to an active or allosteric regulatory site of enzyme may lead conformational changes or changes in protein dynamics. The aim of this thesis is to explore the effect of ligand binding on vibrational dynamics of proteins, specifically the collective modes that are biologically relevant. For this aim, the mixed coarse-grained version of anisotropic network model, named MCG_ANM, was applied to more than 30 crystal structures including different monomeric and multimeric enzymes. In MCG_ANM, the ligands are considered at atomic (high) resolution, whereas the protein is at low resolution with only alpha-carbons considered. Solvents, catalytic ligands, catalytic loop conformational changes, allosteric ligands and coenzymes were considered in terms of their effects on vibrational frequencies of the enzymes. The frequencies of slow modes mostly shifted to higher values due to binding. Swapping of modes and changes in mode character were also observed. Solvents bound to specific regions, mainly catalytic and allosteric sites, were more effective in shifting frequencies. For the enzymes with catalytic loops that close over the active site, the frequency shifts due to the conformational change from open to closed loop were found to dominate the ligand binding effect. Among 17 allosteric protein structures considered, shifts in vibrational frequencies were higher for of three (out of four) monomers compared to dimers and tetramers based on cutoff distance of 7 Å. Moreover, mode swapping and character change was observed dominantly for these monomers. Specifically, allosteric ligand binding to monomeric, dimeric and tetrameric enzymes lead to 3.2%, 0.8% and 1.6% frequency changes, respectively, averaged over first five modes. The binding of allosteric ligands to monomers and dimers also lead to significant changes in the orientational correlations of catalytic residues. Finally, coenzymes bound to tetramers lead to higher frequency shifts compared to allosteric ligands and cofactors.