Structural Investigation of Binding Events in Proteins
Clark, Jordan
2018
Abstract
Understanding the biophysical properties that describe protein binding events has allowed for the advancement of drug discovery through structure-based drug design and in silico methodology. The accuracy of these in silico methods depends entirely on the parameters that we determine for them. Many of these parameters are derived from the structural information we have obtained as a community and therein resides the importance of integrity of the quality of this structural data. First, the curation and contents of the Binding MOAD database are extensively described. This database serves as a repository of 25,759 high-quality, ligand-bound X-ray protein crystal structures complemented by 9138 hand-curated binding affinity data for as many of those ligands as appropriate. The newly implemented extended binding site feature is presented, establishing more robust definitions of ligand binding sites than those provided by other databases. Finally, the contents of Binding MOAD are compared to similar databases, establishing the value of our dataset and which purposes it best serves. Second, a robust dataset of 305 unique protein sequences with at least two ligand-bound and two ligand-free structures for each unique protein is cultivated from Binding MOAD and the PDB. Protein flexibility is assessed using C-alpha RMSD for backbone motion and chi-1 angles to quantify side-chain motions. We establish that there is no statistically significant difference between the available conformational space for the backbones or the side chains of unbound proteins when compared to their bound structures. Examining the change in occupied conformational space upon ligand binding reveals a statistically significant increase in backbone conformational space of miniscule magnitude, but a significant increase of side-chain conformational space. To quantify the conformational space available to the side chains, flexibility profiles are established for each amino acid. We found no correlation between backbone and side-chain flexibility. Parallels are then made to common practices in flexible docking techniques. Six binding-site prediction algorithms are then benchmarked on a derivation of the previously established dataset of 305 proteins. We assessed the performance of ligand-bound vs ligand-free structures with these methods and concluded that five of the six methods showed no preference for either structure type. The remaining method, Fpocket, showed decreased performance for ligand-free structures. There was a staggering amount of inconsistency in performance with the methods; different structures of the exact same protein could achieve wildly different rates of success with the same method. The performance of individual structures for all six methods indicated that success and failure rates were seemingly random. Finally, we establish no correlation between the performance of the same structures with different methods, or the performance of the structures with structure resolution, Cruickshank DPI, or number of unresolved residues in their binding sites. Last, we examine the chemical and physical properties of protein-protein interactions (PPIs) with regard to their geometric location in the interface. First, we found that the relative elevation changes of the protein interface landscapes demonstrate that these interfaces are not as flat as previously described. Second, the hollows of druggable PPI interfaces are more sharply shaped and nonpolar in nature, and the protrusions of these druggable PPI interfaces are very polar in character. Last, no correlations exist between the binding affinity describing the subunits of a PPI and other physical and chemical parameters that we measured.Subjects
Protein flexibility Protein structure database Protein-ligand binding Protein-protein interaction (PPI)
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