| This dissertation discusses two main projects from my thesis work. The first project focuses on the development of a small molecule docking program, SKATE, for drug discovery. The second project focuses on the critical analysis of the thermal stability of a mini-protein, FSD-1.;SKATE is a novel approach to small molecule docking. It removes any inter-dependence between sampling and scoring to improve docking accuracy. SKATE systematically and exhaustively samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. A total of 266 ligands were re-docked to their respective receptors to assess SKATE's performance. The results show that SKATE was able to sample poses within 2 A RMSD of the native structure for 97% of the cases. The best performing scoring function was able to rank a pose that is within 2 A RMSD of the native structure as the top-scoring pose for 83% of the cases. Compared to published data, SKATE has a higher self-docking accuracy rate than or is at least comparable to GOLD, Glide, MolDock and Surflex. The cross-docking accuracy of SKATE was assessed by docking 83 ligands to their respective receptors. The cross-docking results were comparable to those in published methods.;Mini-proteins that contain fewer than 50 amino acids often serve as model systems for studying protein folding because their small size makes long time-scale simulations possible. However, not all mini-proteins are created equal. The stability and structure of FSD-1, a 28-residue mini-protein that adopts the betabetaalpha zinc-finger motif independent of zinc binding, was investigated using circular dichroism (CD), differential scanning calorimetry (DSC), and replica-exchange molecular dynamics (REMD). FSD-1's broad melting transition, similar to that of a helix-to-coil transition, was observed in CD, DSC, and REMD experiments. The N-terminal beta-hairpin was found to be flexible. FSD-1's apparent melting temperature of 41°C may be a reflection of the melting of its alpha-helical segment instead of the entire protein. Thus, FSD-1's status as a model system for studying protein folding should be reconsidered despite its attractiveness for being small in size and it was designed to contain essential helix, sheet, and turn secondary structures.;An electronic copy of this dissertation is available online at www.ccb.wustl.edu/ ∼jafeng... |
