We study the effect of remote residues in enzyme catalysis using computational predictions and experimental verification by site-directed mutagenesis, kinetics assays, and ligand binding studies. The big news is that the participation of remote residues in enzyme catalysis is predictable with a simple calculation. Here are some examples:
Figure 1: Variants made of the remote residues predicted by THEMATICS in the enzyme Nitrile Hydratase show significant decrease in catalytic efficiency. [See Heather R. Brodkin, W.R.P. Novak, et al. Biochemistry 50(22), 4923-4935 (2011).]
Figure 2: THEMATICS predicts a single-layered active site for Ketosteroid isomerase and a multilayered active site for PGI. Site-directed mutagenesis and kinetics assays confirm these predictions. [See Srinivas Somarowthu, Heather R. Brodkin, J.A. D’Aquino, Dagmar Ringe, Mary Jo Ondrechen, and Penny J. Beuning, Biochemistry 50(43), 9283-9295 (2011).]
This work is funded by the National Science Foundation via grant # MCB-1158176.