This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project has immediate two goals: (i) to implement a simple algorithm for identifying conserved residues from a set of protein structure alignments and, (ii) to identify ways this approach can be used to better understand the coupling between protein structure and function. Our quintessential goal is to understand how proteins deliver biological function, and to be able to modify or engineer new functionality in order to benefit humankind. Briefly, our algorithm overlays a three-dimensional voxel grid on top of a set of proteins that have been structurally aligned by an alignment algorithm such as CE or Dali. The voxels that have a residue from each protein are recorded, and their contents are the conserved residues for this alignment. The voxel grid is then systematically moved along each {x,y,z} axis independently to possibly identify additional conserved residues. Once we have a list of structurally conserved residues, we can focus on: Identification of additional active site/superfamily residues: We have investigated this in the cAMP and the enolase enzyme family/superfamily. Working with the cAMP proteins, we were able to recover a conserved hydrophobic residue on the distant side of the active site pocket. This residue is obscured in the sequence alignment, and was previously only identified by visual inspection (Berman, PNAS 2005). For the enolase family/superfamiy, we were able to recover the existing family/superfamily residues. Identification of residues that may affect enzyme catalysis: We want to investigate the effect of distal residues on enzyme catalysis. For this analysis we used the DHFR superfamily and a diverse set of TIM proteins. Working with the DHFR superfamily, we were able to identify the movable loop region as well as additional residues implicated in the stabilization of the co-enzyme NADPH (Agarwal, PNAS 2002). For the TIM proteins, we identified 2/3 of the residues previously identified from point mutations as having significant effects on catalytic rates (Silverman, PNAS 2001).
Showing the most recent 10 out of 508 publications
