Computational Studies of the NUDIX Hydrolase Superfamily

Abstract

The Protein Structure Initiative (PSI) was an effort by consortiums to solve as many unique protein structures as possible; the Protein Data Bank contains a number of enzymes whose structures have been solved, but for which no enzymatic activity has been determined. The Enzyme Function Initiative (EFI) is an effort to determine as many unique enzyme functions as possible. There are a number of putative NUDIX Hydrolase superfamily members for which structures have been solved, but for which no enzymatic activity has been determined. We have catalogued the structurally‐determined enzymes within the NUDIX Hydrolase superfamily using the PDB, BLAST, Dali, and SCOP. We are now in the process of characterizing these enzymes in the biochemistry teaching laboratory.Computational programs, such as ProMOL and UCSF Chimera, aid in annotating uncharacterized enzymes. ProMOL works by aligning the relative spatial arrangement of the catalytic residues of a reference enzyme with query searches. Chimera is a molecular visualization program that provides various tools for the structural analysis of proteins, including comparative modeling and conformational analysis. We are using these programs to design catalytic motifs for the NUDIX hydrolase superfamily and subfamilies within, which then can be used to uncover family members whose structures have been solved. Likewise, we have used the docking program PyRx, which utilizes AutoDock Vina, to predict substrate specificity, and have discovered that due to its “static” nature, it does not satisfactorily predict substrate specificity. Thus, next we will use a “dynamic” docking program to reevaluate substrate specificity prediction. Through this process, we have discovered the strengths and limitations of these programs.Bioinformatics tools, including databases and computational programs, are good starting points for determining protein function; however, the only way to definitively determine protein function is through experimentally determining activity. Our ultimate goal is to discover and characterize new enzymes from human pathogens as potential novel antibiotic targets.Support or Funding InformationNSF IUSE grant (PAC, JLM, and SOH). RIT College of Science FEAD grant (SOH and JLM).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.