The Paetzel lab investigates the structure and mechanism of proteases and peptidases, a class of hydrolytic enzymes that catalyze the cleavage of specific peptide bonds within proteins. These enzymes play essential roles in signal transduction, protein secretion, membrane homeostasis, protein quality control, viral protein processing and many other essential physiological functions. We design inhibitors to these enzymes that can serve as a starting point for drug development. Specific examples of enzymes currently being investigated are listed below. We are also investigating the structure and function of the molecular machinery involved in protein targeting and translocation of secretory proteins and the assembly of proteins within membranes. In addition, we discover, design, and develop novel enzymes for biotechnology systems.
The gene products of many RNA viruses are synthesized as polyproteins that contain structural proteins (sp) such as the proteins used to construct the virion capsid and non-structural proteins (nsp) that include enzymes such the protease that is used to process the polyprotein into individual proteins at the correct time and place. These viral proteases are critical for virion assemble and are often targeted for drug design. A famous example is HIV protease inhibitors. Viral proteases utilize many different catalytic mechanisms and oligomeric assemblies. They are also an interesting example of enzymes that can catalyze an intramolecular reaction as well as an intermolecular reaction. This flexible yet specific class of enzyme provides the opportunity to trap complexes of these enzymes in each of the catalytic steps of its reaction such as Michaelis complexes (substrate bound complexes), acyl-enzyme complexes (for the serine and cysteine proteases), and product complexes. The crystal structures and functional analysis of these enzymes will aid in the development of novel compounds that will lead to new therapies.
For papers on viral proteases studied in our lab, such as Birnavirus VP4 and SARS-CoV-2 Mpro, see our publication page sorted by project.Signal peptidase (SPase) is the membrane bound serine endoprotease responsible for cleaving off the N-terminal signal peptide extensions from secretory proteins. Crystallographic analysis of SPase has revealed a novel proteolytic mechanism that utilizes a serine nucleophile, lysine general base and an unusual oxyanion-hole made up of a serine side chain hydroxyl group and a main chain amide group. Structural analysis has also revealed a shallow hydrophobic binding pocket adjacent to the active-site which explained the observed substrate specificity (small, neutral residues at the -1 and -3 positions relative to the cleavage-site). We are currently investigating the structure and mechanism of SPases from a variety of bacterial species, archaea, mitochondria, and the endoplasmic reticulum.
For a review on Escherichia coli SPase see:
For a review on bacterial SPase see:
For a review on the endoplasmic reticulum SPase see:
For other papers on SPase see our publication page sorted by project.
Signal peptide peptidase A (SppA) functions to hydrolyze the remnant signal peptides left behind in the membrane from secretory protein processing by SPase. SppA is a homo-oligomeric membrane bound protein with either tetrameric or octomeric cyclic symmetry. It creates a bowl shaped structure with either four or eight active sites. Many of these enzymes are synthesized with a type II intramolecular chaperone that is self-processed during assembly. This is another example of an enzyme with a serine/lysine catalytic dyad mechanism, but with no sequence or structural homology to SPase.
For papers on SppA see our publication page sorted by project.