The design of enzymes with tailored physical and catalytic properties is one of the fundamental thrusts of modern protein science, with the potential for profound technological and medical impact. Laboratory directed evolutionary approaches along with rational design principles have now been successfully applied to enhance protein properties and function. What remains is the important next step of """"""""rolling up our sleeves"""""""" and attacking important problems with an eye toward details, which are likely to be enzyme specific. This proposal extends our enzyme directed evolution program in important enabling directions in the area of engineered proteases. Our most recent work with the OmpT protease represents by far the most general manipulation of P1 and P1' substrate specificity of a protease while retaining high overall levels of catalytic activity. Beyond their use in the detergent industry, engineered proteases have tremendous practical potential as either proteomic tools or catalytic therapeutics. In particular, proteases specific for substrates containing modifications such as phosphorylation or O- GlcNAc would represent useful new tools for identifying modified proteins in high throughput proteomics assays.
Under Specific Aim 1, we will engineer OmpT variants specific for cleaving only substrates containing phosphorylated or O-GlcNAc serine. We will also investigate whether we can engineer """"""""restriction-like"""""""" proteases that can very selectively recognize an extended sequence comprising residues well beyond P1 and P1'.
Under Specific Aim 2, we will extend precise OmpT protease recognition to include P2, P3, P2', and P3'. In particular, we will target Gln-His-Ala-Arg-Ala-Ser (QHA$RAS), residues 68-73 of the C-terminus of the C3a anaphylatoxin peptide. C- terminal cleavage of C3a interferes with its biological effects in complement activation. We recognize that creating highly specific subsites in OmpT by mutagenesis and sorting is an exciting yet risky goal and that an engineered OmpT is an unlikely therapeutic clinical candidate because of its bacterial origin. Therefore, for Specific Aim 3, we will engineer precise C3a cleavage activity into the secreted human trypsin-like protease granzyme A in hopes of producing a clinical candidate. As a practical deliverable, following the functional assays of our best variants (Section D6) we will, for the first time, be able to validate the proteolytic approach to complement inhibition, applicable to a wide variety of inflammatory disease therapies.

Public Health Relevance

In general terms, current therapies for almost every disease involve molecules that interact with specific disease targets in a one-for-one ratio, i.e. one drug molecule is required to interact with each disease molecule. We are proposing a route to the engineering of molecules, called proteases, that will catalytically destroy many disease target molecules (i.e. a new paradigm in which one drug molecule destroys hundreds, thousands or even more disease molecules)! In particular, we will be attempting to generate a potent catalyst capable of zeroing in on a target (called the C3a anaphylatoxin) that would allow effective treatment of a wide range of inflammatory diseases including asthma and sepsis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Barski, Oleg
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Texas Austin
Schools of Arts and Sciences
United States
Zip Code
Yi, Li; Gebhard, Mark C; Li, Qing et al. (2013) Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci U S A 110:7229-34
Yoo, Tae Hyeon; Pogson, Mark; Iverson, Brent L et al. (2012) Directed evolution of highly selective proteases by using a novel FACS-based screen that capitalizes on the p53 regulator MDM2. Chembiochem 13:649-53
Cantor, Jason R; Yoo, Tae Hyeon; Dixit, Aakanksha et al. (2011) Therapeutic enzyme deimmunization by combinatorial T-cell epitope removal using neutral drift. Proc Natl Acad Sci U S A 108:1272-7
Chu, Yongjun; Hoffman, David W; Iverson, Brent L (2009) A pseudocatenane structure formed between DNA and A cyclic bisintercalator. J Am Chem Soc 131:3499-508
Pogson, Mark; Georgiou, George; Iverson, Brent L (2009) Engineering next generation proteases. Curr Opin Biotechnol 20:390-7
Varadarajan, Navin; Pogson, Mark; Georgiou, George et al. (2009) Proteases that can distinguish among different post-translational forms of tyrosine engineered using multicolor flow cytometry. J Am Chem Soc 131:18186-90
Varadarajan, Navin; Georgiou, George; Iverson, Brent L (2008) An engineered protease that cleaves specifically after sulfated tyrosine. Angew Chem Int Ed Engl 47:7861-3
Varadarajan, Navin; Rodriguez, Sarah; Hwang, Bum-Yeol et al. (2008) Highly active and selective endopeptidases with programmed substrate specificities. Nat Chem Biol 4:290-4
Li, Hai-Xin; Hwang, Bum-Yeol; Laxmikanthan, Gurunathan et al. (2008) Substrate specificity of human kallikreins 1 and 6 determined by phage display. Protein Sci 17:664-72
Varadarajan, Navin; Gam, Jongsik; Olsen, Mark J et al. (2005) Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc Natl Acad Sci U S A 102:6855-60

Showing the most recent 10 out of 11 publications