| 168 | Karl Schmitz, Ph.D. | <p>Assistant Professor <br></p> | (302) 831-6100 | | schmitzk@udel.edu | 309 Wolf Hall | | | <ul>
<li><strong>B.S.</strong> - Rensselaer Polytechnic Institute
</li><li><strong>Ph.D.</strong> - Perleman School of Medicine, University of Pennsylvania
</li><li><strong>Postdoc</strong> - Massachusetts Institute of Technology </li></ul> | | <p>All bacteria possess ATP-fueled machines that degrade folded proteins in the cytoplasm. These enzymes remodel the proteome in response to environmental cues, enforce protein quality control, and modulate specific cellular pathways. My lab studies the Clp proteases from <em>Mycobacterium tuberculosis</em>, a highly infectious human pathogen. These proteolytic complexes are essential for viability in mycobacteria, and have emerged as attractive antibacterial targets.</p>
<p>Clp proteases mechanically unfold and degrade protein substrates through the collaboration of an ATP-dependent unfoldase and a barrel-shaped peptidase. Our research aims to establish how their activity is regulated in the cell, how they select specific substrates from the complex cytoplasmic proteome, and how structural features relate to their proteolytic activity. We use a variety of experimental tools, including biophysical and biochemical assays to probe protease assembly and function, X-ray crystallography to reveal protein structure, and molecular microbiology approaches to interrogate proteolytic processes in the cell. We hope to exploit our understanding of these enzymes to identify novel antibacterial compounds that target Clp proteolysis in <em>M. tuberculosis</em> and other pathogenic bacteria.</p> | <p><strong>Clp protease assembly and disassembly</strong></p>
<p>The mycobacterial Clp proteases are large oligomeric complexes that comprise a hexameric unfoldase (ClpX or ClpC1) and a heteromeric barrel-shaped peptidase (ClpP1P2). Biochemical evidence suggests that protease assembly is dynamic, and that the active form exists in equilibrium with unassembled inactive species. We aim to characterize the assembly and disassembly pathways, the kinetics of activation and inactivation, and the mechanisms by which substrates stimulate activity.</p>
<p><strong>Substrate identification and selectivity</strong></p>
<p>Clp proteases selectively recognize protein substrates, which minimizes wasteful and deleterious off-target proteolysis. However, few <em>bona fide</em> substrates are known in mycobacteria, and the rules that govern substrate discrimination are not understood. Through targeted screening and capture-based methods, we aim to identify novel physiological substrates. We use cell-based and phage-based screening approaches to define the sequence-based rules by which these proteases select substrates. We also aim to crystallize protease components in complex with substrate polypeptides, to determine the specific interactions and motifs that guide substrate recognition. These studies will help us understand the role that Clp proteases play in mycobacterial biology, and will guide the development of novel <em>in vivo</em> reporter substrates.</p>
<p><strong>High-throughput screening and compound characterization</strong></p>
<p>A major motivation for studying Clp protease function is to improve our ability to develop compounds that disrupt their activity in <em>M. tuberculosis</em>. While we have a rich toolbox of reagents and assays useful for probing protease activity <em>in vitro</em>, few of these tools are well-suited to high-throughput screening applications. We are working to develop robust assay platforms with higher signal-to-noise, improved dynamic range, and the ability to multiplex reporters for unfolding, peptidase, and protease activities. We also collaborate with talented synthetic chemists to characterize and optimize compounds that target these essential mycobacterial enzymes.</p> | <p><strong><em>​Lab Members</em></strong></p><ul><li>Emmanuel Ogbonna (BISC PhD)</li><li>Christopher Presloid (BISC PhD)</li><li>Jialiu Jiang (CHEM PhD)</li><li>Monika Prorok (CHEM PhD)</li><li>Patrick Beardslee (CHEM PhD)</li><li>Priyanka Bheemreddy (undergrad)</li></ul><p><strong><em>Lab Alumni</em></strong></p><ul><li>Thomas Swayne (undergrad, 2017-2020)</li><li>Jennifer Vorn (undergrad, 2019-2020)</li><li>Christian Sullivan (undergrad, 2020)<br></li><li>Leah Ferguson (undergrad, 2019)<br></li><li>Gaury Dhamdhere (BISC MS, 2019-2020)</li><li>Jeffrey Hudson (undergrad, 2018-2020)</li><li>Darian Yang (undergrad, 2017-2018)</li></ul> | <p>
<strong>​Schmitz KR</strong>, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK.
<a href="https://pubmed.ncbi.nlm.nih.gov/32083462/">Acyldepsipeptide antibiotics and a bioactive fragment thereof differentially perturb mycobacterium tuberculosis ClpXP1P2 activity<em> in vitro</em></a><em>. </em>
<em>ACS Chem Biol</em>. 2020. </p><p>
Amor AJ, <strong>Schmitz KR</strong>, Sello JK, Baker TA, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/27003103">Highly dynamic interactions maintain kinetic stability of the ClpXP protease during the ATP-fueled mechanical cycle</a>.
<em>ACS Chem Biol.</em> 2016.
</p><p>Carney DW,
<strong>Schmitz KR</strong>, Scruse AC, Sauer RT, Sello JK.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/26147653">Examination of a structural model of peptidomimicry by cyclic acyldepsipeptide antibiotics in their interaction with the ClpP peptidase</a>.
<em>ChemBioChem</em>. 2015. 16(13):1875-1879. </p><p>Moravcevic K, Alvarado D,
<strong>Schmitz KR</strong>, Kenniston JA, Mendrola JM, Ferguson KM, Lemmon MA.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25620000">Comparison of
<em>Saccharomyces cerevisiae</em> F-BAR domain structures reveals a conserved inositol phosphate binding site</a>. 2015.
<em>Structure</em>. 2015. 23(2):352-63. </p><p>Stinson BM, Baytshtok V,
<strong>Schmitz KR</strong>, Baker TA, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25866879">Subunit asymmetry and roles of conformational switching in the hexameric AAA+ ring of ClpX</a>.
<em>Nat Struct Mol Biol</em>. 2015. 22(5):411-6. </p><p>
<strong>Schmitz KR</strong>, Carney DW, Sello JK, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25267638">Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery</a>.
<em>PNAS</em>. 2014. 111(43):E4587-95. </p><p>Carney DW, Compton CL,
<strong>Schmitz KR</strong>, Stevens JP, Sauer RT, Sello JK.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25212124">A Simple fragment of cyclic acyldepsipeptides is necessary and sufficient for ClpP activation and antibacterial activity</a>.
<em>ChemBioChem</em>. 2014. 15(15):2216-20 </p><p>Cordova JC, Olivares AO, Shin Y, Stinson BM, Calmat S,
<strong>Schmitz KR</strong>, Aubin-Tam ME, Baker TA, Lang MJ, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25083874">Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine</a>.
<em>Cell</em>. 2014. 158(3):647-58. </p><p>
<strong>Schmitz KR</strong>, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/24976069">Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase</a>.
<em>Mol Microbiol.</em> 2014. 93(4):617-28. </p><p>Carney DW,
<strong>Schmitz KR</strong>, Truong JV, Sauer RT, Sello JK.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/24422534">Restriction of the conformational dynamics of the cyclic acyldepsipeptide antibiotics improves their antibacterial activity</a>.
<em>J Am Chem Soc</em>. 2014. 136(5):1922-9. </p><p>Compton CL,
<strong>Schmitz KR</strong>, Sauer RT, Sello JK.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/24047344">Antibacterial activity of and resistance to small molecule inhibitors of the ClpP peptidase</a>.
<em>ACS Chem Biol.</em> 2013. 8(12):2669-77. </p><p>
<strong>Schmitz KR</strong>, Bagchi A, Roovers RC, van Bergen en Henegouwen PM, Ferguson KM.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/23791944">Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains</a>.
<em>Structure</em>. 2013. 21(7):1214-24. </p><p>Stinson BM, Nager AR, Glynn SE,
<strong>Schmitz KR</strong>, Baker TA, Sauer RT.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/23622246">Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine</a>.
<em>Cell</em>. 2013 153(3):628-39. </p><p>Moravcevic K, Mendrola JM,
<strong>Schmitz KR</strong>, Wang YH, Slochower D, Janmey PA, MA Lemmon.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21145462">Kinase associated-1 domains drive MARK/PAR1 kinases to membrane targets by binding acidic phospholipids</a>.
<em>Cell</em>. 2010 143(6):966-77. </p><p>
<strong>Schmitz KR</strong>, Ferguson KM.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18992239">Interaction of antibodies with ErbB receptor extracellular regions</a>.
<em>Exp Cell Res</em>. 2009 315(4):659-70. </p><p>Wood CS,
<strong>Schmitz KR</strong>, Bessman NJ, Setty TG, Ferguson KM, Burd CG.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20026658">PtdIns4<em>P</em> recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking</a>.
<em>J Cell Biol</em>. 2009 187(7):967-75. </p><p>Lin CC, Huoh Y-S,
<strong>Schmitz KR</strong>, Jensen JE, Ferguson KM.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19081057">Pellino proteins contain a cryptic FHA domain that mediates interaction with phosphorylated IRAK1</a>.
<em>Structure</em>. 2008 16(12):1806-16. </p><p>
<strong>Schmitz KR</strong>, Liu J, Li S, Setty TG, Wood CS, Burd CG, Ferguson KM.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18410729">Golgi localization of glycosyltransferases requires a Vps74p oligomer</a>.
<em>Dev Cell</em>. 2008 14(4):523-34. </p><p>Li Y,
<strong>Schmitz KR</strong>, Salerno JC, Koretz JF.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17960114/">The role of the conserved COOH-terminal triad in alphaA-crystallin aggregation and functionality</a>.
<em>Mol Vis</em>. 2007 13:1758-68. </p><p>Li S,
<strong>Schmitz KR</strong>, Jeffrey PD, Wiltzius JJ, Kussie P, Ferguson KM.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15837620">Structural basis for inhibition of the epidermal growth factor receptor by cetuximab</a>.
<em>Cancer Cell</em>. 2005 7(4):301-11. </p><br> | | | <img alt="" src="/Images%20Bios/KRS_20170326.jpg" style="BORDER:0px solid;" /> | |
