Patricia Kane, PhD
Chair and Professor
The central goals of scientists in the Biochemistry and Molecular Biology department are to research fundamental mechanisms in cells and organisms at the molecular level and to train the next generation of scientists. Read More...
Faculty Research Interests
Stewart N Loh, PhD
- Professor of Biochemistry and Molecular Biology
- Vice Chair of Biochemistry and Molecular Biology
Research Programs and Affiliations
- Biochemistry and Molecular Biology
- Biomedical Sciences Program
Education & Fellowships
- Postdoctoral Fellow: Stanford University, Biochemistry, 1996
- PhD: University of Wisconsin at Madison, 1993, Biochemistry
- BS: University of Utah, 1987, Chemistry
Protein engineering, design, and folding
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Our philosophy is to test central hypotheses regarding the kinetic mechanism and thermodynamics of protein folding, while at the same time improving properties of existing proteins and creating novel proteins with completely new functions.
To achieve this goal we employ a variety of structural, biophysical, biochemical, and molecular biological approaches including:
- Nuclear magnetic resonance and X-ray crystallography
- Optical spectroscopy (fluorescence, circular dichroism)
- Thermodynamic and kinetic analysis of protein folding
- Hydrogen and thiol-disulfide exchange mechanisms
- Protein functional assays
Protein-based molecular switches. We have developed two approaches (alternate frame folding (AFF) and mutually exclusive folding (MEF)) for engineering an allosteric conformational change into a protein where none may have existed previously. AFF and MEF transduce a triggering signal into an output event. In this way, an ordinary binding protein can be converted to a molecular switch. This technology is being used to create (for example) fluorescent biosensors and artificial zymogens that selectively attack viruses and diseased cells.
Kinetic mechanism of protein folding. Why do some proteins fold in milliseconds while others require hours? Are partially structured intermediates necessary or do they represent opportunistic traps? We are addressing these questions by applying a variety of spectroscopic techniques to characterize the structure and stability of folding intermediates, and the kinetics of their formation.
p53 and cancer. The p53 tumor suppressor is the most heavily mutated protein in human cancer. Our work has shown that the folding mechanism of p53 is unusually complex. It involves multiple pathways with both productive and dead-end intermediates. We are particularly interested in how folding and misfolding mechanisms are affected by loss of the bound zinc ion and by the natural dimerization and tetramerization of p53. Our goal is to understand how tumorigenic mutations affect p53 folding and cause it to fail, and how small molecules can be designed to offset the effects of mutation.
DeGrave, A.J., Ha, J.-H., Loh, S.N.* & Chong, L.T*. (2018). Large enhancement of response times of a protein conformational switch by computational design. Nature Comm. 9, 1013 (*corresponding authors).
Yu, X., Blanden, A., Tsang, A.T., Zaman, S., Liu, Y., Gilleran, J., Bencivenga, A., Kimball, S.D., Loh, S.N. & Carpizo, D.R. (2017). Thiosemicarbazones functioning as zinc metallochaperones to reactivate mutant p53. Molecular Pharm 91, 567-575.
Karchin, J. M., Ha, J.-H., Namitz, K.E., Cosgrove, M.S. & Loh, S.N. (2017). Small molecule-induced domain swapping as a mechanism for controlling protein function and assembly. Scientific Reports 7, 44388.
Ha, J.-H., Karchin, J.M., Walker-Kopp, N., Castañeda, C.A. & Loh, S.N. (2015). Engineered domain swapping as an on/off switch for protein function. Chemistry & Biology 22, 1384-1393.
Ha, J.-H. & Loh, S.N. (2017). Construction of allosteric protein switches by alternate frame folding and intermolecular fragment exchange. Methods Mol Biol 1596, 27-41.
Blanden, A.R., Yu, X., Loh, S.N., Levine, A.R., & Carpizo, D.R. (2015). Reactivating mutant p53 using small molecules as zinc metallochaperones: awakening a sleeping giant in cancer. Drug Discovery Today 20, 1391-1397
Blanden, A.R., Yu, X., Wolfe, A.J., Gilleran, J.A., Augeri, D.J., O'Dell, R.S., Olson, E.C., Kimball, S.D., Emge, T.J., Movileanu, L., Carpizo, D.R. & Loh, S.N. (2015) Synthetic metallochaperone ZMCI rescues mutant p53 conformation by transporting zinc into cells as an ionophore. Molecular Pharm. 87, 825-831.
Zheng, H., Bi, J., Krendel, M. & Loh, S. N. (2014). Converting a binding protein into a biosensing conformational switch using protein fragment exchange. Biochemistry 53, 5505-5514. (see Comment in Chemical & Engineering News, August 28, 2014)
Yu, X.*, Blanden, A. R.*, Narayanan, S., Jayakumar, L., Lubin, D., Augeri, D., Kimball, S. D., Loh, S. N.**, Carpizo, D. R.** (2014). Small molecule restoration of wildtype structure and function of mutant p53 using a novel zinc metallochaperone based mechanism. Oncotarget 5, 8879-8892. *These authors contributed equally. **Corresponding authors
Ha, J.-H., Shinsky, S.A. & Loh, S.N. (2013).Stepwise conversion of a binding protein to a fluorescent switch:application to Thermoanaerobacter tengcongensis ribose binding protein. Biochemistry 52, 600-612
Ha, J.-H. & Loh, S.N. (2012). Protein conformational switches: from nature to design. Chem. Eur. J. 18, 7984-7999
Ha, J.-H., Karchin, J.M., Walker-Kopp, N., Huang, L.-S., Berry, E.A. & Loh, S.N. (2012). Engineering domain-swapped binding interfaces by mutually exclusive folding. J. Mol. Biol., Vol 416: 495-502
Zheng, H. & Loh, S.N. (2012). Switchable proteins as platforms for biosensor design. Biotech International 23, 17-20
Stratton, M.M., McClendon, S., Eliezer, D. & Loh, S.N. (2011). Structural characterization of two alternate conformations in a calbindin D9k-based molecular switch. Biochemistry 50, 5583-5589.
Stratton, M.M. & Loh, S.N. (2011). Converting a protein into a switch for biosensing and functional regulation. Protein Science, 20, 19-29.
Stratton, M.M. & Loh, S.N. (2010). On the Mechanism of Protein Fold-Switching by a Molecular Sensor. Proteins Struct. Funct. Bioinf. 78, 3260-3269.
Butler, J.S. & Loh, S.N. (2010). Zinc and p53 misfolding. In Protein Folding and Metal Ions: Mechanisms, Biology, and Disease (C.M Gomes and P. Wittung-Stafshede, Eds.), CRC Press.
Stratton, M.M., Cutler, T.A., Ha, J.-H. & Loh, S.N. (2010). Probing local structural fluctuations in myoglobin by size-dependent thiol-disulfide exchange. Protein Sci. 19, 1587-1594.
Loh, S.N. (2010). The missing zinc: p53 misfolding and cancer. Metallomics 2, 442-449 (cover article)
Mitrea D.M., Parsons, L.S. & Loh, S.N. (2010) "Engineering an Artificial Zymogen by Alternate Frame Protein Folding", Proc. Natl. Acad. Sci. USA, Proc. Natl. Acad. Sci. USA 107, 2824-2829.
Lubin DJ, Butler JS & Loh, SN (2010) "Folding of Tetrameric p53: Oligomerization and Tumorigenic Mutations Induce Misfolding and Loss of Function", J. Mol. Biol. 395, 705-716.
Butler JS, Mitrea DM, Mitrousis G, Cingolani G, Loh SN. Structural and thermodynamic analysis of a conformationally strained circular permutant of barnase. Biochemistry. 2009 Apr 12; 48(15): 3497-507.
Cutler TA, Mills BM, Lubin DJ, Chong LT, Loh SN. Effect of Interdomain Linker Length on an Antagonistic Folding-Unfolding Equilibrium between Two Protein Domains. J Mol Biol. 2008 Nov 8. 386(3): 854-68. [Epub ahead of print]
Stratton MM, Mitrea DM, Loh SN. A Ca2+-sensing molecular switch based on alternate frame protein folding. ACS Chem Biol. 2008 Nov 21;3(11):723-32.
Loh SN. Disrupting proteins to treat cancer. ACS Chem Biol. 2008 Mar 20;3(3):140-1.
Cutler TA, Loh SN. Thermodynamic analysis of an antagonistic folding-unfolding equilibrium between two protein domains. J Mol Biol. 2007 Aug 10;371(2):308-16. Epub 2007 Jun 2.
Chen H, Rhoades E, Butler JS, Loh SN, Webb WW. Dynamics of equilibrium structural fluctuations of apomyoglobin measured by fluorescence correlation spectroscopy. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10459-64. Epub 2007 Jun 7.
Butler JS, Loh SN. Zn(2+)-dependent misfolding of the p53 DNA binding domain. Biochemistry. 2007 Mar 13;46(10):2630-9. Epub 2007 Feb 13.