Oliver Smithies investigator, Professor of Biochemistry and Biophysics
Co-Director, UNC Molecular and Cellular Biophysics Program
(PhD – State University of New York, Stony Brook)
HONORS & AWARDS
- ASBMB DeLano Award for Computational Biosciences, 2019
- UNC Oliver Smithies Investigator, 2019
- W.M.Keck Foundation Distinguished Young Scholar in Medical Research, 2005-2010
- Searle Scholar, 2004-2007
- Beckman Young Investigator, 2004-2007
- AAAS Newcomb Cleveland Prize, 2004
- Foresight Institute Feynman Prize in Nanotechnology, 2004
- Alfred P. Sloan Fellow, 2004
Computational Protein Design / Protein-Protein Interactions / Antibodies / Structural Biology / Optogenetics / Rosetta
What is protein design? Most ambitiously it is the creation of novel proteins to perform useful tasks. At a more modest level it might be identifying amino acid mutations that enhance protein stability, alter binding specificity, or increase solubility.
How do we design proteins? We are co-developers of a molecular modeling program called Rosetta that identifies low energy sequences for a target structure or interface. In essence, it is like solving a jigsaw puzzle. The pieces, in this case amino acids, must fit together so that there are no overlaps and little empty space. In addition, specific interactions such as hydrogen bonds must be satisfied.
What have we designed in the past? In the past we have used our program to enhance protein stabilities, design new protein structures, manipulate protein-protein interactions, and engineer protein switches.
What would we like to design in the future? Currently we are focusing on a variety of design goals including the design of light-activatable proteins, new strategies for creating therapeutic antibodies, the de novo design of protein structure.
What techniques do we use? Computer programming (primarily C++ and Python), molecular cloning, protein expression, biophysical analysis of protein-protein interactions (circular dichroism, isothermal titration calorimetry, surface plasmon resonance), directed evolution/yeast display, X-ray crystallography, live cell imaging and microscopy.
Optogenetics. Optogenetics describes the use of genetically encoded light-activatable proteins to control biological processes in living cells. Using a variety of protein engineering techniques, we have created a family of protein switches that can be used to control protein localization with light (see here for relevant papers). We have shown that these proteins can be used to activate GTPase signaling, control cell motility, and turn on gene transcription.
Antibody engineering. Antibodies are invaluable reagents for biological research, and have emerged over the last 20 years as an important class of therapeutic. For the last five year, we have been engaged in a productive collaboration with Eli Lilly focused on the development of new strategies for engineering bispecific antibodies. Bispecific antibodies recognize two antigens simultaneously and can be used to enhance specificity to particular cell types as well as allow the co-localization of different cell types, for instance the recruitment of t-cells to tumor cells in order to fight cancer.
De novo protein design. A long standing area of research in our laboratory is the development of computational methods for designing new protein structures from scratch. These projects allow us to probe the minimal determinants of protein structure, and provides the foundation for building new functional sites in proteins.
Protein interface design. Protein-protein interactions are central to all biological processes, and proteins with new binding properties can be used to manipulate biological pathways for applications in research and medicine. We have developed computational strategies for increasing protein-protein binding affinities, manipulating binding specificities, and creating novel interactions. We have also explored approaches for effectively combining computational predictions with high throughput screening approaches like yeast display and phage display.
Rosetta methods development. Rosetta is a powerful modeling package with modules for protein structure prediction, docking and design. It is being developed by a consortium of over 30 universities and is continually being modified to improve performance and expand capabilities. Our laboratory has played an important role in parameterizing the current energy functions used by Rosetta, and we are now focused on enhanced strategies for parallel computing.
- Froning KJ, Leaver-Fay A, Wu X, Phan S, Gao L, Huang F, Pustilnik A, Bacica M,Houlihan K, Chai Q, Fitchett JR, Hendle J, Kuhlman B, Demarest SJ. Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies. Protein Sci. 2017 Oct;26(10):2021-2038. doi:10.1002/pro.3240. Epub 2017 Jul 31. PubMed PMID: 28726352; PubMed Central PMCID: PMC5606552.
- Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T,Kuhlman B. Design of structurally distinct proteins using strategies inspired by evolution. Science. 2016 May 6;352(6286):687-90. doi:10.1126/science.aad8036. PubMed PMID: 27151863; PubMed Central PMCID: PMC4934125.
- Yumerefendi H, Lerner AM, Zimmerman SP, Hahn K, Bear JE, Strahl BD, Kuhlman B. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. Nat Chem Biol. 2016 Jun;12(6):399-401. doi: 10.1038/nchembio.2068. Epub 2016 Apr 18. PubMed PMID: 27089030; PubMed Central PMCID: PMC4888063.
- Leaver-Fay A, Froning KJ, Atwell S, Aldaz H, Pustilnik A, Lu F, Huang F, Yuan R, Hassanali S, Chamberlain AK, Fitchett JR, Demarest SJ, Kuhlman B. Computationally Designed Bispecific Antibodies using Negative State Repertoires. Structure. 2016 Apr 5;24(4):641-651. doi: 10.1016/j.str.2016.02.013. Epub 2016 Mar 17. PubMed PMID: 26996964; PubMed Central PMCID: PMC4866497.
- Yumerefendi H, Dickinson DJ, Wang H, Zimmerman SP, Bear JE, Goldstein B, Hahn K, Kuhlman B. Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation. PLoS One. 2015 Jun 17;10(6):e0128443. doi:10.1371/journal.pone.0128443. eCollection 2015. PubMed PMID: 26083500; PubMed Central PMCID: PMC4471001.
- Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B: Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide. ACS Synth Biol 2016, 5:53–64.
- Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B: Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. Protein Eng Des Sel 2016, 29:1–9.
- O’Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, et al.: A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. J. Chem. Theory Comput. 2015, 11:609–622.
- Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B: UbSRD: The Ubiquitin Structural Relational Database. Journal of Molecular Biology 2015, doi:10.1016/j.jmb.2015.09.011.
- Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H: Labeling and optical erasure of synaptic memory traces in the motor cortex. Nature 2015, 525:333–338.
- Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B: Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proceedings of the National Academy of Sciences 2015, 112:112–117.
- Lewis SM, Wu X, Pustilnik A, Sereno A, Huang F, Rick HL, Guntas G, Leaver-Fay A, Smith EM, Ho C, et al.: Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Nat Biotechnol 2014, 32:191–198.
- Murphy GS, Mills JL, Machius M, Szyperski T: Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core. Structure 2012, 20:1086–1096.
- Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B: Computational design of a symmetric homodimer using -strand assembly. Proceedings of the National Academy of Sciences 2011, 108:20562–20567.