Contact
Faculty Assistant

Sarah Porter
sp7@princeton.edu
Frick Laboratory, 327
609-258-5705

Research Focus

Tom Muir video interviewsThe Muir lab investigates the physiochemical basis of protein function in complex systems of biomedical interest. By combining tools of organic chemistry, biochemistry, biophysics and cell biology, the Muir lab has developed a suite of new technologies that provide fundamental insight into how proteins work. The chemistry-driven approaches pioneered by the Muir lab are now widely used by chemical biologists around the world.

 

 

We are interested in studying protein function by integrating the tools of synthetic organic and physical chemistry with those of molecular genetics. Driven by a series of biological questions, we have developed general chemical biology approaches that allow the covalent structure of proteins to be manipulated with a similar level of control to that possible with smaller organic molecules. These technologies, which can be applied both in vitro and in vivo, allow the insertion of unnatural amino acids, posttranslational modifications and isotopic probes site-specifically anywhere into proteins. Our methods are now used by numerous laboratories worldwide, and have allowed a large number of biomedical questions to be addressed. A summary of ongoing work in the Muir group is provided below

 

 

Chromatin

The eukaryotic genome is organized as a DNA-protein complex called chromatin. This architecture enables dynamic compaction of DNA within the confined space of the nucleus, and facilitates access to desired genomic loci through post-translational modification of scaffold proteins (histones). In the Muir lab, we use synthetic ‘designer’ chromatin to investigate the molecular basis of how histone modifications control DNA-templated processes, and how aberrant chromatin signaling pathways contribute to pathologies.

Some recent papers:

Nguyen, U. T. T.; Bittova, L.; Müller, M. M.; Fierz, B.; David, Y.; Houck-Loomis, B.; Feng, V.; Dann, G. P.; Muir, T. W. 2014, Nat. Meth., 11, 834.
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3022.html

Holt, M.T., David, Y., Pollock, S., Tang, Z., Jeon, J., Kim, J., Roeder, R.G. and Muir T.W. 2015, Proc. Natl. Acad. Sci. USA, 112, 10365-10370

Lu, C., Jain, S.U., Hoelper, D., et al. 2016, Science, 352, 844-849

Muller, M.M., Fierz, B., Bitova, L., Liszczak, G. and Muir, T.W. 2016, Nature Chemical Biology, 12, 188-193

Debelouchina, G.T., Gerecht, K. and Muir, T.W. 2017, Nature Chemical Biology, 13, 105-117

 

Schematic representation of genome architecture (left) and synthesis of ‘designer’ nucleosomes (right).

 

Inteins

Inteins, found in a variety of unicellular organisms, are polypeptide sequences that are able to excise themselves from flanking protein regions (exteins) and to ligate the exteins together.  While the biological function of inteins remains a mystery, this class of proteins has found widespread use in the fields of chemical and cell biology.  Our lab recognizes the unique intein splicing reaction as a platform for the development of chemical biological tools.  At a fundamental level, we aim to characterize the precise biochemical requirements for intein splicing and to engineer inteins with enhanced properties for the development of novel intein-based technologies.

Some recent papers:

Liu, Z., Frutos, S., Bick, M., Vila-Perello, M., Debelouchina, G.T., Darst, S.A. and Muir, T.W. 2014, Proc. Natl. Acad. Sci. USA, 111, 8422-8427

David, Y., Vila-Perello, M., Verma, S. and Muir, T.W. 2015, Nature Chemistry, 7, 394-402

Stevens AJ, Brown ZZ, Shah NH, Sekar G, Cowburn D. and Muir TW. 2016, J. Am. Chem. Soc. 138, 2162-2165

Liszczak, G., Brown, Z.Z., Kim, S., Oslund, R.C., David, Y. and Muir, T.W. 2017, Proc. Natl. Acad. Sci. USA, 114, 681-686

 

Mechanism of intein-mediated protein splicing.

 

Agr

Bacteria communicate through small-molecule signals. A commensal pathogen, Staphylococcus aureus, secretes a peptide pheromone, AIP, which acts as an extracellular indicator of the population density and coordinates its virulence response. Production and sensing of AIP involves four Agr (accessory gene regulator) proteins. The Muir lab uses highly purified recombinant or synthetic components to reconstitute these processes and to investigate how each Agr protein carries out its function at the molecular level. 

Some recent papers:

Wang, B., Zhao, A., Novick, R.P. and Muir, T.W. 2014, Molecular Cell, 53, 929-940

Wang, B., Zhao, A., Novick, R.P. and Muir, T.W. 2015, Proc. Natl. Acad. Sci. USA, 112, 10679-10684

Wang, B. and Muir, T.W. 2016, Cell Chemical Biology, 23, 214-224

Wang, B. Zhao, A., Xie, Q., Novick, R.P. and Muir, T.W. 2017, Cell Chemical Biology, 24, 76-86

 

Schematic representation of the S. aureus quorum sensing pathway.

 

Phosphohistidine

Although protein histidine phosphorylation (pHis) was discovered over 50 years ago, investigating its functional role has proven extremely difficult due to its chemical instability and the lack of adequate chemical and biochemical tools and approaches. The Muir lab has developed the first pan-pHis specific antibodies, which enables the select detection of pHis-modified proteins from complex biological samples. Currently, we are utilizing this antibody, along with other methods, to investigate the functional roles played by pHis in signaling, metabolism, and epigenetics.

Some recent papers:

Kee, J.-M.; Villano, B.; Carpenter, L.R.; Muir, T.W. 2010, JACS, 132, 14327.
http://pubs.acs.org/doi/abs/10.1021/ja104393t

Kee, J.-M.; Oslund, R.C.; Perlman, D.H.; Muir, T.W. 2013, Nat. Chem. Biol., 9, 416.
http://www.nature.com/nchembio/journal/v9/n7/full/nchembio.1259.html

Oslund, R.C., Kee, J.-M., Perlman, D.H. and Muir, T.W. 2014, J. Am. Chem. Soc.  136, 12899-12911

 

The development of pHis analogs and antibodies enables the investigation of the biological role of this elusive protein modification. 
Research Areas
Chemical Biology
Honors

Emil Thomas Kaiser Award, The Protein Society (2017)

Winner of the Breslow Award in Biomimetic Chemistry from the American Chemical Society (2016)

Fellow of The Royal Society of Edinburgh (2013)

Arthur C. Cope Scholar Award, American Chemical Society (2013)

Elected Fellow of the Royal Society of Chemistry (2012)

Jeremy Knowles Award, Royal Society of Chemistry (2012)

MERIT Award, US National Institutes of Health (2012)

Vincent du Vigneaud Award in Peptide Chemistry, American Peptide Society (2008)

Fellow of the American Association for the Advancement of Science (2007)

Kavli Fellow, U.S. National Academy of Sciences (2007)

Leonidas Zervas Award from The European Peptide Society (2002)

Alfred P. Sloan Research Fellow (2000)

Pew Scholar in the Biomedical Sciences (1998)

Selected Recent Publications

Shah, N. H.; Muir, T. W., "Inteins: nature's gift to protein chemists." Chemical Science 2014, 5 (2), 446-461.

Wang, B.; Zhao, A.; Novick, R. P.; Muir, T. W., "Activation and Inhibition of the Receptor Histidine Kinase AgrC Occurs through Opposite Helical Transduction Motions." Molecular Cell 2014, 53 (6), 929-940.

Eryilmaz, E.; Shah, N. H.; Muir, T. W.; Cowburn, D., "Structural and dynamical features of inteins and implications on protein splicing." Journal of Biological Chemistry 2014, 289 (28), 19278-19278.

Barbuto, S.; Idoyaga, J.; Vila-Perello, M.; Longhi, M. P.; Breton, G.; Steinman, R. M.; Muir, T. W., "Induction of innate and adaptive immunity by delivery of poly dA:dT to dendritic cells." Nature Chemical Biology 2013, 9 (4), 250-256.

Kim, D.-H.; Tang, Z.; Shimada, M.; Fierz, B.; Houck-Loomis, B.; Bar-Dagen, M.; Lee, S.; Lee, S.-K.; Muir, T. W.; Roeder, R. G.; Lee, J. W., "Histone H3K27 Trimethylation Inhibits H3 Binding and Function of SET1-Like H3K4 Methyltransferase Complexes." Molecular and Cellular Biology 2013, 33 (24), 4936-4946.

Wu, L.; Lee, S. Y.; Zhou, B.; Nguyen, U. T. T.; Muir, T. W.; Tan, S.; Dou, Y., "ASH2L Regulates Ubiquitylation Signaling to MLL: trans-Regulation of H3 K4 Methylation in Higher Eukaryotes." Molecular Cell 2013, 49 (6), 1108-1120.

Kim, J.; Kim, J.-A.; McGinty, R. K.; Nguyen, U. T. T.; Muir, T. W.; Allis, C. D.; Roeder, R. G., "The n-SET Domain of Set1 Regulates H2B Ubiquitylation-Dependent H3K4 Methylation." Molecular Cell 2013, 49 (6), 1121-1133.

Vila-Perello, M.; Liu, Z.; Shah, N. H.; Willis, J. A.; Idoyaga, J.; Muir, T. W., "Streamlined Expressed Protein Ligation Using Split Inteins." Journal of the American Chemical Society 2013, 135 (1), 286-292.

Shah, N. H.; Eryilmaz, E.; Cowburn, D.; Muir, T. W., "Extein Residues Play an Intimate Role in the Rate-Limiting Step of Protein Trans-Splicing." Journal of the American Chemical Society 2013, 135 (15), 5839-5847.

Shah, N. H.; Eryilmaz, E.; Cowburn, D.; Muir, T. W., "Naturally Split Inteins Assemble through a "Capture and Collapse" Mechanism." Journal of the American Chemical Society 2013, 135 (49), 18673-18681.

Tang, Z.; Chen, W.-Y.; Shimada, M.; Nguyen, U. T. T.; Kim, J.; Sun, X.-J.; Sengoku, T.; McGinty, R. K.; Fernandez, J. P.; Muir, T. W.; Roeder, R. G., "SET1 and p300 Act Synergistically, through Coupled Histone Modifications, in Transcriptional Activation by p53." Cell 2013, 154 (2), 297-310.

Lewis, P. W.; Mueller, M. M.; Koletsky, M. S.; Cordero, F.; Lin, S.; Banaszynski, L. A.; Garcia, B. A.; Muir, T. W.; Becher, O. J.; Allis, C. D., "Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma." Science 2013, 340 (6134), 857-861.

Kee, J.-M.; Muir, T. W., "Chasing Phosphohistidine, an Elusive Sibling in the Phosphoamino Acid Family." Acs Chemical Biology 2012, 7 (1), 44-51.

Fierz, B.; Muir, T. W., "Chromatin as an expansive canvas for chemical biology." Nature Chemical Biology 2012, 8 (5), 417-427.

Shah, N. H.; Dann, G. P.; Vila-Perello, M.; Liu, Z.; Muir, T. W., "Ultrafast Protein Splicing is Common among Cyanobacterial Split Inteins: Implications for Protein Engineering." Journal of the American Chemical Society 2012, 134 (28), 11338-11341.

Fierz, B.; Kilic, S.; Hieb, A. R.; Luger, K.; Muir, T. W., "Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis." Journal of the American Chemical Society 2012, 134 (48), 19548-19551.

Fierz, B.; Chatterjee, C.; McGinty, R. K.; Bar-Dagan, M.; Raleigh, D. P.; Muir, T. W., "Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction." Nature Chemical Biology 2011, 7 (2), 113-119.

Allis, C. D.; Muir, T. W., "Spreading Chromatin into Chemical Biology." Chembiochem 2011, 12 (2), 264-279.

Cho, J.-H.; Muralidharan, V.; Vila-Perello, M.; Raleigh, D. P.; Muir, T. W.; Palmer, A. G., III, "Tuning protein autoinhibition by domain destabilization." Nature Structural & Molecular Biology 2011, 18 (5), 550-U163.

Shah, N. H.; Vila-Perello, M.; Muir, T. W., "Kinetic Control of One-Pot Trans-Splicing Reactions by Using a Wild-Type and Designed Split Intein." Angewandte Chemie-International Edition 2011, 50 (29), 6511-6515.

Shah, N. H.; Muir, T. W., "Split Inteins: Nature's Protein Ligases." Israel Journal of Chemistry 2011, 51 (8-9), 854-861.

Nguyen, D. P.; Elliott, T.; Holt, M.; Muir, T. W.; Chin, J. W., "Genetically Encoded 1,2-Aminothiols Facilitate Rapid and Site-Specific Protein Labeling via a Bio-orthogonal Cyanobenzothiazole Condensation." Journal of the American Chemical Society 2011, 133 (30), 11418-11421.

Janz, J. M.; Ren, Y.; Looby, R.; Kazmi, M. A.; Sachdev, P.; Grunbeck, A.; Haggis, L.; Chinnapen, D.; Lin, A. Y.; Seibert, C.; McMurry, T.; Carlson, K. E.; Muir, T. W.; Hunt, S., III; Sakmar, T. P., "Direct Interaction between an Allosteric Agonist Pepducin and the Chemokine Receptor CXCR4." Journal of the American Chemical Society 2011, 133 (40), 15878-15881.

Ruthenburg, A. J.; Li, H.; Milne, T. A.; Dewell, S.; McGinty, R. K.; Yuen, M.; Ueberheide, B.; Dou, Y.; Muir, T. W.; Patel, D. J.; Allis, C. D., "Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions." Cell 2011, 145 (5), 692-706.

Moyle, P. M.; Muir, T. W., "Method for the Synthesis of Mono-ADP-ribose Conjugated Peptides." Journal of the American Chemical Society 2010, 132 (45), 15878-15880.