Tom Muir

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(609) 258-5778	Frick Lab, 325
Faculty Assistant	Meghan krause
This email address is being protected from spambots. You need JavaScript enabled to view it.	(609) 258-5705

Research Focus

Dr. Muir's laboratory investigates the physiochemical basis of protein function in complex systems of biomedical interest. By combining tools of organic chemistry, biochemistry 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 Dr. Muir has developed are now widely used by chemical biologists around the world.

The Muir lab is using novel methods to study molecular recognition in prokaryotic and eukaryotic signaling processes. One of these techniques is a general approach to investigating protein activity called expressed protein ligation, which allows synthetic peptides (or other molecules) and recombinant proteins to be chemoselectively and regioselectively linked together. This is done by introducing molecular "sticky ends," which act like Velcro, at the complementary ends of the pieces, causing them to react when mixed together in water. Introduction of these sticky ends can either be achieved chemically or biosynthetically, and it is possible to append the synthetic molecule at either end of the recombinant protein, or even insert the synthetic cassette right into the middle. This technology opens up proteins to the tools of organic chemistry by allowing researchers to incorporate unnatural amino acids, posttranslational modifications and isotopic probes into proteins at specific sites. The major focus of Dr. Muir's current research is in the broad area of epigenetics where his group is applying in vitro protein chemistry methods to study how histone modifications control the local structure and function of chromatin.

Because expressed protein ligation is an in vitro technique, the Muir laboratory simultaneously pursues complementary approaches for studying protein function in vivo. The group has developed two ways to do this, both of which exploit protein splicing, in which an intervening sequence — termed an intein — catalyzes its removal from a host protein, the extein. In trans-splicing, the intein is split into two pieces and splicing occurs only upon reconstitution of these fragments.

The first of the methods is a platform technology that allows protein trans-splicing to occur only in the presence of a user specified stimulus such as a small cell-permeable molecule or red light; this "conditional protein trans-splicing" method provides a means to trigger posttranslational synthesis of a target protein from two fragments, thereby controlling that protein's function. Conditional protein trans-splicing provides a level of temporal and spatial control over protein function that is impossible to achieve using standard genetic approaches, and Dr. Muir's laboratory has shown that the methods works well in various cultured mammalian cell lines and in living animals.

The second technique developed by the lab allows for protein semisynthesis to be performed inside living cells. Using a different type of protein trans-splicing with peptide-transduction domain technology, this method allows a targeted cellular protein to be specifically ligated to an artificial probe delivered into the cell, effectively expanding the genetic code for cell biological studies. Currently we are developing second-generation versions of this technology specifically geared towards applications in the epigenetics area.

Another active area of research in the Muir lab focuses on quorum sensing in the pathogen Staphylococcus aureus. The Muir laboratory studies a class of the secreted peptides produced by the bacterium that have the ability to activate or inhibit expression of virulence, depending on which strain of S. aureus the peptides encounter. Dr. Muir and collaborators at New York University Medical Center have found that the peptides contain an unusual thiolactone structure, and further studies have suggested a mechanism that accounts for the changes in virulence. This discovery made it possible for them to design peptide analogues that globally inhibit virulence expression. These molecules are powerful tools for studying this quorum-sensing circuit both in vitro and in vivo. The Muir laboratory is currently studying the biosynthesis of these peptides and their mechanism of secretion. The group is also interested in how these peptides are recognized by their cognate cell surface receptors and how binding translates to receptor activation.

Selected Publications

100. McGinty, R.K., Kim, J., Chatterjee, C., Roeder, R.G. and Muir, T. W. 2008, Nature, 453, 812-816 Chemically ubiquitylated histone 2B stimulates hDot1L-mediated intranucleosomal methylation

102. Vila-Perelló, M., Hori, Y., Ribó, M. and Muir, T.W 2008, Angew. Chemie. Int. Ed. 47, 7764-7767 Activation of Protein Splicing by Protease or Light Triggered O-N Acyl Migration

103. Schwartz, E.C., Shekhtman, A., Dutta, K., Pratt, M.R., Cowburn, D., Darst, S., and Muir, T.W. 2008 Chemistry and Biology, 15, 1091-1103 A Full Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

107. Geisinger, E., Muir, T.W. and Novick, R.P. 2009, Proc. Natl. Acad. Sci. USA. 106, 1216-1221 agr receptor mutants reveal distinct modes of inhibition by staphylococcal autoinducing peptides.

108.Kim, J., Guermah, M., McGinty, R.K., Lee, J.-S., Tang, Z., Milne, T.A., Shilatifard, A., Muir, T.W. and Roeder, R.G., 2009, Cell, 137, 459-471 RAD6-Mediated Transcription-Coupled H2B Ubiquitylation Directly Stimulates H3K4 Methylation in Human Cells.

110. Lockless, S.W. and Muir. T.W., 2009, Proc. Natl. Acad. Sci. USA, 106, 10999-11004 Traceless Protein Ligation Using Evolved Split Inteins

111. Ceccarini, G., Flavell, R.R., Butelman, E.R. Synan, M. Willnow, T.E., Bar-Dagan, M., Goldsmith, S.J. Kreek, M.J., Kothari, P., Vallabhajosula, S., Muir, T.W., and Friedman, J.M. 2009, Cell Metabolism, 10, 148-159. PET Imaging of Leptin Biodistribution and Metabolism in Rodents and Primates

112. Chiang, K.P., Jensen, M.S., McGinty, R.K. and Muir, T.W. 2009, ChemBioChem, 13, 2182-2187 A Semi-Synthetic Strategy to Generate Phosphorylated and Acetylated Histone H2B

113. Pratt, M.R., Sekedat, M.D., Chiang, K.P. and Muir, T.W. 2009, Chemistry and Biology, 16, 1001-1012 Direct measurement of cathepsin-B activity in the cytosol of apoptotic cells by an activity based probe.

114. Cisar, E.A., Geisinger, E., Novick, R.P. and Muir, T.W 2009, Molecular Microbiology. 74, 44-57 Symmetric Signaling within Asymmetric Dimers of the Staphylococcus aureus Receptor Histidine Kinase AgrC

117. McGinty, R.K., Köhn, M., Chatterjee, C., Chiang, K.P., Pratt, M.R. and Muir, T.W. 2009, ACS Chemical Biology, 4, 958-968 Structure activity analysis of semisynthetic nucleosomes: Mechanistic insights of the stimulation of Dot1L by ubiquitylated histone H2B

119. Chatterjee, C., McGinty, R.K., Fierz, B. and Muir, T.W. 2010, Nature Chemical Biology, 6, 267-269 Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation

120. Frutos, S., Goger, M., Giovani, B., Cowburn, D. and Muir, T.W. 2010, Nature Chemical Biology, 6, 527-533 Branched Intermediate Formation Stimulates Peptide Bond Cleavage in the Mxe GyrA Intein Protein Splicing Reaction

121. Scheuermann, J.C., Gaytan de Ayala Alonso, A., Oktaba, K., Ly-Hartig, Nga., McGinty, R.K., Fraterman, S., Wilm, M., Muir, TW., Muller, J., 2010, Nature, 465, 243-247. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB

123. Vila-Perelló, M. and Muir, T.W 2010, Cell, 143, 191-200 Biological Applications of Protein Splicing

124. Kee, J-M., Villani, B., Carpenter, L., and Muir, T.W. 2010, J. Am. Chem. Soc, 132, 14327-14329 Development of Stable Phosphohistidine Analogs For commentary, see 2010, Chemistry and Engineering News, 88, (41) 10.

125. Moyle, P.M. and Muir, T.W. 2010, J. Am. Chem. Soc, 132, 15878-15880 Method for the Synthesis of Mono-ADP-Ribose Conjugated Peptides

126. Fierz, B., Chatterjee, C. McGinty, R.K., Bar-Dagan, M. and Muir, T.W. 2011, Nature Chemical Biology, 7, 113-119 H2B Ubiquitylation Disrupts Local and Higher-Order Chromatin Compaction

127.Allis, C.D. and Muir, T.W. 2011, ChemBioChem, 12, 264-279 Spreading Chromatin into Chemical Biology

128. Singla, N., Himanen, J.P. Muir, T.W. and Nikolov, D.B. 2011, Chemistry and Biology, 18, 361-371 A semisynthetic Eph receptor tyrosine kinase provides insight into ligand- induced kinase activation

129. Cho, J.-H., Muralidharan, V., Vila-Perello, M., Raleigh, D.P., Palmer III, A.G. and Muir, T.W. 2011, Nature Structural Mol. Biol. 18, 550-555. Tuning protein autoinhibition by domain destabilization

130. Ruthenburg, A.J., Li, H., Milne, T.A., Dewell, S., McGinty, R.K., Yuen, M., Ueberheide, B., Dou, Y., Muir, T.W., Patel, D.P. and Allis,, C.D. 2011, Cell, 145, 692-706 BPTF recognizes a mononucleosome-level histone modification pattern via multivalent interactions

131. Nguyen, D.P., Elliott, T., Holt, M., Muir, T.W. and Chin, J.W. 2011, J. Am. Chem. Soc. 133, 11418-11521 Genetically Encoded 1,2-Aminothiols Facilitate Rapid and Site-Specific Protein Labeling via a Bio-orthogonal Cyanobenzothiazole Condensation

132. Shah, N.H., Vila-Perelló, M. and Muir, T.W. 2011, Angew. Chemie. Int. Ed. 50, 6511-6515 Kinetic Control of One-Pot Trans-Splicing Reactions Using a Wild-Type and Designed Split Intein