Faculty & Research

Associated Faculty

Tom Muir

Associated Faculty, Chemistry

Tom Muir

Phone (609) 258-5778
locationFrick Lab, 325
Faculty Assistant
Sarah porter
Phone (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

Stevens AJ, Brown ZZ, Shah NH, Sekar G, Cowburn D, Muir TW.  Design of a Split Intein with Exceptional Protein Splicing Activity. J Am Chem Soc. 2016 Feb 24;138(7):2162-5. [PubMed - in process]

Zhou L, Holt MT, Ohashi N, Zhao A, Müller MM, Wang B, Muir TW. (2016) Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation. Nat Commun. 7:10589. Pubmed

Müller MM, Fierz B, Bittova L, Liszczak G, Muir TW. (2016) A two-state activation mechanism controls the histone methyltransferase Suv39h1. Nat Chem Biol. [Epub ahead of print]

Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF. (2015) DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res. 25(11):1727-38. Pubmed

Wang B, Zhao A, Novick RP, Muir TW. (2015) Key driving forces in the biosynthesis of autoinducing peptides required for staphylococcal virulence. Proc Natl Acad Sci U S A. 112 (34): 10679-84. Pubmed

Holt MT, David Y, Pollock S, ... Roeder RG, Muir TW. (2015) Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin.  Proc Natl Acad Sci U S A. 112 (33): 10365-70. Pubmed

David Y, Vila-Perelló M, Verma S, Muir TW. (2015) Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat Chem. 7:394-402. Pubmed

Brown ZZ, Müller MM, Kong HE, Lewis PW, Muir TW. (2015) Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin. Angew Chem Int Ed Engl. 54(22):6457-61. Pubmed

 Johnson JG, Wang B, Debelouchina GT, Novick RP, Muir TW. (2015) Increasing AIP macrocycle size reveals key features of agr activation in Staphylococcus aureus. Chembiochem. 16:1093-100. Pubmed

Kee J, Oslund RC, Couvillon AD, Muir TW. (2014) A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org Lett. 17:187-9. Pubmed

Müller MM, Muir TW. (2014) Histones: At the crossroads of peptide and protein chemistry. Chem Rev. 115:2296-349. Pubmed

Brown ZZ, Müller MM, Jain SU, Allis CD, Lewis PW, Muir TW. (2014) Strategy for "detoxification" of a cancer-derived histone mutant based on mapping its interaction with the methyltransferase PRC2. J Am Chem Soc. 136: 13498-501. Pubmed

Oslund RC, Kee JM, Couvillon AD, Bhatia VN, Perlman DH, Muir TW. (2014) A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J Am Chem Soc. 136: 12899-911. Pubmed

Eryilmaz E, Shah NH, Muir TW, Cowburn D. (2014) Structural and dynamical features of inteins and implications on protein splicing. J Biol Chem. 289: 14506-11. Pubmed

Nguyen UT, Bittova L, Müller MM,...Muir TW. (2014) Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods. 11: 834-40. Pubmed

Liu Z, Frutos S, Bick MJ,...Muir TW. (2014) Structure of the branched intermediate in protein splicing. Proc Natl Acad Sci. 111: 8422-27. Pubmed

Wang B, Zhao A, Novick RP, Muir TW. (2014) Activation and inhibition of the receptor histidine kinase AgrC occurs through opposite helical transduction motions. Mol Cell. 53: 929-40. Pubmed

Shah NH, Muir TW. (2014) Inteins: nature's gift to protein chemists. Chem Sci. 5: 446-61. Pubmed

Shah NH, Eryilmaz E, Cowburn D, Muir TW. (2013) Naturally split inteins assemble through a "capture and collapse" mechanism. J Am Chem Soc. 135: 18673-81. Pubmed

Kee JM, Oslund RC, Perlman DH, Muir TW. (2013) A pan-specific antibody for direct detection of protein histidine phosphorylation. Nat Chem Biol. 9: 416-21. Pubmed

Shah NH, Eryilmaz E, Cowburn D, Muir TW. (2013) Extein residues play an intimate role in the rate-limiting step of protein trans-splicing. J Am Chem Soc. 135: 5839-47. Pubmed

Vila-Perelló M, Liu Z, Shah NH, Willis JA, Idoyaga J, Muir TW. (2012) Streamlined expressed protein ligation using split inteins. J Am Chem Soc. 135: 286-92. Pubmed

Fierz B, Kilic S, Hieb AR, Luger K, Muir TW. (2012) Stability of nucleosomes containing homogenously ubiquitylated H2A and H2B prepared using semisynthesis. J Am Chem Soc. 134: 19548-51. Pubmed

Shah NH, Dann GP, Vila-Perelló M, Liu Z, Muir TW. (2012) Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering. J Am Chem Soc. 134: 11338-41. Pubmed

Brown ZZ, Muir TW. (2012) From EPOthilone to EPO: Aa challenge for natural product synthesis. Proc Natl Acad Sci. 109: 7134-35. Pubmed

Shah NH, Vila-Perelló M and Muir TW. (2011) Kinetic control of one-pot trans-splicing reactions using a wild-type and designed split intein. Angew Chemie Int Ed. 50: 6511-15. PubMed

Nguyen DP, Elliott T, Holt M, Muir TW and Chin JW. (2011) Genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation. J Am Chem Soc. 133: 11418-521. PubMed

Ruthenburg AJ, Li H, Milne TA,...Muir TW, et al. (2011) BPTF recognizes a mononucleosome-level histone modification pattern via multivalent interactions. Cell 145: 692-706. PubMed

Cho J-H, Muralidharan V, Vila-Perello M, Raleigh DP, Palmer III AG and Muir TW. (2011) Tuning protein autoinhibition by domain destabilization. Nature Structural Mol Biol. 18: 550-55. PubMed

Singla N, Erdjument-Bromage H, Himanen JP, Muir TW, Nikolov DB. (2011) A semisynthetic Eph receptor tyrosine kinase provides insight into ligand-induced kinase activation. Chem Biol. 18: 361-71. PubMed

Allis CD, Muir TW. (2011) Spreading chromatin into chemical biology. Chembiochem. 12: 264-79. PubMed

Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW. (2011) Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol. 7: 113-19. PubMed

Moyle PM, Muir TW. (2010) Method for the synthesis of mono-ADP-ribose conjugated peptides. J Am Chem Soc. 132: 15878-80. PubMed

Kee JM, Villani B, Carpenter LR, Muir TW. (2010) Development of stable phosphohistidine analogues. J Am Chem Soc. 132: 14327-29. Pubmed

Vila-Perelló M, Muir TW. (2010) Biological applications of protein splicing. Cell. 143: 191-200. Pubmed

Scheuermann JC, de Ayala Alonso AG, Oktaba K,...Muir TW, Müller J. (2010) Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature. 465: 243-47. Pubmed

Frutos S, Goger M, Giovani B, Cowburn D, Muir TW. (2010) Branched intermediate formation stimulates peptide bond cleavage in protein splicing. Nat Chem Biol. 6: 527-33. Pubmed

Chatterjee C, McGinty RK, Fierz B, Muir TW. (2010) Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nat Chem Biol. 6: 267-69. Pubmed

McGinty RK, Köhn M, Chatterjee C, Chiang KP, Pratt MR, Muir TW. (2009) Structure-activity analysis of semisynthetic nucleosomes: mechanistic insights into the stimulation of Dot1L by ubiquitylated histone H2B. ACS Chem Biol. 4: 958-68. Pubmed

George Cisar EA, Geisinger E, Muir TW, Novick RP. (2009) Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC. Mol Microbiol. 74: 44-57. Pubmed

Pratt MR, Sekedat MD, Chiang KP, Muir TW. (2009) Direct measurement of cathepsin B activity in the cytosol of apoptotic cells by an activity-based probe. Chem Biol. 16: 1001-12. Pubmed

Chiang KP, Jensen MS, McGinty RK and Muir TW. (2009)A semisynthetic strategy to generate phosphorylated and acetylated histone H2B. ChemBioChem. 13: 2182-87. Pubmed

Ceccarini G, Flavell RR, Butelman ER,...Muir TW, Friedman JM. (2009) PET imaging of leptin biodistribution and metabolism in rodents and primates. Cell Metab. 10: 148-59. Pubmed

Lockless SW, Muir TW. (2009) Traceless protein splicing utilizing evolved split inteins. Proc Natl Acad Sci. 106: 10999-1004. Pubmed

Kim J, Guermah M, McGinty RK,...Muir TW, Roeder RG. (2009) RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137: 459-71. Pubmed

Geisinger E, Muir TW, Novick RP. (2009) agr receptor mutants reveal distinct modes of inhibition by staphylococcal autoinducing peptides. Proc Natl Acad Sci. 106: 1216-21. Pubmed

Schwartz EC, Shekhtman A, Dutta K,...Muir TW. (2008) A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Chem Biol. 15: 1091-103. Pubmed

Vila-Perelló M, Hori Y, Ribó M, Muir TW. (2008) Activation of protein splicing by protease- or light-triggered O to N acyl migration. Angew Chem Int Ed Engl. 47: 7764-67. Pubmed

McGinty RK, Kim J, Chatterjee C, Roeder RG, Muir TW. (2008) Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature. 453: 812-16. Pubmed

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