Tom Muir

The Muir lab investigates the physiochemical basis of protein function in complex systems of biomedical interest. We study protein function using an integration of  synthetic organic and physical chemistry tools in combination 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 those 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 innovative methods are now used by numerous laboratories worldwide to address a large number of biomedical questions. 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:

Dao, H.T.; Dul, B.E.; Dann, G.P.; Liszczak, G.P.; Muir, T.W. “A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing.” Nat. Chem. Biol. 2020. 16, 134-142. doi: 10.1038/s41589-019-0413-4

Valencia, A.M.; Collings, C.K.; Dao, H.T.; St. Pierre, R.; Cheng, Y.-C.; Huang, J.; Sun, Z.-Y.; Seo, H.-S.; Mashtalir, Nazar; Comstock, D.E.; Bolonduro, O.; Vangos, N.E.; Yeoh, Z.C.; Dornan, M.K.; Hermawan, C.; Barrett, L.; Dhe-Paganon, S.; Woolf, C.J.; Muir, T.W.; Kadoch, C. “Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling.” Cell. 2019. 179, 1342–1356. doi: 10.1016/j.cell.2019.10.044

Diehl, K.L.; Ge, E.J.; Weinberg, D.N.; Jani, K.S.; Allis, C.D.; Muir, T.W. “PRC2 engages a bivalent H3K27M-H3K27me3 dinucleosome inhibitor.” PNAS. 2019. 116, 44, 22152-22157. doi: 10.1073/pnas.1911775116

Ge, E.J.; Jani, K.S.; Diehl, K.L.; Muller, M.M.; Muir, T.W. “Nucleation and Propagation of Heterochromatin by the Histone Methyltransferase PRC2: Geometric Constraints and Impact of the Regulatory Subunit JARID2.” J. Am. Chem. Soc. 2019. 141, 38, 15029-15039. doi: 10.1021/jacs.9b02321

Beh, L.Y.; Debelouchina, G.T.; Clay, D.M.; Thompson, R.E.; Lindblad, K.A.; Hutton, E.R.; Bracht, J.R.; Sebra, R.P.; Muir, T.W.; Landweber, L.F. “Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.” Cell. 2019. 177, 1781–1796 doi: 10.1016/j.cell.2019.04.028

Jani, K.S.; Jain, S.U.; Ge, E.J.; Diehl, K.L.; Lundgren, S.M.; Müller, M.M.; Lewis, P.W.; Muir, T.W. “Histone H3 tail binds a unique sensing pocket in EZH2 to activate the PRC2 methyltransferase.” PNAS. 2019, 116 (17), 8295-8300. doi: 10.1073/pnas.1819029116

Nacev, B.A.; Feng, L; Bagert, J.D.; Lemiesz, A.E; Gao, J.J.; Soshnev, A.A.; Kundra, R.; Schultz, N; Muir, T.W.; Allis, C.D. “The expanding landscape of ‘oncohistone’ mutations in human cancers.” Nature. 2019, 567, 473-478. doi: 10.1038/s41586-019-1038-1

Farrelly, L.A.; Thompson, R.E.; Zhao, S.; Lepack, A.E.; Lyu, Y.; Bhanu, N.V.; Zhang, B.; Loh, Y.E.; Ramakrishnan, A.; Vadodaria, K.C.; Heard, K.J.; Erikson, G.; Nakadai, T.; Bastle, R.M.; Lukasak, B.J.; Zebroski, H. 3rd; Alenina, N.; Bader, M.; Berton, O.; Roeder, R.G.; Molina, H.; Gage, F.H.; Shen, L.; Garcia, B.A.; Li, H.; Muir, T.W.; Maze, I. “Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3.” Nature. 2019, 567, 535-539. doi: 10.1038/s41586-019-1024-7

 

Oncohistones

Mutations in histone proteins, such as H3K27M, H3G34R/V, and H3K36M, have been associated with cancers. Recently, we and other researchers have uncovered thousands more cancer-associated histone mutations which remain largely uncharacterized. Using a cross-disciplinary, chemical biology approach, our lab seeks to dissect the molecular mechanisms by which these so-called “oncohistones” contribute to the development and progression of cancer.

Some recent papers:

Nacev, B.A.; Feng, L; Bagert, J.D.; Lemiesz, A.E; Gao, J.J.; Soshnev, A.A.; Kundra, R.; Schultz, N; Muir, T.W.; Allis, C.D. “The expanding landscape of ‘oncohistone’ mutations in human cancers.” Nature. 2019, 567, 473-478. doi: 10.1038/s41586-019-1038-1

 

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.  Recognizing the unique intein splicing reaction as a platform for the development of chemical biological tools, the Muir Lab aims 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:

Thompson, R.E.; Muir, T.W. “Chemoenzymatic Semisynthesis of Proteins.” Chem. Rev. 2020. doi: 10.1021/acs.chemrev.9b00450

Gramespacher, J.A.; Burton, A.J.; Guerra, L.F.; Muir, T.W. “Proximity Induced Splicing Utilizing Caged Split Inteins.” J. Am. Chem. Soc. 2019. 141, 35, 13708-13712. doi: 10.1021/jacs.9b05721

Thompson, R.E.; Stevens, A. J.; Muir, T.W. “Protein engineering through tandem transamidation.” Nature Chemistry. 2019. 11, 737-749. doi: 10.1038/s41557-019-0281-2

 

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:

Xie, Q.; Zhao, A.; Jeffrey, P.D.; Kim, M.K.; Bassler, B.L.; Stone, H.A.; Novick, R.P.; Muir, T.W. “Identification of a Molecular Latch that Regulates Staphylococcal Virulence.” Cell Chem Biol. 2019, 26, 1-11. doi: 10.1016/j.chembiol.2019.01.006

Wang B, Zhao A, Xie Q, Olinares PD, Chait BT, Novick RP, Muir TW. Functional Plasticity of the AgrC Receptor Histidine Kinase Required for Staphylococcal Virulence. Cell Chem Biol. 2017 Jan 19;24(1):76-86. doi: 10.1016/j.chembiol.2016.12.008.