Publications – The Muir Lab

Preprints

Hua, Y. *; Tay, N.E.S. *; Ye, X.; Owen, J. A.; Liu, H.; Thompson, R.; Muir, T.W. Protein Editing using a Concerted Transposition Reaction. bioRxiv 2024. doi: https://www.biorxiv.org/content/10.1101/2024.06.03.597171v1

Kofoed, C.; Tay, N. E. S.; Ye, X.; Erkalo, G.; Muir, T. W. Cell surface sculpting using logic-gated protein actuators. bioRxiv 2023. doi: https://www.biorxiv.org/content/10.1101/2023.12.18.572113v1

Park S.; Athreya A.; Carrizo, G. E.; Benning, N. A.; Mitchener, M. M.; Bhanu, N. V.;Garcia, B. A.; Zhang, B.; Muir, T. W.; Pearce, E. L.; Ha T. Electrostatic encoding of genome organization principles within single native nucleosomes. bioRxiv 2023. doi: https://www.biorxiv.org/content/10.1101/2023.12.08.570828v1

Hallinen, K. M.; Bodine, S. P.; Stone, H. A.; Muir, T. W.; Wingreen, N. S.; Gitai, Z. Distinct microcolony morphologies promote flow-dependent bacterial colonization. bioRxiv 2023. doi: https://www.biorxiv.org/content/10.1101/2023.11.22.568348v2

Zheng, Q.; Bastle, R. M.; Zhao, S.; Kong, L.; Vostal, L.; Ramakrishnan, A.; Shen, L.; Fulton, S. L.; Wang, H.; Zhang, B.; Upad, A.; Dierdorff, L.; Thompson, R. E.; Molina, H.; Stransky, S.; Sidoli, S.; Muir, T. W.; Li, H.; David, Y.; Maze, I. Histone monoaminylation dynamics are regulated by a single enzyme and promote neural rhythmicity. bioRxiv 2022. doi: https://www.biorxiv.org/content/10.1101/2022.12.06.519310v3

2024

Lee, G.; Muir, T. W. Distinct phases of cellular signaling revealed by time-resolved protein synthesis. Nat. Chem. Biol. 2024. doi: https://www.nature.com/articles/s41589-024-01677-3

B. A. Nacev, Y. Dabas, M. R. Paul, C. Pacheco, M. Mitchener, Y. Perez, Y. Fang, A. A. Soshnev, D. Barrows, T. Carroll, N. D. Socci, S. C. St. Jean, S. Tiwari, M. J. Gruss, S. Monette, W. D. Tap, B. A. Garcia, T. Muir, C. D. Allis, Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nat Commun 2024 15, 5155. https://www.nature.com/articles/s41467-024-49486-5

2023

Hananya, N.; Koren, S.; Muir, T. W. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2023. doi: https://doi.org/10.1038/s41576-023-00664-z

Hananya, N.*, Ye, X.*, Koren, S.; Muir, T. W. A genetically encoded photoproximity labeling approach for mapping protein territories. Proceedings of the National Academy of Sciences2023 120(16) e2219339120 doi: https://doi.org/10.1073/pnas.2219339120

Seath, C.P.*, Burton, A.J.*, Sun, X.; Lee, G.; Kleiner, R. E.; MacMillan, D. W. C.; Muir, T. W. Tracking chromatin state changes using nanoscale photo-proximity labelling. Nature 2023 616, 574-580 doi: 10.1038/s41586-023-05914-y

2022

Lukasak, B. J.; Mitchener, M. M.; Kong, L.; Dul, B. E.; Lazarus, C. D.; Ramakrishnan, A.; Ni, J.; Shen, L.; Maze, I.; Muir, T. W. TGM2-mediated histone transglutamination is dictated by steric accessibility. Proceedings of the National Academy of Sciences 2022, 119 (43), e2208672119.

Sekar, G.; Stevens,A. J.; Mostafavi, A. Z.; Sashi, P.; Muir, T. W.; Cowburn, D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J. Am. Chem. Soc. 2022144 (41), 19196-19203 doi: 10.1021/jacs.2c08985

Mitchener, M. M.; Muir, T. M. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation. Mol. Cell, 2022. 82(16): 2925-2938. doi: 10.1016/j.molcel.2022.07.008

Zhao, A.*; Bodine, S. P.*; Xie, Q.; Wang, B.; Ram, G.; Novick, R.P.; Muir, T. W. Reconstitution of the S. aureus agr quorum sensing pathway reveals a direct role for the integral membrane protease MroQ in pheromone biosynthesis. Proc. Natl. Acad. Sci. USA.2022. 119(33): e2202661119. doi: 10.1073/pnas.2202661119

Park, S.; Mitchener, M. M.; Dao, H. T.; Muir, T. W.; Ha, T. Biophysical driving forces of heterochromatin organization. Biophys. J. 2022. 121(3): 159a. doi: 10.1016/j.bpj.2021.11.1926

Lukasak, B. J.*; Thompson, R. E.*; Mitchener, M. M.; Feng, V. J.; Bagert, J. D.; Muir, T. W. A Genetically Encoded Approach for Breaking Chromatin Symmetry. ACS. Cent. Sci. 2022. 8(2): 176-183. doi: 10.1021/acscentsci.1c01332

Dao, H. T.*; Liu, H.*; Mashtalir, N.; Kadoch, C.; Muir, T. W. Synthesis of Oriented Hexasomes and Asymmetric Nucleosomes Using a Template Editing Process. J. Am. Chem. Soc. 2022. 144(5): 2284-2291. doi: 10.1021/jacs.1c12420

2021

Burton, A. J.; Hamza, G. M.; Zhang, A. X.; Muir, T. W. Chemical biology approaches to study histone interactors. Biochem. Soc. Trans.2021. 49(5): 2431-2441. doi: 10.1042/BST20210772

Mitchener, M. M.; Muir, T. M. Janus Bioparticles: Asymmetric Nucleosomes and Their Preparation Using Chemical Biology Approaches. Acc. Chem. Res,2021. 54(16): 3215-3227. doi:doi.org/10.1021/acs.accounts.1c00313[pdf]

Mashtalir, N.*; Dao, H. T.*; Sankar, A.; Liu, H.; Corin, A.J.; Bagert, J. D.; Ge, E. J.; D’Avino, A. R.; Filipovski, M.; Michel, B. C.; Dann, G. P.; Muir, T. M.; Kadoch, C. Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes. Science.2021. 373(6552):306-315. doi: 10.1126/science.abf8705.

Hananya, N.; Daley, S.; Bagert, J. D.; Muir, T. W.; Synthesis of ADP-Ribosylated Histones Reveals Site-Specific Impacts on Chromatin Structure and Function. J. Am. Chem. Soc. 2021. 143(29): 10847-10852. doi: doi.org/10.1021/jacs.1c05429.

Wu, A.; Zhi, J.; Tian, T.; Cihan, A.; Cevher, M. A.; Liu, Z.; David, Y.; Muir, T. W.; Roeder, R. G.; Yu, M. DOT1L complex regulates transcriptional initiation in human erythroleukemic cells. Proc Natl Acad Sci U S A. 2021. 118(27), e2106148118. doi:10.1073/pnas.2106148118

Bagert, J. D., & Muir, T. W. Molecular Epigenetics: Chemical Biology Tools Come of Age. Annual Review of Biochemistry, 2021. 90(1), 287-320. doi:10.1146/annurev-biochem-080120-021109

Naismith JH, Song H, Burton AJ, Shirran SL, Fahrig-Kamarauskaitė J, Kaspar H, Muir TW, Künzler M. Engineering of a peptide α-N-methyltransferase to methylate non-proteinogenic amino acids. Angew Chem Int Ed Engl. 2021 Apr 15. doi: 10.1002/anie.202100818

Bagert JD*, Mitchener MM*, Patriotis AL**, Dul BE**, Wojcik F, Nacev BA, Feng L, Allis CD, Muir TW. Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat Chem Biol. 2021 Apr;17(4):403-411. doi: 10.1038/s41589-021-00738-1

Zhao S*, Chuh KN*, Zhang B, Dul BE, Thompson RE, Farrelly LA, Liu X, Xu N, Xue Y, Roeder RG, Maze I, Muir TW, Li H. Histone H3Q5 serotonylation stabilizes H3K4 methylation and potentiates its readout. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2016742118. doi: 10.1073/pnas.2016742118

Seath CP , Trowbridge AD , Muir TW , MacMillan DWC . Reactive intermediates for interactome mapping. Chem Soc Rev. 2021 Mar 7;50(5):2911-2926. doi: 10.1039/d0cs01366h

2020

Leicher, R.; Ge, E.J.; Lin, X.; Reynolds, M.J.; Xie, W.; Walz, T.; Zhang, B.; Muir, T.W.; Liu, S. “Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin.” Proc Natl Acad Sci USA. 2020. 117(48) 30465-30475. doi: 10.1073/pnas.2003395117

Xu, G.; van Bruggen, R.; Gualtieri, C.O.; Moragin, N.; Fois, A.; Vallerand, D.; De Sa Tavares Russo, M.; Bassenden, A.; Lu, W.; Tam, M.; Lesage, S.; Girouard, H.; Avizonis, D.Z.; Deblois, G.; Prchal, J.T.; Stevenson, M.; Berghuis, A.; Muir, T.W.; Rabinowitz, J.D.; Vidal, S.M.; Fodil, N.; Gros, P. “Bisphosphoglycerate Mutase Deficiency Protects against Cerebral Malaria and Severe Malaria-Induced Anemia.” Cell Rep.2020. 32(12), 108170. doi: 10.1016/j.celrep.2020.108170

Xie, Q.; Wiedmann, M.M.; Zhao, A.; Pagan, I.R.; Novick, R.P.; Suga, H.; Muir, T.W. “Discovery of quorum quenchers targeting the membrane-embedded sensor domain of the Staphylococcus aureus receptor histidine kinase, AgrC.” Chem. Commun.2020. 56(76), 11223-11226. doi: 10.1039/d0cc04873a

McBride, M.J.*; Mashtalir, N.*; Winter, E.B.; Dao, H.T.; Filipovski, M.; D’Avino, A.R.; Seo, H.S.; Umbreit, N.T.; St. Pierre, R.; Valencia, A.M.; Qian, K.; Zullow, H.J.; Jaffe, J.D.; Dhe-Paganon, S.; Muir, T.W.; Kadoch, C. “The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.” Nat Struct. Mol. Biol.2020. 27(9), 836-845. doi: 10.1038/s41594-020-0466-9

Burton, A.J.; Haugbro, M.; Gates, L.A.; Bagert, J.D.; Allis, C.D.; Muir, T.W. “In situ chromatin interactomics using a chemical bait and trap approach.” Nat. Chem. 2020. 12, 520–527. doi: 10.1038/s41557-020-0474-8

Diehl, K.L.; Muir, T.W. “Chromatin as a key consumer in the metabolite economy.” Nat. Chem. Biol. 2020. 16, 620–629. doi: 10.1038/s41589-020-0517-x

Burton, A.J.*; Haugbro, M.*; Parisi, E.; Muir, T.W. “Live-cell protein engineering with an ultra-short split intein.” Proc. Natl. Acad. Sci. USA.2020. 117(22), 12041–12049. doi: 10.1073/pnas.2003613117

Kwon, M.; Park, K.; Hyun, K.; Lee, J.H.; Zhou, L.; Cho, Y.W.; Ge, K.; Skalnik, D.G.; Muir, T.W.; Kim, J. “H2B ubiquitylation enhances H3K4 methylation activities of human KMT2 family complexes.” Nucleic Acids Res. 2020. 48(10), 5442–5456. doi: 10.1093/nar/gkaa317

Wan, L.; Chong, S.; Xuan, F.; Liang, A.; Cui, X.; Gates, L.; Carroll, T.S.; Li, Y.; Feng, L.; Chen, G.; Wang, S.P.; Ortiz, M.V.; Daley, S.K.; Wang, X.; Xuan, H.; Kentsis, A.; Muir, T.W.; Roeder, R.G.; Li, H.; Li, W.; Tjian, R.; Wen, H.; Allis, C.D. “Impaired cell fate through gain-of-function mutations in a chromatin reader.” Nature.2020. 577(7788), 121-126. doi: 10.1038/s41586-019-1842-7

Murawska, M.; Schauer, T.; Matsuda, A.; Wilson, M.D.; Pysik, T.; Wojcik, F.; Muir, T.W.; Hiraoka, Y.; Straub, T.; Ladurner, A.G. “The Chaperone FACT and Histone H2B Ubiquination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions.” Mol. Cell.2020. 77(3), 501-513.e7. doi: 10.1016/j.molcel.2019.11.016

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

Thompson, R.E.; Muir, T.W. “Chemoenzymatic Semisynthesis of Proteins.” Chem Rev. 2020. 120(6), 3051-3126. doi: 10.1021/acs.chemrev.9b00450

2019

Albig, C.; Wang, C.; Dann, G.P.; Wojcik, F.; Schauer, T.; Krause, S.; Maenner, S.; Cai, W.; Li, Y.; Girton, J.; Muir, T.W.; Johansen, H.; Johansen, K.M.; Becker, P.B.; Regnard, C. “JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila.” Nat. Commun. 2019. 10(1), 5343. doi: 10.1038/s41467-019-13174-6

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

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

Guerra, L.F.; Muir, T.W.; Yang, H. “Single-Particle Dynamic Light Scattering: Shapes of Individual Nanoparticles.” Nano Lett.2019. 19(8), 5530-5536. doi: 10.1021/acs.nanolett.9b02066

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

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

Jain, S.U.; Do, T.J.; Lund, P.J.; Rashoff, A.Q.; Diehl, K.L.; Cieslik, M; Bajic, A.; Juretic, N.; Deshmukh, S.; Venneti, S.; Muir, T.W.; Garcia, B.A.; Jabado, N.; Lewis, P.W. “PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism.” Nat. Commun.2019. doi: 10.1038/s41467-019-09981-6

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

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

Liszczak, G. and Muir, T.W. “Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter.” Angew Chem Int Ed. 2019, 58, 2-21. doi: 10.1002/anie.201808956

2018

Stevens, A.J.; Sekar, G.; Gramespacher, J.A.; Cowburn, D.; Muir, T.W. “An Atypical Mechanism of Split Intein Molecular Recognition and Folding.” J Am Chem Soc. 2018, 140(37), 11791-11799. doi: 10.1021/jacs.8b07334

Liszczak, G.*; Diehl, K.L.*; Dann, G.P.; Muir, T.W. “Acetylation blocks DNA damage-induced chromatin ADP-ribosylation.” Nat. Chem. Biol. 2018, 14(9), 837-840. doi: 10.1038/s41589-018-0097-1

Jeon, J.; McGinty, R.K.; Muir, T.W.; Kim, J.A.; Kim, J. “Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation.” Nucleic Acids Res. 2018, 46(21), 11129-11143. doi: 10.1093/nar/gky920

Wojcik F, Dann GP, Beh LY, Debelouchina GT, Hofmann R, Muir TW. Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat Commun. 2018 Apr 11;9(1):1394. doi: 10.1038/s41467-018-03895-5

Bos J, Muir TW. A Chemical Probe for Protein Crotonylation. J Am Chem Soc. 2018 Apr 11;140(14):4757-4760. doi: 10.1021/jacs.7b13141

Jenness C, Giunta S, Müller MM, Kimura H, Muir TW, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):E876-E885. doi:10.1073/pnas.1717509115.

2017

Debelouchina GT, Muir TW. A molecular engineering toolbox for the structural biologist. Q Rev Biophys. 2017 Jan;50:e7. doi: 10.1017/S0033583517000051.

Gramespacher JA, Stevens AJ, Thompson RE, Muir TW. Improved protein splicing using embedded split inteins. Protein Sci. 2017 Dec 11. doi: 10.1002/pro.3357.

Wang X, Paucek RD, Gooding AR, Brown ZZ, Ge EJ, Muir TW, Cech TR. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017 Dec;24(12):1028-1038. doi: 10.1038/nsmb.3487.

Oslund RC*, Su X*, Haugbro M*, Kee JM, Esposito M, David Y, Wang B, Ge E, Perlman DH, Kang Y, Muir TW, Rabinowitz JD. Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate. Nat Chem Biol. 2017 Oct;13(10):1081-1087. doi: 10.1038/nchembio.2453.

Dann GP, Liszczak GP, Bagert JD, Müller MM, Nguyen UTT, Wojcik F, Brown ZZ, Bos J, Panchenko T, Pihl R, Pollock SB, Diehl KL, Allis CD, Muir TW. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature. 2017 Aug 31;548(7669):607-611. doi: 10.1038/nature23671.

Winer BY, Huang TS, Pludwinski E, Heller B, Wojcik F, Lipkowitz GE, Parekh A, Cho C, Shrirao A, Muir TW, Novik E, Ploss A. Long-term hepatitis B infection in a scalable hepatic co-culture system. Nat Commun. 2017 Jul 25;8(1):125. doi: 10.1038/s41467-017-00200-8.

Stevens AJ, Sekar G, Shah NH, Mostafavi AZ, Cowburn D, Muir TW. A promiscuous split intein with expanded protein engineering applications. Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8538-8543. doi: 10.1073/pnas.1701083114.

David Y, Muir TW. Emerging Chemistry Strategies for Engineering Native Chromatin. J Am Chem Soc. 2017 Jul 12;139(27):9090-9096. doi: 10.1021/jacs.7b03430.

Gramespacher JA, Stevens AJ, Nguyen DP, Chin JW, Muir TW. Intein Zymogens: Conditional Assembly and Splicing of Split Inteins via Targeted Proteolysis. J Am Chem Soc. 2017 Jun 21;139(24):8074-8077. doi: 10.1021/jacs.7b02618.

Kim MK, Zhao A, Wang A, Brown ZZ, Muir TW, Stone HA, Bassler BL. Surface-attached molecules control Staphylococcus aureus quorum sensing and biofilm development. Nat Microbiol. 2017 May 22;2:17080. doi: 10.1038/nmicrobiol.2017.80.

Liszczak GP, Brown ZZ, Kim SH, Oslund RC, David Y, Muir TW. Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):681-686. doi: 10.1073/pnas.1615723114.

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.

Debelouchina GT, Gerecht K, Muir TW. Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol. 2017 Jan;13(1):105-110. doi: 10.1038/nchembio.2235.

2016

Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW. Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. Science. 2016 May 13;352(6287):844-9.

Müller MM, Fierz B, Bittova L, Liszczak G, Muir TW. A two-state activation mechanism controls the histone methyltransferase Suv39h1. Nat Chem Biol. 2016 Mar;12(3):188-93. doi: 10.1038/nchembio.2008.

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. doi: 10.1021/jacs.5b13528.

Wang B, Muir TW. Regulation of Virulence in Staphylococcus aureus: Molecular Mechanisms and Remaining Puzzles. Cell Chem Biol. 2016 Feb 18;23(2):214-24. doi: 10.1016/j.chembiol.2016.01.004. Review.

Zhou L, Holt MT, Ohashi N, Zhao A, Müller MM, Wang B, Muir TW. Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation. Nat Commun. 2016 Feb 2;7:10589.

2015

Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res. 2015 Nov;25(11):1727-38. doi: 10.1101/gr.188516.114.

Wang B, Zhao A, Novick RP, Muir TW. Key driving forces in the biosynthesis of autoinducing peptides required for staphylococcal virulence. Proc Natl Acad Sci U S A. 2015 Aug 10. pii: 201506030

Holt MT, David Y, Pollock S, Tang Z, Jeon J, Kim J, Roeder RG, Muir TW. Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc Natl Acad Sci U S A. 2015 Aug 3. pii: 2015 04483

David Y, Vila-Perelló M, Verma S, Muir TW. Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat Chem. 2015 May;7(5):394-402

Brown ZZ, Müller MM, Kong HE, Lewis PW, Muir TW. Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin. Angew Chem Int Ed Engl. 2015 May 26;54(22):6457-61

Johnson JG, Wang B, Debelouchina GT, Novick RP, Muir TW. Increasing AIP Macrocycle Size Reveals Key Features of agr Activation in Staphylococcus aureus. Chembiochem. 2015 May 4;16(7):1093-100

Kee JM, Oslund RC, Couvillon AD, Muir TW.A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org Lett. 2015 Jan 16;17(2):187-9

Müller MM, Muir TW.Histones: at the crossroads of peptide and protein chemistry. Chem Rev. 2015 Mar 25;115(6):2296-349

2014

Brown ZZ, Müller MM, Jain SU, Allis CD, Lewis PW, Muir TW. Strategy for “detoxification” of a cancer-derived histone mutant based on mapping its interaction with the methyltransferase PRC2. J Am Chem Soc. 2014 Oct 1;136(39):13498-501

Oslund RC, Kee JM, Couvillon AD, Bhatia VN, Perlman DH, Muir TW. A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J Am Chem Soc. 2014 Sep 17;136(37):12899-911

Nguyen UT, Bittova L, Müller MM, Fierz B, David Y, Houck-Loomis B, Feng V, Dann GP, Muir TW. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods. 2014 Aug;11(8):834-40.

Eryilmaz, E., Shah, N.H., *Muir, T.W and *Cowburn, D. Structural and Dynamical Features of Inteins and Implications on Protein Splicing. J. Biol. Chem. 2014, May 23;289(21):14506-11.

Liu, Z., Frutos, S., Bick, M., Vila-Perello, M., Debelouchina, G.T., Darst, S.A. and *Muir, T.W. Structure of the Branched Intermediate in Protein Splicing. Proc. Natl. Acad. Sci. USA, 2014, Jun 10;111(23):8422-7.

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.

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

2013

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.

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.

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.

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.

Muir, T. W., Award Address (Arthur C. Cope Scholar Awards (CSM) sponsored by Arthur C. Cope Fund). Chromatin: An expansive canvas for chemical biology. Abstracts of Papers of the American Chemical Society 2013, 246.

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.

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.

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.

Kee, J.-M.; Oslund, R. C.; Perlman, D. H.; Muir, T. W., A pan-specific antibody for direct detection of protein histidine phosphorylation. Nature Chemical Biology 2013, 9 (7), 416-U28.

Casadio, F.; Lu, X.; Pollock, S. B.; LeRoy, G.; Garcia, B. A.; Muir, T. W.; Roeder, R. G.; Allis, C. D., H3R42me2a is a histone modification with positive transcriptional effects. Proceedings of the National Academy of Sciences of the United States of America 2013, 110 (37), 14894-14899.

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.

2012

Whitcomb, S. J.; Fierz, B.; McGinty, R. K.; Holt, M.; Ito, T.; Muir, T. W.; Allis, C. D., Histone Monoubiquitylation Position Determines Specificity and Direction of Enzymatic Cross-talk with Histone Methyltransferases Dot1L and PRC2. Journal of Biological Chemistry 2012, 287 (28), 23718-23725.

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.

Muir, T. W., Chromatin: An Expansive Canvas for Chemical Biology. Journal of Peptide Science 2012, 18, S20-S21.

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

Geisinger, E.; George, E. A.; Chen, J.; Muir, T. W.; Novick, R. P., Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor. (vol 283, pg 8930, 2008). Journal of Biological Chemistry 2012, 287 (22), 18588-18588.

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

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.

Brown, Z. Z.; Muir, T. W., From EPOthilone to EPO: A challenge for natural product synthesis. Proceedings of the National Academy of Sciences of the United States of America 2012, 109 (19), 7134-7135.

2011

Singla, N.; Erdjument-Bromage, H.; Himanen, J. P.; Muir, T. W.; Nikolov, D. B., A Semisynthetic Eph Receptor Tyrosine Kinase Provides Insight into Ligand-Induced Kinase Activation. Chemistry & Biology 2011, 18 (3), 361-371.

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.

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.

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.

Jarraud, S.; Lyon, G. J.; Figueiredo, A. M. S.; Lina, G.; Vandenesch, F.; Etienne, J.; Muir, T. W.; Novick, R. P., Exfoliatin-Producing Strains Define a Fourth agr Specificity Group in Staphylococcus aureus (vol 182, pg 6517, 2000). Journal of Bacteriology 2011, 193 (24), 7027-7027.

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.

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.

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.

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

2010

Vila-Perello, M.; Muir, T. W., Biological Applications of Protein Splicing. Cell 2010, 143 (2), 191-200.

Scheuermann, J. C.; Alonso, A. G. d. A.; Oktaba, K.; Ly-Hartig, N.; McGinty, R. K.; Fraterman, S.; Wilm, M.; Muir, T. W.; Mueller, J., Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 2010, 465 (7295), 243-U138.

Muir, T. W.; McGinty, R.; Chatterjee, D., Testing the ‘Histone Code’ Hypothesis Using Synthesis. Journal of Peptide Science 2010, 16, 22-22.

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.

Kee, J.-M.; Villani, B.; Carpenter, L. R.; Muir, T. W., Development of Stable Phosphohistidine Analogues. Journal of the American Chemical Society 2010, 132 (41), 14327-14329.

Frutos, S.; Goger, M.; Giovani, B.; Cowburn, D.; Muir, T. W., Branched intermediate formation stimulates peptide bond cleavage in protein splicing. Nature Chemical Biology 2010, 6 (7), 527-533.

Chatterjee, C.; Muir, T. W., Chemical Approaches for Studying Histone Modifications. Journal of Biological Chemistry 2010, 285 (15), 11045-11050.

Chatterjee, C.; McGinty, R. K.; Fierz, B.; Muir, T. W., Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nature Chemical Biology 2010, 6 (4), 267-269.

2009

Pratt, M. R.; Sekedat, M. D.; Chiang, K. P.; Muir, T. W., Direct Measurement of Cathepsin B Activity in the Cytosol of Apoptotic Cells by an Activity-Based Probe. Chemistry & Biology 2009, 16 (9), 1001-1012.

Novick, R. P.; Geisinger, E.; Cisar, E. G.; Muir, T. W., Symmetrical Signaling in Asymmetric AgrC Heterodimers in Staphylococcus aureus. Abstracts of the General Meeting of the American Society for Microbiology 2009, 109.

Muir, T. W., Non-natural amino acids. Preface. Methods in enzymology 2009, 462, xiii-xv.

Muir, T. W., Chemical Biology in a Time of Transition. Acs Chemical Biology 2009, 4 (4), 241-243.

McGinty, R. K.; Koehn, M.; Chatterjee, C.; Chiang, K. P.; Pratt, M. R.; Muir, T. W., Structure-Activity Analysis of Semisynthetic Nucleosomes: Mechanistic Insights into the Stimulation of Dot1L by Ubipuitylated Histone H2B. Acs Chemical Biology 2009, 4 (11), 958-968.

McGinty, R. K.; Chatterjee, C.; Muir, T. W., SEMISYNTHESIS OF UBIQUITYLATED PROTEINS. In Methods in Enzymology: Non-Natural Amino Acids, Muir, T. W.; Abelson, J. N., Eds. 2009; Vol. 462, pp 225-243.

McGinty, R.; Chatterjee, C.; Muir, T. W., TESTING THE “HISTONE CODE” HYPOTHESIS USING SYNTHESIS. Biopolymers 2009, 92 (4), 295-295.

Lockless, S. W.; Muir, T. W., Traceless protein splicing utilizing evolved split inteins. Proceedings of the National Academy of Sciences of the United States of America 2009, 106 (27), 10999-11004.

Kim, J.; Guermah, M.; McGinty, R. K.; Lee, J.-S.; Tang, Z.; Milne, T. A.; Shilatifard, A.; Muir, T. W.; Roeder, R. G., RAD6-Mediated Transcription-Coupled H2B Ubiquitylation Directly Stimulates H3K4 Methylation in Human Cells. Cell 2009, 137 (3), 459-471.

George Cisar, E. A.; Geisinger, E.; Muir, T. W.; Novick, R. P., Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC. Molecular microbiology 2009, 74 (1), 44-57.

Geisinger, E.; Muir, T. W.; Novick, R. P., agr receptor mutants reveal distinct modes of inhibition by staphylococcal autoinducing peptides. Proceedings of the National Academy of Sciences of the United States of America 2009, 106 (4), 1216-1221.

Flavell, R. R.; Muir, T. W., Expressed Protein Ligation (EPL) in the Study of Signal Transduction, Ion Conduction, And Chromatin Biology. Accounts of Chemical Research 2009, 42 (1), 107-116.

Cisar, E. A. G.; Geisinger, E.; Muir, T. W.; Novick, R. P., Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC. Molecular Microbiology 2009, 74 (1), 44-57.

Chiang, K. P.; Jensen, M. S.; McGinty, R. K.; Muir, T. W., A Semisynthetic Strategy to Generate Phosphorylated and Acetylated Histone H2B. Chembiochem 2009, 10 (13), 2182-2187.

Chatterjee, C.; McGinty, R. K.; Fierz, B.; Muir, T. W., Interrogating the histone ubiquitylation mark by semisynthesis. Abstracts of Papers of the American Chemical Society 2009, 238.

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.; Friedman, J. M., PET Imaging of Leptin Biodistribution and Metabolism in Rodents and Primates. Cell Metabolism 2009, 10 (2), 148-U7.

Averette, K. M.; Pratt, M. R.; Yang, Y.; Bassilian, S.; Whitelegge, J. P.; Loo, J. A.; Muir, T. W.; Bradley, K. A., Anthrax Lethal Toxin Induced Lysosomal Membrane Permeabilization and Cytosolic Cathepsin Release Is Nlrp1b/Nalp1b-Dependent. Plos One 2009, 4 (11).

2008

Vila-Perello, M.; Hori, Y.; Ribo, M.; Muir, T. W., Activation of protein splicing by protease- or light-triggered O to N acyl migration. Angewandte Chemie-International Edition 2008, 47 (40), 7764-7767.

Tyszkiewicz, A. B.; Muir, T. W., Activation of protein splicing with light in yeast. Nature Methods 2008, 5 (4), 303-305.

Singla, N.; Himanen, J. P.; Muir, T. W.; Nikolov, D. B., Toward the semisynthesis of multidomain transmembrane receptors: Modification of Eph tyrosine kinases. Protein Science 2008, 17 (10), 1740-1747.

Schwartz, E. C.; Shekhtman, A.; Dutta, K.; Pratt, M. R.; Cowburn, D.; Darst, S.; Muir, T. W., A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding. Chemistry & Biology 2008, 15 (10), 1091-1103.

Ottesen, J. J.; Bar-Dagan, M.; Giovani, B.; Muir, T. W., An amalgamation of solid phase peptide synthesis and ribosomal peptide synthesis. Biopolymers 2008, 90 (3), 406-414.

Muir, T. W.; McGinty, R.; Pratt, M.; Chatterjee, C.; Schwartz, E., Making and Breaking Ubiquitin. Faseb Journal 2008, 22.

Muir, T. W., Studying Protein Structure and Function Using Semisynthesis. Biopolymers 2008, 90 (6), 743-750.

McGinty, R. K.; Kim, J.; Chatterjee, C.; Roeder, R. G.; Muir, T. W., Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature 2008, 453 (7196), 812-U12.

McGinty, R.; Chatterjee, C.; Muir, T. W., BIOL 106-Testing the “Histone Code” hypothesis using synthesis. Abstracts of Papers of the American Chemical Society 2008, 236.

Kent, S. B. H.; Muir, T. W.; Dawson, P. E. Synthesis of proteins by native chemical ligation. US 07408026, Aug 5 2008, 2008.

George, E. A.; Novick, R. P.; Muir, T. W., Cyclic peptide inhibitors of staphylococcal virulence prepared by Fmoc-based thiolactone peptide synthesis. Journal of the American Chemical Society 2008, 130 (14), 4914-4924.

Geisinger, E.; George, E. A.; Muir, T. W.; Novick, R. P., Identification of Ligand Specificity Determinants in AgrC, the S. aureus Quorum Sensing Receptor. Abstracts of the General Meeting of the American Society for Microbiology 2008, 108, 294-294.

Geisinger, E.; George, E. A.; Muir, T. W.; Novick, R. P., Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor. Journal of Biological Chemistry 2008, 283 (14), 8930-8938.

Flavell, R. R.; Kothari, P.; Bar-Dagan, M.; Synan, M.; Vallabhajosula, S.; Friedman, J. M.; Muir, T. W.; Ceccarini, G., Site-specific F-18-labeling of the protein hormone leptin using a general two-step ligation procedure. Journal of the American Chemical Society 2008, 130 (28), 9106-9112.

Chiang, K. P.; Muir, T. W., Systems- and Molecular-Level Elucidation of Signaling Processes Through Chemistry. Science Signaling 2008, 1 (42).

Vila-Perello, M.; Pratt, M. R.; Tulin, F.; Muir, T. W., Covalent capture of phospho-dependent protein oligomerization by site-specific incorporation of a diazirine photo-cross-linker. Journal of the American Chemical Society 2007, 129 (26), 8068-+.

2007

Valiyaveetil, F. I.; Sekedat, M.; Leonetti, M.; Mackinnon, R.; Muir, T. W., The ins and outs of K+ channels revealed through synthesis. Biopolymers 2007, 88 (4), 525-525.

Schwartz, E. C.; Saez, L.; Young, M. W.; Muir, T. W., Post-translational enzyme activation in an animal via optimized conditional protein splicing. Nature Chemical Biology 2007, 3 (1), 50-54.

Pratt, M. R.; Schwartz, E. C.; Muir, T. W., Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt. Proceedings of the National Academy of Sciences of the United States of America 2007, 104 (27), 11209-11214.

Muir, T. W., BIOL 7-Site specific histone ubiquitylation. Abstracts of Papers of the American Chemical Society 2007, 234.

Hahn, M. E.; Pellois, J.-P.; Vila-Perello, M.; Muira, T. W., Tunable photoactivation of a post-translationally modified signaling protein and its unmodified counterpart in live cells. Chembiochem 2007, 8 (17), 2100-2105.

George, E. A.; Muir, T. W., Molecular mechanisms of agr quorum sensing in virulent staphylococci. Chembiochem 2007, 8 (8), 847-855.

Chatterjee, C.; McGinty, R. K.; Pellois, J.-P.; Muir, T. W., Auxiliary-mediated site-specific peptide ubiquitylation. Angewandte Chemie-International Edition 2007, 46 (16), 2814-2818.

2006

Valiyaveetil, F. I.; Sekedat, M.; MacKinnon, R.; Muir, T. W., Structural and functional consequences of an amide-to-ester substitution in the selectivity filter of a potassium channel. Journal of the American Chemical Society 2006, 128 (35), 11591-11599.

Valiyaveetil, F. I.; Leonetti, M.; Muir, T. W.; MacKinnon, R., Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. Science 2006, 314 (5801), 1004-1007.

Pellois, J.-P.; Muir, T. W., Semisynthetic proteins in mechanistic studies: using chemistry to go where nature can’t. Current Opinion in Chemical Biology 2006, 10 (5), 487-491.

Muralidharan, V.; Muir, T. W., Protein ligation: an enabling technology for the biophysical analysis of proteins. Nature Methods 2006, 3 (6), 429-438.

Muralidharan, V.; Dutta, K.; Cho, J.; Vila-Perello, M.; Raleigh, D. P.; Cowburn, D.; Muir, T. W., Solution structure and folding characteristics of the C-terminal SH3 domain of c-Crk-II. Biochemistry 2006, 45 (29), 8874-8884.

Muir, T. W., Chemical biology – Cutting out the middle man. Nature 2006, 442 (7102), 517-518.

2005

Tyszkiewicz, A. B.; Muir, T. W., Light-activated protein splicing. Biopolymers 2005, 80 (4), 545-545.

Shi, J. X.; Muir, T. W., Development of a tandem protein trans-splicing system based on native and engineered split inteins. Journal of the American Chemical Society 2005, 127 (17), 6198-6206.

Schwartz, E. C.; Saez, L.; Young, M. W.; Muir, T. W., Rapid in vivo control of enzyme function through Conditional Protein Splicing. Biopolymers 2005, 80 (4), 544-544.

Pratt, M. R.; Muir, T. W., Small molecule mediated, targeted protein degradation using conditional protein splicing. Biopolymers 2005, 80 (4), 601-601.

Pellois, J. P.; Muir, T. W., Photo-control of the activity, concentration, and localization of proteins in live cells. Biopolymers 2005, 80 (4), 519-519.

Pellois, J. P.; Muir, T. W., A Ligation and photorelease strategy for the temporal and spatial control of protein function in living cells. Angewandte Chemie-International Edition 2005, 44 (35), 5713-5717.

Ottesen, J. J.; Muir, T. W., Synthesis of artificial FG-nucleoporins by solid phase chemical ligation. Biopolymers 2005, 80 (4), 525-525.

Muir, T. W.; Cole, P. A.; Sondhi, D.; Severinov, K. Methods of ligating expressed proteins. US 06875594, Apr 5 2005, 2005.

Muir, T. W., 2005 Irving Sigal Young Investigator Award. Protein science : a publication of the Protein Society 2005, 14 (12), 3140-4.

Hahn, M. E.; Pellois, J. P.; Muir, T. W., Photoactivation of signal transduction in live cells and animals. Biopolymers 2005, 80 (4), 545-545.

Hahn, M. E.; Muir, T. W., Manipulating proteins with chemistry: a cross-section of chemical biology. Trends in Biochemical Sciences 2005, 30 (1), 26-34.

George, E. A.; Wright, J. S.; Novick, R. P.; Muir, T. W., Synthesis of dimeric quorum sensing peptides to probe virulence in S. aureus. Biopolymers 2005, 80 (4), 541-541.

Flavell, R. R.; Ceccarini, G.; Giriat, I.; Friedman, J. M.; Muir, T. W., Towards better weight loss by engineering leptin using Expressed Protein Ligation (EPL). Biopolymers 2005, 80 (4), 520-520.

2004

Wright, J. S.; Lyon, G. J.; George, E. A.; Muir, T. W.; Novick, R. P., Hydrophobic interactions drive ligand-receptor recognition for activation and inhibition of staphylococcal quorum sensing. Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (46), 16168-16173.

Valiyaveetil, F. I.; Sekedat, M.; Muir, T. W.; MacKinnon, R., Why are glycine residues absolutely conserved in the selectivity filter of potassium channels? Biophysical Journal 2004, 86 (1), 130A-130A.

Valiyaveetil, F. I.; Sekedat, M.; Muir, T. W.; MacKinnon, R., Semisynthesis of a functional K+ channel. Angewandte Chemie-International Edition 2004, 43 (19), 2504-2507.

Valiyaveetil, F. I.; Sekedat, M.; MacKinnon, R.; Muir, T. W., Glycine as a D-amino acid surrogate in the K+-selectivity filter. Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (49), 17045-17049.

Tyszkiewicz, A. B.; Muir, T. W., Expanding the flexibility of the conditional protein splicing system. Protein Science 2004, 13, 158-158.

Shi, J.; Muir, T. W., Protein trans-splicing mediated segmental isotopic labeling for NMR analysis. Protein Science 2004, 13, 155-155.

Sekedat, M.; Valiyaveetil, F.; MacKinnon, R.; Muir, T. W., The semisynthesis of the potassium channel KcsA. 2004; p 276-277.

Schwartz, E. C.; Shekhtman, A.; Darst, S. A.; Cowburn, D.; Muir, T. W., Segmental isotopic labeling of RNA polymerase for NMR studies. 2004; p 466-467.

Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T. W., Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (17), 6397-6402.

Pellois, J. P.; Hahn, M. E.; Muir, T. W., Simultaneous triggering of protein activity, and fluorescence. Journal of the American Chemical Society 2004, 126 (23), 7170-7171.

Ottesen, J. J.; Muir, T. W., Design of bisubstrate inhibitors for the T beta RI kinase. Protein Science 2004, 13, 144-144.

Ottesen, J. J.; Huse, M.; Sekedat, M. D.; Muir, T. W., Semisynthesis of phosphovariants of Smad2 reveals a substrate preference of the activated T beta RI kinase. Biochemistry 2004, 43 (19), 5698-5706.

Muralidharan, V.; Cho, J. H.; Trester-Zedlitz, M.; Kowalik, L.; Chait, B. T.; Raleigh, D. P.; Muir, T. W., Domain-specific incorporation of noninvasive optical probes into recombinant proteins. Journal of the American Chemical Society 2004, 126 (43), 14004-14012.

Muralidharan, V.; Cho, J.; Trester-Zedlitz, M.; Kowalik, L.; Chait, B. T.; Raleigh, D. P.; Muir, T. W., Domain specific incorporation of tryptophan analogues into multi-domain proteins. Protein Science 2004, 13, 159-159.

Muir, T. W., Chemical biology of protein splicing. Abstracts of Papers of the American Chemical Society 2004, 227, U45-U45.

Muir, T. W., Chemical biology of protein splicing. Abstracts of Papers of the American Chemical Society 2004, 228, U211-U211.

Mootz, H. D.; Blum, E. S.; Muir, T. W., Activation of an autoregulated protein kinase by conditional protein splicing. Angewandte Chemie-International Edition 2004, 43 (39), 5189-5192.

Hahn, M. E.; Muir, T. W., Photocontrol of Smad2, a multiphosphorylated cell-signaling protein, through caging of activating phosphoserines. Angewandte Chemie-International Edition 2004, 43 (43), 5800-5803.

Cowburn, D.; Shekhtman, A.; Xu, R.; Ottesen, J. J.; Muir, T. W., Segmental isotopic labeling for structural biological applications of NMR. Methods in molecular biology (Clifton, N.J.) 2004, 278, 47-56.

Blum, E. S.; Mootz, H. D.; Giriat, I.; Romanelli, A.; Shekhtman, A.; Muir, T. W., The chemical biology of protein splicing. 2004; p 269-275.

2003

Trester-Zedlitz, M.; Kamada, K.; Burley, S. K.; Fenyo, D.; Chait, B. T.; Muir, T. W., A modular cross-linking approach for exploring protein interactions. Journal of the American Chemical Society 2003, 125 (9), 2416-2425.

Sekedat, M.; Valiyaveetil, F.; MacKinnon, R.; Muir, T. W., Semisynthesis of the potassium channel KcsA. Biopolymers 2003, 71 (3), 364-365.

Schwartz, E. C.; Shekhman, A.; Darst, S. A.; Cowburn, D.; Muir, T. W., Segmental isotopic labeling of bacterial RNA polymerase for NMR studies. Biopolymers 2003, 71 (3), 315-315.

Schwartz, E. C.; Muir, T. W.; Tyszkiewicz, A. B., “The splice is right”: how protein splicing is opening new doors in protein science. Chemical Communications 2003, (17), 2087-2090.

Pellois, J. P.; Hahn, M. E.; Muir, T. W., Photo-control of the activity of proteins via caging of their C-terminus. Biopolymers 2003, 71 (3), 352-352.

Ottesen, J. J.; Blaschke, U. K.; Cowburn, D.; Muir, T. W., Segmental isotopic labeling: Prospects for a new tool to study the structure-function relationships in multi-domain proteins. In Protein NMR for the millennium, Krishna, N. R.; Berliner, L. J., Eds. 2003; Vol. Volume 20, pp 35-51.

Muir, T. W., Semisynthesis of proteins by expressed protein ligation. In Annual Review of Biochemistry. Volume 72, Richardson, C. C., Ed. 2003; Vol. Volume 72, pp 249-289.

Muir, T. W., From protein semisythesis to chemical genetics: The chemical biology of protein splicing. Biopolymers 2003, 71 (3), 280-280.

Muir, T. W., Semisynthesis of proteins by expressed protein ligation. Annual Review of Biochemistry 2003, 72, 249-289.

Muir, T. W., From protein semisynthesis to chemical genetics: the chemical biology of protein splicing. FASEB Journal 2003, 17 (4-5), Abstract No. 115.2-Abstract No. 115.2.

Muir, T. W., Turning virulence on and off in Staphylococci. Journal of Peptide Science 2003, 9 (10), 612-619.

Mootz, H. D.; Blum, E. S.; Tyszkiewicz, A. B.; Muir, T. W., Conditional protein splicing: A new tool to control protein structure and function in vitro and in vivo. Journal of the American Chemical Society 2003, 125 (35), 10561-10569.

Miller, J. S.; Dudkin, V. Y.; Lyon, G. J.; Muir, T. W.; Danishefsky, S. J., Toward fully synthetic N-linked glycoproteins. Angewandte Chemie-International Edition 2003, 42 (4), 431-+.

Lyon, G. J.; Muir, T. W., Chemical signaling among bacteria and its inhibition. Chemistry & Biology 2003, 10 (11), 1007-1021.

Giriat, I.; Muir, T. W., Protein semi-synthesis in living cells. Journal of the American Chemical Society 2003, 125 (24), 7180-7181. link

2002

Valiyaveetil, F. I.; MacKinnon, R.; Muir, T. W., Semisynthesis and folding of the potassium channel KcsA. Journal of the American Chemical Society 2002, 124 (31), 9113-9120. link

Mootz, H. D.; Muir, T. W., Protein splicing triggered by a small molecule. Journal of the American Chemical Society 2002, 124 (31), 9044-9045. link

Lyon, G. J.; Wright, J. S.; Muir, T. W.; Novick, R. P., Key determinants of receptor activation in the agr autoinducing peptides of Staphylococcus aureus. Biochemistry 2002, 41 (31), 10095-10104. link

Lyon, G. J.; Wright, J. S.; Christopoulos, A.; Novick, R. P.; Muir, T. W., Reversible and specific extracellular antagonism of receptor-histidine kinase signaling. Journal of Biological Chemistry 2002, 277 (8), 6247-6253. link

Hofmann, R. M.; Muir, T. W., Recent advances in the application of expressed protein ligation to protein engineering. Current Opinion in Biotechnology 2002, 13 (4), 297-303. link

Flavell, R. R.; Huse, M.; Goger, M.; Trester-Zedlitz, M.; Kuriyan, J.; Muir, T. W., Efficient semisynthesis of a tetraphosphorylated analogue of the type I TGF beta receptor. Organic Letters 2002, 4 (2), 165-168. link

Camarero, J. A.; Shekhtman, A.; Campbell, E. A.; Chlenov, M.; Gruber, T. M.; Bryant, D. A.; Darst, S. A.; Cowburn, D.; Muir, T. W., Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proceedings of the National Academy of Sciences of the United States of America 2002, 99 (13), 8536-8541. link

2001

Wu, J. W.; Hu, M.; Chai, J. J.; Seoane, J.; Huse, M.; Li, C.; Rigotti, D. J.; Kyin, S.; Muir, T. W.; Fairman, R.; Massague, J.; Shi, Y. G., Crystal structure of a phosphorylated Smad2: Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Molecular Cell 2001, 8 (6), 1277-1289. link

Minakhin, L.; Camarero, J. A.; Holford, M.; Parker, C.; Muir, T. W.; Severinov, K., Mapping the molecular interface between the σ⁷⁰ subunit of E. coli RNA polymerase and T4 AsiA. Journal of Molecular Biology 2001, 306 (4), 631-642. link

Huse, M.; Muir, T. W.; Xu, L.; Chen, Y. G.; Kuriyan, J.; Massague, J., The TGF beta receptor activation process: An inhibitor- to substrate-binding switch. Molecular Cell 2001, 8 (3), 671-682. link

Hofmann, R. M.; Cotton, G. J.; Chang, E. J.; Vidal, E.; Veach, D.; Bornmann, W.; Muir, T. W., Fluorescent monitoring of kinase activity in real time: Development of a robust fluorescence-based assay for abl tyrosine kinase activity. Bioorganic & Medicinal Chemistry Letters 2001, 11 (24), 3091-3094. link

Giriat, I.; Muir, T. W.; Perler, F. B., Protein splicing and its applications. Genetic Engineering: Principles and Methods 2001, 23, 171-99. link

Cowburn, D.; Muir, T. W., Segmental isotopic labeling using expressed protein ligation. Nuclear Magnetic Resonance of Biological Macromolecules, Pt B 2001, 339, 41-54. link

Camarero, J. A.; Muir, T. W., Native chemical ligation of polypeptides. Current protocols in protein science / editorial board, John E. Coligan … [et al.] 2001, Chapter 18, Unit 18.4-Unit 18.4.

Camarero, J. A.; Fushman, D.; Sato, S.; Giriat, I.; Cowburn, D.; Raleigh, D. P.; Muir, T. W., Rescuing a destabilized protein fold through backbone cyclization. Journal of Molecular Biology 2001, 308 (5), 1045-1062. link

Camarero, J. A.; Fushman, D.; Cowburn, D.; Muir, T. W., Peptide chemical ligation inside living cells: In vivo generation of a circular protein domain. Bioorganic & Medicinal Chemistry 2001, 9 (9), 2479-2484. link

2000

Merrifield, B., Barany, G., Deber, C.M., Goodman, M., Hodges, R.S., Hruby, V.J., Muir, T.W., Offord, R., Spatola, A.F., Veber, D.F. & Fields, G.B. (2000) Perspectives for the new peptide millennium. In G.B. Fields, J.P. Tam & G. Barany (Eds.), Peptides for the New Millennium. (pp. 797-804).

Lyon, G. J.; Mayville, P.; Muir, T. W.; Novick, R. P., Rational design of a global inhibitor of the virulence response in Staphylococcus aureus, based in part on localization of the site of inhibition to the receptor-histidine kinase, AgrC. Proceedings of the National Academy of Sciences of the United States of America 2000, 97 (24), 13330-13335. link

Jarraud, S.; Lyon, G. J.; Figueiredo, A. M. S.; Gerard, L.; Vandenesch, F.; Etienne, J.; Muir, T. W.; Novick, R. P., Exfoliatin-producing strains define a fourth agr specificity group in Staphylococcus aureus. Journal of Bacteriology 2000, 182 (22), 6517-6522. link

Cotton, G. J.; Muir, T. W., Generation of a dual-labeled fluorescence biosensor for Crk-II phosphorylation using solid-phase expressed protein ligation. Chemistry & Biology 2000, 7 (4), 253-261. link

Camarero, J. A.; Adeva, A.; Muir, T. W., 3-thiopropionic acid as a highly versatile multidetachable thioester resin linker. Letters in Peptide Science 2000, 7 (1), 17-21. link

Blaschke, U. K.; Silberstein, J.; Muir, T. W., Protein engineering by expressed protein ligation. Applications of Chimeric Genes and Hybrid Proteins, Pt C 2000, 328, 478-496. link

Blaschke, U. K.; Cotton, G. J.; Muir, T. W., Synthesis of multi-domain proteins using expressed protein ligation: Strategies for segmental isotopic labeling of internal regions. Tetrahedron 2000, 56 (48), 9461-9470. link

1999

Xu, R.; Ayers, B.; Cowburn, D.; Muir, T. W., Chemical ligation of folded recombinant proteins: Segmental isotopic labeling of domains for NMR studies. Proceedings of the National Academy of Sciences of the United States of America 1999, 96 (2), 388-393. link

Novick, R. P.; Muir, T. W., Virulence gene regulation by peptides in staphylococci and other Gram-positive bacteria. Current Opinion in Microbiology 1999, 2 (1), 40-45. link

Mayville, P.; Ji, G. Y.; Beavis, R.; Yang, H. M.; Goger, M.; Novick, R. P.; Muir, T. W., Structure-activity analysis of synthetic autoinducing thiolactone peptides from Staphylococcus aureus responsible for virulence. Proceedings of the National Academy of Sciences of the United States of America 1999, 96 (4), 1218-1223. link

Cotton, G. J.; Muir, T. W., Peptide ligation and its application to protein engineering. Chemistry & Biology 1999, 6 (9), R247-R256. link

Ayers, B.; Blaschke, U. K.; Camarero, J. A.; Cotton, G. J.; Holford, M.; Muir, T. W., Introduction of unnatural amino acids into proteins using expressed protein ligation. Peptide Science 1999, 51 (5), 343-354. link

1998

Severinov, K.; Muir, T. W., Expressed protein ligation, a novel method for studying protein-protein interactions in transcription. Journal of Biological Chemistry 1998, 273 (26), 16205-16209. link

Muir, T. W.; Sondhi, D.; Cole, P. A., Expressed protein ligation: A general method for protein engineering. Proceedings of the National Academy of Sciences of the United States of America 1998, 95 (12), 6705-6710. link

Holford, M.; Muir, T. W., Adding ‘splice’ to protein engineering. Structure with Folding & Design 1998, 6 (8), 951-956. link

Camarero, J. A.; Cotton, G. J.; Adeva, A.; Muir, T. W., Chemical ligation of unprotected peptides directly from a solid support. Journal of Peptide Research 1998, 51 (4), 303-316. link

Camarero, J. A.; Ayers, B.; Muir, T. W., Studying receptor-ligand interactions using encoded amino acid scanning. Biochemistry 1998, 37 (20), 7487-7495. link

1997

Muir, T. W.; Dawson, P. E.; Kent, S. B. H., Protein synthesis by chemical ligation of unprotected peptides in aqueous solution. In Solid-Phase Peptide Synthesis, Fields, G. B., Ed. 1997; Vol. 289, pp 266-298.

Muir, T. W.; Dawson, P. E.; Fitzgerald, M. C.; Kent, S. B. H., Protein signature analysis: A practical new approach for studying structure-activity relationships in peptides and proteins. In Solid-Phase Peptide Synthesis, Fields, G. B., Ed. 1997; Vol. 289, pp 545-564.

Love, S. G.; Muir, T. W.; Ramage, R.; Shaw, K. T.; Alexeev, D.; Sawyer, L.; Kelly, S. M.; Price, N. C.; Arnold, J. E.; Mee, M. P.; Mayer, R. J., Synthetic, structural and biological studies of the ubiquitin system: Synthesis and crystal structure of an analogue containing unnatural amino acids. Biochemical Journal 1997, 323 (3), 727-734. link

1996

Muir, T. W.; Dawson, P. E.; Fitzgerald, M. C.; Kent, S. B. H., Probing the chemical basis of binding activity in an SH3 domain by protein signature analysis. Chemistry & Biology 1996, 3 (10), 817-825. link

Zhao, Y.; Muir, T. W.; Kent, S. B. H.; Tischer, E.; Scardina, J. M.; Chait, B. T., Mapping protein-protein interactions by affinity-directed mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 1996, 93 (9), 4020-4024. link

1995

Muir, T. W.; Williams, M. J.; Kent, S. B. H., DETECTION OF SYNTHETIC PROTEIN ISOMERS AND CONFORMERS BY ELECTROSPRAY MASS-SPECTROMETRY. Analytical Biochemistry 1995, 224 (1), 100-109. link

Muir, T. W., A CHEMICAL APPROACH TO THE CONSTRUCTION OF MULTIMERIC PROTEIN ASSEMBLIES. Structure 1995, 3 (7), 649-652. link

1994

Williams, M. J.; Muir, T. W.; Ginsberg, M. H.; Kent, S. B. H., Total chemical synthesis of a folded beta-sandwich protein domain: An analog of the tenth fibronectin type 3 module. Journal of the American Chemical Society 1994, 116 (23), 10797-10798. link

Ramage, R.; Green, J.; Muir, T. W.; Ogunjobi, O. M.; Love, S.; Shaw, K., SYNTHETIC, STRUCTURAL AND BIOLOGICAL STUDIES OF THE UBIQUITIN SYSTEM – THE TOTAL CHEMICAL SYNTHESIS OF UBIQUITIN. Biochemical Journal 1994, 299 (1), 151-158. link

Muir, T. W.; Williams, M. J.; Ginsberg, M. H.; Kent, S. B. H., DESIGN AND CHEMICAL SYNTHESIS OF A NEOPROTEIN STRUCTURAL MODEL FOR THE CYTOPLASMIC DOMAIN OF A MULTISUBUNIT CELL-SURFACE RECEPTOR – INTEGRIN ALPHA(IIB)BETA(3) (PLATELET GPIIB-IIIA). Biochemistry 1994, 33 (24), 7701-7708. link

Jongewaard, I. N.; Muir, T. W.; Ingham, K. C.; Novokhatny, V.; Smith, J. W., Expression and characterization of recombinant type III connecting segment from human fibronectin. Molecular Biology of the Cell 1994, 5 (SUPPL.), 54A-54A. link

Dawson, P. E.; Muir, T. W.; Clarklewis, I.; Kent, S. B. H., SYNTHESIS OF PROTEINS BY NATIVE CHEMICAL LIGATION. Science 1994, 266 (5186), 776-779. link

Alexeev, D.; Bury, S. M.; Turner, M. A.; Ogunjobi, O. M.; Muir, T. W.; Ramage, R.; Sawyer, L., SYNTHETIC, STRUCTURAL AND BIOLOGICAL STUDIES OF THE UBIQUITIN SYSTEM – CHEMICALLY SYNTHESIZED AND NATIVE UBIQUITIN FOLD INTO IDENTICAL 3-DIMENSIONAL STRUCTURES. Biochemical Journal 1994, 299 (1), 159-163. link

1993

Muir, T. W.; Kent, S. B. H., The chemical synthesis of proteins. Current Opinion in Biotechnology 1993, 4 (4), 420-427. link