Matthew D. Daugherty, Ph.D. - Publications

Affiliations: 
2009 Chemistry and Chemical Biology University of California, San Francisco, San Francisco, CA 
Area:
Molecular Biology, General Biophysics

24/31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Tsu BV, Beierschmitt C, Ryan AP, Agarwal R, Mitchell PS, Daugherty MD. Diverse viral proteases activate the NLRP1 inflammasome. Elife. 10. PMID 33410748 DOI: 10.7554/eLife.60609  0.32
2019 Daugherty MD, Zanders SE. Gene conversion generates evolutionary novelty that fuels genetic conflicts. Current Opinion in Genetics & Development. 58: 49-54. PMID 31466040 DOI: 10.1016/j.gde.2019.07.011  0.64
2016 Chavarría-Smith J, Mitchell PS, Ho AM, Daugherty MD, Vance RE. Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation. Plos Pathogens. 12: e1006052. PMID 27926929 DOI: 10.1371/journal.ppat.1006052  0.32
2016 Daugherty MD, Schaller AM, Geballe AP, Malik HS. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. Elife. 5. PMID 27240734 DOI: 10.7554/eLife.14228  0.44
2015 Chou S, Daugherty MD, Peterson SB, Biboy J, Yang Y, Jutras BL, Fritz-Laylin LK, Ferrin MA, Harding BN, Jacobs-Wagner C, Yang XF, Vollmer W, Malik HS, Mougous JD. Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature. 518: 98-101. PMID 25470067 DOI: 10.1038/nature13965  0.44
2014 Daugherty MD, Malik HS. How a virus blocks a cellular emergency access lane to the nucleus, STAT! Cell Host & Microbe. 16: 150-2. PMID 25121743 DOI: 10.1016/j.chom.2014.07.013  0.6
2014 Daugherty MD, Young JM, Kerns JA, Malik HS. Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. Plos Genetics. 10: e1004403. PMID 24875882 DOI: 10.1371/journal.pgen.1004403  0.6
2014 Tenthorey JL, Kofoed EM, Daugherty MD, Malik HS, Vance RE. Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Molecular Cell. 54: 17-29. PMID 24657167 DOI: 10.1016/j.molcel.2014.02.018  0.6
2013 Carter JJ, Daugherty MD, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA. Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proceedings of the National Academy of Sciences of the United States of America. 110: 12744-9. PMID 23847207 DOI: 10.1073/pnas.1303526110  0.6
2012 Daugherty MD, Malik HS. Rules of engagement: molecular insights from host-virus arms races. Annual Review of Genetics. 46: 677-700. PMID 23145935 DOI: 10.1146/annurev-genet-110711-155522  0.6
2010 Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, Musier-Forsyth K, Barbara PF. Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1. Biophysical Journal. 99: 3454-62. PMID 21081095 DOI: 10.1016/j.bpj.2010.09.051  0.6
2010 Daugherty MD, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nature Structural & Molecular Biology. 17: 1337-42. PMID 20953181 DOI: 10.1038/nsmb.1902  0.6
2010 Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD. HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proceedings of the National Academy of Sciences of the United States of America. 107: 12481-6. PMID 20616058 DOI: 10.1073/pnas.1007022107  0.6
2008 Daugherty MD, D'Orso I, Frankel AD. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Molecular Cell. 31: 824-34. PMID 18922466 DOI: 10.1016/j.molcel.2008.07.016  0.6
2006 Fuhrmann CN, Daugherty MD, Agard DA. Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis. Journal of the American Chemical Society. 128: 9086-102. PMID 16834383 DOI: 10.1021/ja057721o  0.6
2006 Mills NL, Daugherty MD, Frankel AD, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. Journal of the American Chemical Society. 128: 3496-7. PMID 16536504 DOI: 10.1021/ja0582051  0.6
2005 Landt SG, Ramirez A, Daugherty MD, Frankel AD. A simple motif for protein recognition in DNA secondary structures. Journal of Molecular Biology. 351: 982-94. PMID 16055152 DOI: 10.1016/j.jmb.2005.07.001  0.6
2005 Calabro V, Daugherty MD, Frankel AD. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein. Proceedings of the National Academy of Sciences of the United States of America. 102: 6849-54. PMID 15857951 DOI: 10.1073/pnas.0409282102  0.6
2003 Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, et al. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. Journal of Bacteriology. 185: 5673-84. PMID 13129938 DOI: 10.1128/JB.185.19.5673-5684.2003  0.6
2003 Cebrat M, Kim CM, Thompson PR, Daugherty M, Cole PA. Synthesis and analysis of potential prodrugs of coenzyme A analogues for the inhibition of the histone acetyltransferase p300. Bioorganic & Medicinal Chemistry. 11: 3307-13. PMID 12837541 DOI: 10.1016/S0968-0896(03)00265-7  0.6
2002 Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, et al. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. Journal of Bacteriology. 184: 4555-72. PMID 12142426 DOI: 10.1128/JB.184.16.4555-4572.2002  0.6
2002 Daugherty M, Polanuyer B, Farrell M, Scholle M, Lykidis A, de Crécy-Lagard V, Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. The Journal of Biological Chemistry. 277: 21431-9. PMID 11923312 DOI: 10.1074/jbc.M201708200  0.6
2001 Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H. Structural basis for the catalysis and substrate specificity of homoserine kinase. Biochemistry. 40: 10810-8. PMID 11535056 DOI: 10.1021/bi010851z  0.6
2000 Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H. Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Structure (London, England : 1993). 8: 1247-57. PMID 11188689 DOI: 10.1016/S0969-2126(00)00533-5  0.6
Low-probability matches
2009 Yeh Y, Wang H, Barbara PF, Daugherty MD, Frankel AD, Musier-Forsyth K. Nucleocapsid Protein Locally Melts The Iib Region Of Hiv-1 Rre Rna, But Rev Protein Does Not: A Single-molecule Spectroscopic Study Biophysical Journal. 96: 292a. DOI: 10.1016/j.bpj.2008.12.1446  0.12
2020 Mudla A, Jiang Y, Arimoto KI, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. Elife. 9. PMID 32945770 DOI: 10.7554/eLife.58825  0.01
2019 Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. Diversification of the heat shock response by Helitron transposable elements. Elife. 8. PMID 31825311 DOI: 10.7554/eLife.51139  0.01
2019 Schwerk J, Soveg FW, Ryan AP, Thomas KR, Hatfield LD, Ozarkar S, Forero A, Kell AM, Roby JA, So L, Hyde JL, Gale M, Daugherty MD, Savan R. RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Nature Immunology. PMID 31740798 DOI: 10.1038/s41590-019-0527-6  0.01
2019 Thibault PA, Ryan AP, Hung C, Daugherty M, Lee B. The long isoform of ZAP widely restricts Paramyxoviruses Access Microbiology. 1. DOI: 10.1099/acmi.ac2019.po0549  0.01
2017 Moens U, Calvignac-Spencer S, Lauber C, Ramqvist T, Feltkamp MCW, Daugherty MD, Verschoor EJ, Ehlers B, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Polyomaviridae. The Journal of General Virology. PMID 28640744 DOI: 10.1099/jgv.0.000839  0.01
2016 Calvignac-Spencer S, Feltkamp MC, Daugherty MD, Moens U, Ramqvist T, Johne R, Ehlers B. A taxonomy update for the family Polyomaviridae. Archives of Virology. PMID 26923930 DOI: 10.1007/s00705-016-2794-y  0.01
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