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Click HERE to search NCBI PubMed for publications by David S. Waugh. |
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SELECTED PUBLICATIONS | |
Bahta, M., Dyas, B., Lountos, G. T., Ulrich, R. G., Waugh, D. S., and Burke, T. R. Jr. 2011. Utilization of nitrophenylphosphates and oxime-based ligation for the development of nanomolar affinity inhibitors of the Yersinia pestis protein-tyrosine phosphatase YopH. J. Med. Chem., in press. |
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Lountos, G. T., Tropea, J. E., and Waugh, D. S. 2011. Structure of human dual-specificity phosphatase 27 at 2.38 Å resolution. Acta Cryst. D, in press. |
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Luke, J. M., Carnes, A. E., Sun, P., Hodgson, C. P., Waugh, D. S., and Williams, J. A. 2011. Thermostable tag (TST) protein expression system: engineering thermotolerant recombinant proteins and vaccines. J. Biotechnol. 151: 242-20. |
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Austin, B. P., Tozser, J, Bagossi, P., Tropea, J. E., and Waugh, D. S. 2011. The substrate specificity of Metarhizium anisopliae and Bos Taurus carboxypeptidases A: insights their use as tools for the removal of affinity tags. Prot. Expr. Purif. 77: 53-61. |
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Sun, P., Tropea, J. E., and Waugh, D. S. 2011. Enhancing the solubility of recombinant proteins in Escherichia coli by using hexahistidine-tagged maltose-binding protein as a fusion partner. Methods Mol. Biol. 705: 259-274. |
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Sun, P., Austin, B. P., Tozser, J., and Waugh, D. S. 2010. Structural determinants of tobacco vein mottling virus protease substrate specificity. Protein Sci. 19: 2240-2251. |
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Muus, U., Hose, C., Yao, W., Kosakowska-Cholody, T., Farnsworth, D., Dyba, M., Waugh, D. S., Lountos, G. T., Monks A. Burke, T. R. Jr., and Michejda, C. 2010. Development of antiproliferative phenymaleiimides that activate the unfolded protein response. Bioorg. Med. Chem. 18: 4535-4541. |
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Subburaman, P., Austin, B. P., Shaw, G. X., Waugh, D. S. and Ji, X. 2010. Cloning, expression purification and preliminary X-ray diffraction analysis of macrophage growth locus A (MglA) protein from Francisella tularensis. Acta Cryst F66: 554-557. |
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Liu, F., Hakami, R. M., Dyas, B., Bahta, M., Lountos, G., Waugh, D. S., Ulrich, R. G., and Burke, T. R. Jr. 2010. A rapid oxime linker-based library approach to identification of bivalent inhibitors of the Yersinia pestis protein tyrosine phosphatase, YopH. Bioorg Med. Chem Lett. 20: 2813-2816. |
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Jobson, A. G., Lountos, G. T., Lorenzi, P. L., Llamas, J., Connelly, J., Cerna, D., Tropea. J. E., Onda, A., Zoppoli, G., Kondapaka, S., Zhang, G., Caplen, N. J., Cardellina, J. H. 2nd, Yoo, S. S., Monks, A., Self, C. Waugh, D. S. Shoemaker, R. H., and Pommier, Y. 2009. Cellular inhibition of checkpoint kinase 2 (Chk2) and potentiation of camptothecins and radiation by the novel Chk2 inhibitor PV1019 [7-nitro-1H-indole-2-carboxylic acid {4-[1-(guanidinohydrazone)ethyl]-phenyl}-amide]. J. Pharmacol. Exp. Ther. 331: 816-828. |
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Tu, C., Tropea, J., Austin, B. P., Court, D. L., Waugh, D. S., and Ji, X. 2009. Structural basis for binding of RNA and cofactor by a KsgA methyltransferase. Structure 17: 374-385. |
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Lountos, G. T., Tropea, J. E., Cherry, S., and Waugh, D. S. 2009. Overproduction, purification, and structure determination of human dual specificity phosphatase 14. Acta Cryst. D65: 1013-1020. |
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Tu, C., Zhou, X., Tropea, J. E., Austin, B. P., Waugh, D. S., Court, D. L., and Ji, X. 2009. Structure of ERA in complex with the 3’ end of 16S rRNA: Implications for ribosome biogenesis. Proc. Natl. Acad. Sci. USA 106: 14843-14848. |
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Lountos, G. T., Austin, B. P., Nallamsetty, S., and Waugh, D. S. 2009. Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion. Protein Sci. 18: 467-474. |
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Zhang, D., Tözsér, J., and Waugh, D. S. 2009. Molecular cloning, purification, and biochemical characterization of the p39 nsp2 protease domains encoded by three alphaviruses. Prot. Expr. Purif. 64: 89-97. |
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Lountos, G. T., Tropea, J. E., Zhang, D., Jobson, A. G., Pommier, Y., Shoemaker, R. H., and Waugh, D. S. 2009. Crystal structure of chekpoint kinase 2 in complex with NSC 109555, a potent and selective inhibitor. Protein Sci. 18: 92-100. |
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Austin, B. P., Nallamsetty, S., and Waugh, D. S. 2009. Hexahistidine-tagged maltose-binding protein as a fusion partner for the production of soluble recombinant proteins in Escherichia coli. Methods Mol. Biol. 498: 157-172. |
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Tropea, J. E., Cherry, S., and Waugh, D. S. 2009. Expression and purification of soluble His6-tagged TEV protease. Methods Mol. Biol. 498: 297-307. |
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Davis, J., Wang, J., Tropea, J. E., Zhang, D., Dauter, Z., Waugh, D. S., and Wlodawer, A. 2008. Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri. Protein Sci. 17: 2167-2173. |
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Sun, P., Tropea, J. E., Austin, B., Cherry, S., and Waugh, D. S. 2008. Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG. J. Mol. Biol. 377, 819830. | |
Das, R., Loss, S., Li, J., Waugh, D. S., Tarasov, S., Wingfield, P. T., Byrd, R. A., and Alteri, A. S. 2008. Structural Biophysics of the NusB:NusE Antitermination Complex. J. Mol. Biol. 376, 705720. | |
Gan, J., Shaw, G., Tropea, J. E., Waugh, D. S., Court, D. L., and Ji, X. 2007. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol. Microbiol. 67: 143-154. | |
McFeeters, R. L., Altieri, A. S., Cherry, S., Tropea, J. E., Waugh, D. S., and Byrd, R. A. 2007. High precision solution structure of Yersinia modulating protein YmoA provides insight into its interaction with H-NS. Biochemistry 46: 13975-13982. | |
Nallamsetty, S., and Waugh, D.S. 2007. Mutations that alter the equilibrium between open and closed conformations of Escherichia coli maltose-binding protein impede its ability to enhance the solubility of passenger proteins. Biochem. Biophys. Res. Comm. 364: 639-644. | |
Blaszczyk, J., Li, Y., Cherry, S. Alexandratos, J., Wu, Y., Shaw, G., Tropea, J. E., Waugh, D. S., Yan, H., and Ji, X. 2007. Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphpkinase as a novel molecular target for the development of antiplague therapeutics. Acta Cryst. D 63: 1169-1177. | |
Sun, P., Austin, B. P., Schubot, F. D., and Waugh, D. S. 2007. New protein fold revealed by 1.65 Å resolution crystal structure of Franciscella tularensis pathogenicity island protein IglC. Protein Sci. 16: 2560-2563. | |
Phan, J., Tropea, J. E., and Waugh, D. S. 2007. Structure-assisted discovery of Variola major H1 phosphatase inhibitors. Acta Cryst. D 63: 698-704. | |
Nallamsetty, S. and Waugh, D. S. 2007. A generic protocol for the expression and purification of recombinant proteins in Escherichia coli using a combinatorial His6-maltose binding protein fusion tag. Nature Protocols 2: 383-391. | |
Tropea, J.E., Cherry, S., Nallamsetty, S., Bignon, C., and Waugh, D.S. 2007. A generic method for the production of recombinant proteins in Escherichia coli using a dual His6-MBP affinity tag. Methods. Mol. Biol. 363:1-19. | |
Saikh, K. U., Kissner, T. L., Dyas, B., Tropea, J. E., Waugh, D. S., and Ulrich, R. G. 2006. Human cytolytic T cell recognition of Yersinia pestis virulence proteins that target innate immune responses. J. Infect. Diseases 194: 1753-1760. | |
Schubot, F. D., Tropea, J. E., and Waugh, D. S. 2006. Structure of the POZ domain of human LRF, a master regulator of oncogenesis. Biochem. Biophys. Res. Commun. 351: 1-6. | |
Tropea, J. E., Phan, J., and Waugh, D. S. 2006. Overproduction, purification, and biochemical characterization of the dual specificity H1 protein phosphatase encoded by variola major virus. Protein Expr. Purif. 50: 31-36. | |
Nallamsetty, S., and Waugh, D.S. 2006. Solubility-enhancing proteins MBP and NusA play a passive role in the folding of their fusion partners. Prot. Expr. Purif. 45: 175-182. | |
Gan, J., Tropea, J. E., Austin, B. P., Court, D. L., Waugh, D. S., and Ji, X. 2006. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124: 355-366. | |
Tözsér, J., Tropea, J.E., Cherry, S., Bagossi, P., Copeland, T.D., Wlodawer, A., and Waugh, D.S. 2005. Comparison of the substrate specificity of two potyvirus proteases. FEBS. J. 272: 514-523. | |
Schubot, F.D., Jackson, M.W., Penrose, K.J., Cherry, S., Tropea, J.E., Plano, G.V., and Waugh, D.S. 2005. Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis. J. Mol. Biol. 346: 1147-1161. | |
Hansen, A.M., Gu, Y., Li, M., Andrykovitch, M., Waugh, D.S., and Ji, X. 2005. Structural basis for the function of stringent starvation protein A as a transcription factor. J. Biol. Chem. 280: 17380-17391. | |
Waugh, D.S. 2005. Making the most of affinity tags. Trends Biotechnol. 23: 316-320. | |
Schubot, F.D., Cherry, S., Austin, B.P., Tropea, J.E., and Waugh, D. S. 2005. Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR. Protein Sci. 14: 1679-1683. | |
Ferracci, F., Schubot, F.D., Waugh, D.S., and Plano, G.V. 2005. Selection and characterization of Yersinia pestis YopN mutants that constitutively block Yop secretion. Mol. Microbiol. 57: 970-987. | |
Lee, K., Boovanahalli, S.K., Nam, K.-Y., Kang, S.-U., Phan, J., Wu, L., Waugh, D.S., Zhang, Z.-Y., No, K.T., Lee, J.-J., and Burke, T.R. Jr. 2005. Synthesis of tripeptides as Yersinia protein-tyrosine phosphatase inhibitors. Bioorg. Med. Chem. Lett. 15: 4037-4042. | |
Gan, J., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S., and Ji, X. 2005. Intermediate States of Ribonuclease III in complex with double-stranded RNA. Structure 13: 1435-1442. | |
Phan, J., Shi, Z.-D., Burke, T.R., and Waugh, D.S. 2005. Crystal structures of a high-affinity macrocyclic compound in complex with the Grb2 SH2 domain. J. Mol. Biol. 353: 104-115. | |
Phan, J., Austin, B.P., and Waugh, D.S. 2005. Crystal structure of the Yersinia type III secretion protein YscE. Protein Sci. 14: 2759-2763. | |
Nallamsetty, S., and Waugh, D.S. 2005. Gateway destination vectors for the production of combinatorially-tagged His6-MBP fusion proteins in the cytoplasm and periplasm of Escherichia coli. Protein Sci. 14: 2964-2971. | |
Blaszczyk, J., Gan, J., Tropea, J.E., Court, D.L., Waugh, D.S., and Xi, J. 2004. Non-catalytic assembly of ribonuclease III with double-stranded RNA. Structure 12: 457-466. | |
Swietnicki, W., O'Brien, S., Holman, K., Brueggeman, E., Tropea, J.E., Hines, H., Waugh, D.S., and Ulrich, R.G. 2004. Novel protein-protein interactions of the Yersinia pestis type III secretion system elucidated with a matrix analysis by surface plasmon resonance and mass spectrometry. J. Biol. Chem. 279: 38693-38700. | |
Waugh, D. S., and Phan, J. 2004. Taking aim at bioterrorism. CCR Frontiers in Research 3: 1-2. | |
Phan, J., Tropea, J.E., and Waugh, D.S. 2004. Crystal structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2. Acta Cryst. D60: 1591-1599. | |
Nallamsetty, S., Kapust, R.B., Tözsér, J., Cherry, S., Tropea, J.E., and Waugh, D.S. 2004. Efficient site-specific processing of fusion proteins by tobacco vein mottling virus protease in vivo and in vitro. Protein Expr. Purif. 38: 108-115. | |
Schubot, F.D. and Waugh, D.S. (2004). A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB. Acta Cryst. D60: 1981-1986. | |
Liang, X., Young, J.J., Boone, S.A., Waugh, D.S., and Duesbery, N.S. 2004. Involvement of domain II in toxicity of anthrax lethal factor. J. Biol. Chem. 279: 52473-52478. | |
Derewenda, U., Mateja, A., Devedjiev, Y., Routzahn, K. M., Evdokimov, A. G., Derewenda, Z. S. and Waugh, D. S. 2004. The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague. Structure 12: 301-306. | |
Phan, J., Lee, K., Cherry, S., Tropea, J. E., Burke, T. R. Jr., and Waugh, D. S. 2003. High-resolution structure of the Yersinia pestis protein tyrosine phosphatase YopH in complex with a phosphotyrosyl mimetic-containing hexapeptide. Biochemistry 42: 13113-13121. | |
Evdokimov, A. G., Phan, J., Tropea, J. E., Routzahn, K. M., Peters, H. P. K., III, and Waugh, D. S. 2003. Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion. Nat. Struct. Biol. 10: 789-793. | |
Lee, K., Gao, Y., Yao, X.-J., Phan, J., Wu, L., Liang, J., Waugh, D. S., Zhang, Z.-Y., and Burke, T. R. Jr. 2003. Tripeptide inhibitors of Yersinia protein-tyrosine phosphatase. Bioorg. Med. Chem. Lett. 13: 2577-2581. | |
Andrykovitch, M., Routzahn, K. M., Li, M., Gu, Y., Waugh, D. S., and Ji, X. Characterization of four orthologs of stringent starvation protein A. 2003. ,Acta Cryst. D59: 881-886. | |
Fox, J. D., Routzahn, K. M., Bucher, M. H., and Waugh, D. S. 2003. Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers. FEBS Lett. 537: 53-57. | |
Knowlton, J. R., Bubunenko, M., Andrykovitch, M., Guo, W., Routzahn, K. M., Waugh, D. S., Court, D. L., and Ji, X. 2003. A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants. Biochemistry 42: 2275-2281. | |
Fox, J. D. and Waugh, D. S. 2003. Maltose-binding protein as a solubility enhancer. Methods Mol. Biol. 205: 99-117. | |
Andrykovitch, M., Guo, W., Routzahn, K. M., Gu, Y., Anderson, D. E., Reshetnikova, L. S., Knowlton, J. R., Waugh, D. S., and Ji, X. 2002. Crystallization and preliminary X-ray diffraction studies of NusG, a protein shared by the transcription and translation machines. Acta Cryst. D58: 2157-2158. | |
Phan, J., Zdanov, A., Evdokimov, A. G., Tropea, J. E., Peters, H. P. K., Kapust, R. B., Li, M., Wlodawer, A., and Waugh, D. S. 2002. Structural basis for the substrate specificity of tobacco etch virus protease. J. Biol. Chem. 277: 50564-50572. | |
Routzahn, K. M. and Waugh, D. S. 2002. Differential effects of supplementary affinity tags on the solubility of MBP fusion proteins. J. Struct. Funct. Genomics 2: 83-92. | |
Kapust, R. B., Tözsér, J., Copeland, T. D., and Waugh, D. S. 2002. The P1' specificity of tobacco etch virus protease. Biochem. Biophys. Res. Commun. 294: 949-955. | |
Evdokimov, A. G., Tropea, J. E., Routzahn, K. M., and Waugh, D. S. 2002. Three-dimensional structure of the type III secretion chaperone SycE from Yersinia pestis. Acta Cryst. D58: 393-406. | |
Bucher, M. H., Evdokimov, A. G., and Waugh, D. S. 2002. Differential effects of short affinity tags on the crystallization of Pyrococcus furiosus maltodextrin-binding protein. Acta Cryst. D58: 392-397. | |
Kapust, R. B., Routzahn, K. M., and Waugh, D. S. 2002. Processive degradation of nascent polypeptides, triggered by tandem AGA codons, limits the accumulation of recombinant TEV protease in Escherichia coli BL21(DE3). Prot. Expr. Purif. 24: 61-70. | |
Evdokimov, A. G., Tropea, J. E., Routzahn, K. M., and Waugh, D. S. 2002. Crystal structure of the Yersinia pestis GTPase activator YopE. Protein Sci. 11: 401-408. | |
Zhou, M., Horita, D. A., Waugh, D. S., Byrd, R. A., and Morrison, D. 2002. Solution structure and functional analysis of the atypical cysteine-rich C1 domain of KSR1. J. Mol. Biol. 315: 435-446. | |
Blaszczyk, J., Tropea, J. E., Bubunenko, M., Routzahn, K. M., Waugh, D. S., Court, D. L., and Ji, X. 2001. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure 9: 1225-1236. | |
Evdokimov, A. G., Anderson, D. E., Routzahn, K. M., and Waugh, D. S. 2001. Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: A leucine-rich repeat protein with the shortest repeating unit. J. Mol. Biol. 312: 807-821. | |
Kapust, R. B., Tözsér, J., Fox, J. D., Anderson, D. E., Cherry, S., Copeland, T. D., and Waugh, D. S. 2001. Tobacco etch virus protease: Mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Prot. Eng. 14: 993-1000. | |
Evdokimov, A. G., Tropea, J. E., Routzahn, K. M., Copeland, T. D., and Waugh, D. S. 2001. Crystal structure of the N-terminal domain of Yersinia pestis YopH at 2.0 Å resolution. Acta Cryst. D57: 793-799. | |
Fox, J. D., Kapust, R. B., and Waugh, D. S. 2001. Single amino acid substitutions on the surface of Escherichia coli maltose-binding protein can have a profound impact on the solubility of fusion proteins. Protein Sci. 10: 622-630. | |
Evdokimov, A. G., Anderson, D. E., Routzahn, K. M., and Waugh, D. S. 2001. Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein. J. Mol. Biol. 305: 891-904. | |
Evdokimov, A. G., Anderson, D. E., Routzahn, K. M., and Waugh, D. S. 2000. Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of YopM, an essential virulence factor extruded by the plague bacterium, Yersinia pestis. Acta Cryst. D56: 1676-1679. | |
Eisenmesser, E. Z., Kapust, R. B., Nawrocki, J. P., Mazzulla, M. J., Pannell, L. K., Waugh, D. S., and Byrd, R. A. 2000. Expression, purification, refolding, and characterization of recombinant human interleukin-13: utilization of intracellular processing. Prot. Expr. Purif. 20: 186-195. | |
Kapust, R. B. and Waugh, D. S. 2000. Controlled intracellular processing of fusion proteins by TEV protease. Prot. Expr. Purif. 19: 312-318. | |
Kireeva, M., Komissarova, N., Waugh, D. S., and Kashlev, M. 2000. The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex. J. Biol. Chem. 275: 6530-6536. | |
Kapust, R. B. and Waugh, D. S. 1999. Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci. 8: 1668-1674. |
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