David Waugh, Ph.D. - Publications

Publications
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SELECTED PUBLICATIONS
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, 819–830.
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, 705–720.
*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.