Biography

Dr. David S. Waugh

Macromolecular Crystallography Laboratory

NCI-Frederick, USA


Email: [email protected]


Qualifications

1989 Ph.D., Biochemistry, Indiana University
1982 B.Sc., Molecular Biophysics & Biochemistry, Yale University


Publications (Selected)

  1. Brabson, G.D. and Waugh, D.S. (1986). Two electrophoresis experiments for freshmen in the health professions.J. Chem. Ed.63: 540-542.
  2. Waugh, D.S. and Pace, N.R. (1986). Catalysis by RNA.Bioessays 4: 56-61.
  3. Pace, N.R., James, B.D., Reich, C., Waugh, D.S., Olsen, G.J., and Marsh, T.L. (1987). TheBacillussubtilisRNase P. In “Molecular Biology of RNA: New Perspectives,” M. Inouye and B. Dudock (eds.), Academic Press, pp. 17-36.
  4. Pace, N.R., Reich, C., James, B.D., Olsen, G.J., Pace, B., and Waugh, D.S. (1987). Structure and catalytic function in ribonuclease P.Cold Spring Harb. Symp. Quant. Biol.52: 239-247.
  5. Waugh, D.S., Sganga, M.W., Raff, M., and Pace, N.R. (1989). A site-directed mutation in theBacillussubtilisRNase P RNA that selectively influences its protein-dependent reaction. In “Molecular Biology of RNA,” T. Cech (ed.), Alan R. Liss, pp. 67-77.
  6. Waugh, D.S., Green, C.J., and Pace, N.R. (1989). The design and catalytic properties of a simplified ribonuclease P RNA.Science244: 1569-1571.
  7. Waugh, D.S. and Pace, N.R. (1990). Complementation of an RNase P RNA (rnpB) gene deletion inEscherichia coliby homologous genes from distantly related eubacteria.J. Bacteriol.172: 6316-6322.
  8. Pace, N.R. and Waugh, D.S. (1991). Design of a simplified ribonuclease P RNA by phylogenetic comparison. Methods Enzymol.203: 500-510.
  9. Waugh, D.S. and Pace, N.R. (1993). Gap-scan deletion analysis ofBacillus subtilisRNase P RNA.FASEB J.7: 188-195.
  10. Waugh, D.S.and Sauer, R.T. (1993). Single amino acid substitutions uncouple the DNA binding and strand scission activities ofFokI endonuclease.Proc. Natl. Acad. Sci. USA90: 9596-9600.
  11. Waugh, D.S. and Sauer, R.T. (1994). A novel class of Fok I restriction endonuclease mutants that cleave hemi-methylated substrates. J. Biol. Chem.269: 12298-12303.
  12. Emerson, S.D., Waugh, D.S., Scheffler, J.E., Tsao, K.-L., Prinzo, K.M., and Fry, D.C. (1994). Chemical shift assignments and folding topology of the ras-binding domain of human raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy. Biochemistry33: 7745-7752.
  13. Scheffler, J.E., Waugh, D.S., Bekesi, E., Kiefer, S.E., Losardo, J.L., Neri, A., Prinzo, K. M., Tsao, K.-L., Wegrzynski, B., Emerson, S.D., and Fry, D.C. (1994). Characterization of a 78-residue fragment of c-raf-1 that comprises a minimal binding domain for the interaction with ras-GTP.J. Biol. Chem.269: 22340-22346.
  14. Emerson, S.D, Madison, V.S., Palermo, R.E., Waugh, D.S., Scheffler, J.E., Tsao, K.-L., Kiefer, S.E., Liu, S.P., and Fry, D.C. (1995). Structure of the ras-binding domain of c-raf-1 and identification of its ras-interaction surface.Biochemistry 34: 6911-6918.
  15. Dracheva, S., Palermo, R.E., Powers, G.D., and Waugh, D.S. (1995). Expression of soluble human interleukin-2 receptor chain inEscherichia coli. Protein Expr. Purif.6: 737-747.
  16. Tsao, K.-L., DeBarbieri, B., Michel, H., and Waugh, D.S. (1996).A versatile plasmid expression vector for the production of biotinylated proteins by site-specific, enzymatic modification inEscherichia coli.Gene169: 59-64.
  17. Emerson, S.D, Madison, V.S., Palermo, R.E., Waugh, D.S., Scheffler, J.E., Tsao, K.-L., Kiefer, S.E., Liu, S.P., and Fry, D.C. (1996). Structure of the ras binding domain of c-raf-1 as determined by NMR spectroscopy and identification of the region that interacts with ras.Drug. Des. Discov.13: 83-93.
  18. Chen, T., Repetto, B., Chizzonite, R., Pullar, C., Burghard, C., Dharm, E., Zhao, Z., Carroll, R., Nunes, P., Basu, M., Danho, W., Visnick, M., Kochan, J., Waugh, D.S., and Gilfillan, A. (1996).
  19. Interaction of phosphorylated FcRI immunoglobulin receptor tyrosine activation motif-based peptides with dual and single SH2 domains of p72syk: Assessment of binding parameters and real time binding kinetics by a novel scintillation proximity assay. J. Biol. Chem. 271: 25308-25315.
  20. Waugh, D.S.(1996). Genetic tools for selective labeling of proteins with -15N amino acids.J. Biomol. NMR8: 184-192.
  21. Tsao, K.-L. and Waugh, D.S.(1997). Balancing the production of two recombinant proteins inEscherichia coliby manipulating plasmid copy number: High-level expression of heterodimeric Ras farnesyl transferase.Protein Expr. Purif.11: 233-240.
  22. Duffy, S., Tsao, K.-L., and Waugh, D.S. (1998). Efficient, site-specific biotinylation of recombinant proteins inSpodoptera frugiperdacells using biotin acceptor peptides. Anal. Biochem.262: 122-128.
  23. Baden, H.A., Sarma, S.P., Kapust, R.B., Byrd, R.A., and Waugh, D.S. (1998). The amino-terminal domain of human STAT4: Overexpression, purification, and biophysical characterization.J. Biol. Chem. 273: 17109-17114.
  24. Kervinen, J., Tobin, G.J., Costa, J.,Waugh, D.S., Wlodawer, A., and Zdanov, A. (1999). Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting.EMBO J.18: 3947-3955.
  25. Kapust, R.B. and Waugh, D.S. (1999).Escherichia colimaltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused.Protein Sci.8: 1668-1674.
  26. 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.
  27. Kapust, R.B. and Waugh, D.S. (2000). Controlled intracellular processing of fusion proteins by TEV protease.Protein Expr. Purif. 19: 312-318.
  28. 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.Protein Expr. Purif. 20: 186-195.
  29. 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.
  30. Evdokimov, A.G., Anderson, D.E., Routzahn, K.M., and Waugh, D.S. (2001). Structural basis for oligosaccharide recognition byPyrococcus furiosusmaltodextrin-binding protein.J. Mol. Biol.305: 891-904.
  31. Fox, J.D., Kapust, R.B., and Waugh, D.S. (2001). Single amino acid substitutions on the surface ofEscherichia colimaltose-binding protein can have a profound impact on the solubility of fusion proteins.Protein Sci.10: 622-630.
  32. Needle, Danielle & Waugh, David. (2014). Rescuing Aggregation-Prone Proteins in Escherichia coli with a Dual His6-MBP Tag. Methods in molecular biology (Clifton, N.J.). 1177. 81-94. 10.1007/978-1-4939-1034-2_7.
  33. Lountos, George & Cherry, Scott & Tropea, Joseph & Waugh, David. (2015). Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate. Acta Crystallographica Section F. 71. 199-205. 10.1107/S2053230X15000217.
  34. Raran-Kurussi, Sreejith & Keefe, Karina & Waugh, David. (2015). Positional effects of fusion partners on the yield and solubility of MBP fusion proteins. Protein expression and purification. 110. 10.1016/j.pep.2015.03.004.
  35. Hewitt, William & Lountos, George & Zlotkowski, Katherine & Dahlhauser, Samuel & Saunders, Lindsey & Needle, Danielle & Tropea, Joseph & Zhan, Chendi & Wei, Guanghong & Ma, Buyong & Nussinov, Ruth & Waugh, David & Schneekloth, John. (2016). Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angewandte Chemie (International ed. in English). 55. 10.1002/anie.201511351.
  36. Raran-Kurussi, Sreejith & Waugh, David. (2016). A Dual Protease Approach for Expression and Affinity Purification of Recombinant Proteins. Analytical biochemistry. 504. 10.1016/j.ab.2016.04.006.
  37. Gumpena, Rajesh & Lountos, George & Raran-Kurussi, Sreejith & Tropea, Joseph & Cherry, Scott & Waugh, David. (2017). Crystal structure of the human dual specificity phosphatase 1 catalytic domain. Protein Science. 27. 10.1002/pro.3328.
  38. Gumpena, Rajesh & Lountos, George & Waugh, David. (2018). MBP-binding DARPins facilitate the crystallization of an MBP fusion protein. Acta Crystallographica Section F. 74. 549-557. 10.1107/S2053230X18009901.
  39. Hogan, Megan & Bahta, Medhanit & Tsuji, Kohei & Nguyen, Trung & Cherry, Scott & Lountos, George & Tropea, Joseph & Zhao, Bryan & Zhao, Xue Zhi & Waugh, David & Burke, Terrence & Ulrich, Robert. (2019). Targeting Protein–Protein Interactions of Tyrosine Phosphatases with Microarrayed Fragment Libraries Displayed on Phosphopeptide Substrate Scaffolds. ACS Combinatorial Science. 21. 10.1021/acscombsci.8b00122.
  40. Jin, Lan & Song, He & Tropea, Joseph & Needle, Danielle & Waugh, David & Gu, Shuo & Ji, Xinhua. (2019). The molecular mechanism of dsRNA processing by a bacterial Dicer. Nucleic acids research. 47. 4707-4720. 10.1093/nar/gkz208.
  41. Bozóki, Beáta & Mótyán, János & Hoffka, Gyula & Waugh, David & Tözsér, József. (2020). Specificity Studies of the Venezuelan Equine Encephalitis Virus Non-Structural Protein 2 Protease Using Recombinant Fluorescent Substrates. International Journal of Molecular Sciences. 21. 7686. 10.3390/ijms21207686.
  42. Zhao, Xue Zhi & Kiselev, Evgeny & Lountos, George & Wang, Wenjie & Tropea, Joseph & Needle, Danielle & Hilimire, Thomas & Schneekloth, John & Waugh, David & Pommier, Yves & Burke, Terrence. (2021). Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites. Chemical Science. 12. 10.1039/D0SC05411A.
  43. Hoffka, Gyula & Lountos, George & Needle, Danielle & Wlodawer, Alexander & Waugh, David & Tözsér, József & Mótyán, János. (2023). Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis. Journal of Molecular Biology. 435. 168012. 10.1016/j.jmb.2023.168012.
  44. Golda, Mária & Hoffka, Gyula & Cherry, Scott & Tropea, Joseph & Lountos, George & Waugh, David & Wlodawer, Alexander & Tözsér, József & Mótyán, János. (2024). P1' specificity of the S219V/R203G mutant tobacco etch virus protease. Proteins. 92. 10.1002/prot.26693.


Personal Profile

https://www.researchgate.net/profile/David-Waugh-4

https://ncifrederick.cancer.gov/ScientificLibrary/Bibliography/Waugh.aspx

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