Biosphysics Resource: Publications

The following are publications resulting from the use of the Biophysics Resource from 2000 to date:


  • Li J, Zhang Y, Soubias O, Khago D, Chao FA, Li Y, Shaw K, Byrd RA. Optimization of sortase A ligation for flexible engineering of complex protein systems. J Biol Chem. 2020 Feb 28;295(9):2664-2675. doi: 10.1074/jbc.RA119.012039. Epub 2020 Jan 23.
  • Zheng Z, Okada R, Kobayashi H, Nagaya T, Wei J, Zhou Q, Lee F, Bera TK, Gao Y, Kuhlman W, Tai CH, Pastan I.Site-Specific PEGylation of Anti-Mesothelin Recombinant Immunotoxins Increases Half-life and Antitumor Activity. Mol Cancer Ther. 2020 Mar;19(3):812-821. doi: 10.1158/1535-7163.MCT-19-0890.
  • Tomas Kroupa, Siddhartha A. K. Datta and Alan Rein, Distinct Contributions of Di_erent Domains within the HIV-1 Gag Polyprotein to Specific and Nonspecific Interactions with RNA, Viruses 2020, 12(4), 394; (registering DOI)
  • Buel GR, Chen X, Chari R, O'Neill MJ, Ebelle DL, Jenkins C, Sridharan V, Tarasov SG, Tarasova NI, Andresson T, Walters KJ. Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10. Nat Commun. 2020 Mar 10;11(1):1291. doi: 10.1038/s41467-020-15073-7.



  • Grkovic T, Evans JR, Akee RK, Guo L, Davis M, Jato J, Grothaus PG, Ahalt-Gottholm M, Hollingshead M, Collins JM, Newman DJ, O'Keefe BR. Erythrofordins D and E, two new cassaine-type diterpenes from Erythrophleum suaveolens. Bioorg Med Chem Lett. 2019 Jan 15;29(2):134-137. doi: 10.1016/j.bmcl.2018.12.019. Epub 2018 Dec 10.
  • Song H, Dharmasena MN, Wang C, Shaw GX, Cherry S, Tropea JE, Jin DJ, Ji X, Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. FEBS J. 2019 Nov 2. doi: 10.1111/febs.15120.
  • ​​​​Stagno JR, Yu P, Dyba MA, Wang YX, Liu Y  Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing. PLoS One. 2019 Apr 15;14(4):e0215555. doi: 10.1371/journal.pone.0215555. eCollection 2019.
  • Jin L, Song H, Tropea JE, Needle D, Waugh DS, Gu S, Ji X. The molecular mechanism of dsRNA processing by a bacterial Dicer. Nucleic Acids Res. 2019 Mar 27. pii: gkz208. doi: 10.1093/nar/gkz208.
  • Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA, Matsuo H. Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA Nucleic Acids Res. 2019 Aug 22;47(14):7676-7689. doi: 10.1093/nar/gkz550.
  • Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR, Waugh DS. Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res. 2019 Jun 14. pii: gkz515. doi: 10.1093/nar/gkz515
  • Neckles C, Boer RE, Aboreden N, Cross AM, Walker RL, Kim BH, Kim S, Schneekloth JS Jr, Caplen NJ. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction. RNA. 2019 Sep 11. pii: rna.072454.119. doi: 10.1261/rna.072454.119
  • Cao B, Lu TW, Martinez Fiesco JA, Tomasini M, Fan L, Simon SM, Taylor SS, Zhang P. Structures of the PKA RIα Holoenzyme with the FLHCC Driver J-PKAcα or Wild-Type PKAcα. Structure. 2019 May 7;27(5):816-828.e4. doi: 10.1016/j.str.2019.03.001.
  • Li Y, Soubias O, Li J, Sun S, Randazzo PA, Byrd RA. Functional Expression and Characterization of Human Myristoylated-Arf1 in Nanodisc Membrane Mimetics. Biochemistry. 2019 Mar 12;58(10):1423-1431. doi: 10.1021/acs.biochem.8b01323.
  • Chao FA, Li Y, Zhang Y, Byrd RA. Probing the Broad Time Scale and Heterogeneous Conformational Dynamics in the Catalytic Core of the Arf-GAP ASAP1 via Methyl Adiabatic Relaxation Dispersion. J Am Chem Soc. 2019 Jul 31;141(30):11881-11891. doi: 10.1021/jacs.9b02602.
  • Gibbs ME, Lountos GT, Gumpena R, Waugh DS. Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague. Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):608-615. doi: 10.1107/S2053230X19011154.



  • Comas-Garcia M, Kroupa T, Datta SA, Harvin DP, Hu WS, Rein A. Efficient support of virus-like particle assembly by the HIV-1 packaging signal. Elife. 2018 Aug 2;7. pii: e38438. doi: 10.7554/eLife.38438.
  • Anchoori RK, Jiang R, Peng S, Soong RS, Algethami A, Rudek MA, Anders N, Hung CF, Chen X, Lu X, Kayode O, Dyba M, Walters KJ, Roden RBS. Covalent Rpn13-Binding Inhibitors for the Treatment of Ovarian Cancer. ACS Omega. 2018 Sep 30;3(9):11917-11929. doi: 10.1021/acsomega.8b01479. Epub 2018 Sep 27.
  • Lountos GT1, Raran-Kurussi S2, Zhao BM3, Dyas BK4, Burke TR Jr5, Ulrich RG4, Waugh DS2. High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design. Acta Crystallogr D Struct Biol. 2018 Oct 1;74(Pt 10):1015-1026. doi: 10.1107/S2059798318011919. Epub 2018 Oct 2.
  • Gumpena R1, Lountos GT2, Waugh DS1. MBP-binding DARPins facilitate the crystallization of an MBP fusion protein. Acta Crystallogr F Struct Biol Commun. 2018 Sep 1;74(Pt 9):549-557. doi: 10.1107/S2053230X18009901. Epub 2018 Aug 29.
  • Calabrese DR1, Chen X2, Leon EC3, Gaikwad SM3, Phyo Z3, Hewitt WM1, Alden S1, Hilimire TA1, He F2, Michalowski AM3, Simmons JK3, Saunders LB1, Zhang S3, Connors D3, Walters KJ4, Mock BA5, Schneekloth JS Jr6 Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex. Nat Commun. 2018 Oct 12;9(1):4229. doi: 10.1038/s41467-018-06315-w.
  • Moon MH1, Hilimire TA1, Sanders AM1, Schneekloth JS Jr1. Measuring RNA-Ligand Interactions with Microscale Thermophoresis. Biochemistry. 2018 Aug 7;57(31):4638-4643. doi: 10.1021/acs.biochem.7b01141. Epub 2018 Jan 31.
  • Calabrese DR1, Zlotkowski K1, Alden S1, Hewitt WM1, Connelly CM1, Wilson RM1, Gaikwad S2, Chen L3, Guha R3, Thomas CJ3, Mock BA2, Schneekloth JS Jr1. Characterization of clinically used oral antiseptics as quadruplex-binding ligands. Nucleic Acids Res. 2018 Apr 6;46(6):2722-2732. doi: 10.1093/nar/gky084.
  • Atanu Maiti,1 Wazo Myint,1 Tapan Kanai,1 Krista Delviks-Frankenberry,2 Christina Sierra Rodriguez,1 Vinay K. Pathak,2 Celia A. Schiffer,3 and Hiroshi Matsuocorresponding author1 Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA Nat Commun. 2018 Jun 25;9(1):2460. doi: 10.1038/s41467-018-04872-8.
  • Yan P1,2, Ritt DA3, Zlotkowski K4, Bokesch HR1,5, Reinhold WC6, Schneekloth JS Jr4, Morrison DK3, Gustafson KR1. Macrophilones from the Marine Hydroid Macrorhynchia philippina Can Inhibit ERK Cascade Signaling. J Nat Prod. 2018 Jul 27;81(7):1666-1672. doi: 10.1021/acs.jnatprod.8b00343. Epub 2018 Jul 6.



  • Zlotkowski K, Hewitt WM, Sinniah RS, Tropea JE, Needle D, Lountos GT, Barchi JJ Jr, Waugh DS, Schneekloth JS Jr. A Small-Molecule Microarray Approach for the Identification of E2 Enzyme Inhibitors in Ubiquitin-Like Conjugation Pathways SLAS Discov. 2017 Jul;22(6):760-766. doi: 10.1177/2472555216683937. Epub 2017 Jan 6.
  • Abulwerdi FA, Shortridge MD, Sztuba-Solinska J, Wilson R, Le Grice SF, Varani G, Schneekloth JS Jr. Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA J Med Chem. 2016 Dec 22;59(24):11148-11160. doi: 10.1021/acs.jmedchem.6b01450. Epub 2016 Dec 2.
  • Lu X, Nowicka U, Sridharan V, Liu F, Randles L, Hymel D, Dyba M, Tarasov SG, Tarasova NI, Zhao XZ, Hamazaki J, Murata S, Burke TR Jr, Walters KJ. Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets. Nat Commun. 2017 Jun 9;8:15540. doi: 10.1038/ncomms15540.
  • Zlotkowski K, Hewitt WM, Yan P, Bokesch HR, Peach ML, Nicklaus MC, O'Keefe BR, McMahon JB, Gustafson KR, Schneekloth JS Jr. Macrophilone A: Structure Elucidation, Total Synthesis, and Functional Evaluation of a Biologically Active Iminoquinone from the Marine Hydroid Macrorhynchia philippina. Org Lett. 2017 Apr 7;19(7):1726-1729. doi: 10.1021/acs.orglett.7b00496. Epub 2017 Mar 27.
  • O'Carroll IP, Thappeta Y, Fan L, Ramirez-Valdez EA, Smith S, Wang YX, Rein A. Contributions of individual domains to function of the HIV-1 Rev response element. J Virol. 2017 Aug 16. pii: JVI.00746-17. doi: 10.1128/JVI.00746-17. [Epub ahead of print]
  • Aguilar-Alonso F, Whiting AL, Kim YJ, Bernal F. Biophysical and biological evaluation of optimized stapled peptide inhibitors of the linear ubiquitin chain assembly complex (LUBAC). Bioorg Med Chem. 2017 Dec 5. pii: S0968-0896(17)31746-7. doi: 10.1016/j.bmc.2017.11.047. 
  • Vrentas CE, Moayeri M, Keefer AB, Greaney AJ, Tremblay J, O'Mard D, Leppla SH, Shoemaker CB, In vivo characterization of an Hfq protein encoded by the Bacillus anthracis virulence plasmid pXO1. J Biol Chem. 2016 Oct 7;291(41):21596-21606. Epub 2016 Aug 18.
  • Chan ST, Nani RR, Schauer EA, Martin GE, Williamson RT, Saurí J, Buevich AV, Schafer WA, Joyce LA, Goey AK, Figg WD, Ransom TT, Henrich CJ, McKee TC, Moser A, MacDonald SA, Khan S, McMahon JB, Schnermann MJ, Gustafson KR, Characterization and Synthesis of Eudistidine C, a Bioactive Marine Alkaloid with an Intriguing Molecular Scaffold. J Org Chem. 2016 Nov 18;81(22):10631-10640. Epub 2016 Nov 10.



  • Chen W, Bardhi A, Feng Y, Wang Y, Qi Q, Li W, Zhu Z, Dyba MA, Ying T, Jiang S, Goldstein H, Dimitrov DS Improving the 5CH1-CK heterodimerization and pharmacokinetics of 4Dm2m, a novel potent CD4-antibody fusion protein against HIV-1. MAbs. 2016 May-Jun;8(4):761-74. doi: 10.1080/19420862.2016.1160180. Epub 2016 Mar 10.
  • Shi Y, Chen X, Elsasser S, Stocks BB, Tian G, Lee BH, Shi Y, Zhang N, de Poot SA, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Finley D, Walters KJ. Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science. 2016 Feb 19;351(6275). pii: aad9421. doi: 10.1126/science.aad9421.
  • Hewitt WM, Lountos GT, Zlotkowski K, Dahlhauser SD, Saunders LB, Needle D, Tropea JE, Zhan C, Wei G, Ma B, Nussinov R, Waugh DS, Schneekloth JS Jr. Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angew Chem Int Ed Engl. 2016 May 4;55(19):5703-7. doi: 10.1002/anie.201511351. Epub 2016 Apr 1.
  • umari V, Dyba MA, Holland RJ, Liang YH, Singh SV, Ji X. Irreversible Inhibition of Glutathione S-Transferase by Phenethyl Isothiocyanate (PEITC), a Dietary Cancer Chemopreventive Phytochemical. PLoS One. 2016 Sep 29;11(9):e0163821. doi: 10.1371/journal.pone.0163821.
  • Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature. 2016 Nov 14. doi: 10.1038/nature20599. [Epub ahead of print]
  • Raran-Kurussi S, Waugh DS A dual protease approach for expression and affinity purification of recombinant proteins. Anal Biochem. 2016 Jul 1;504:30-7. doi: 10.1016/j.ab.2016.04.006. Epub 2016 Apr 19.
  • Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Applications of PLOR in labeling large RNAs at specific sites. Methods. 2016 Jul 1;103:4-10. doi: 10.1016/j.ymeth.2016.03.014. Epub 2016 Mar 23.
  • Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ. Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure. 2016 Aug 2;24(8):1257-70. doi: 10.1016/j.str.2016.05.018. Epub 2016 Jul 7.


  • Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, De Chen, Ying J, Lockett S, Nesbitt DJ, Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature. 2015 May 4. doi: 10.1038/nature14352. [Epub ahead of print
  • Kim Y, Maciag AE, Cao Z, Deschamps JR, Saavedra JE, Keefer LK, Holland RJ PABA/NO lead optimization: Improved targeting of cytotoxicity to glutathione S-transferase P1-overexpressing cancer cells. Bioorg Med Chem. 2015 May 19. pii: S0968-0896(15)00420-4. doi: 10.1016/j.bmc.2015.05.020. [Epub ahead of print]
  • Lountos GT, Cherry S, Tropea JE, Waugh DS. Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate. Acta Crystallogr F Struct Biol Commun. 2015 Feb;71(Pt 2):199-205. doi: 10.1107/S2053230X15000217. Epub 2015 Jan 28.
  • Lountos GT, Austin BP, Tropea JE, Waugh DS., Structure of human dual-specificity phosphatase 7, a potential cancer drug target, Acta Crystallogr F Struct Biol Commun. 2015 Jun;71(Pt 6):650-6. doi: 10.1107/S2053230X1500504X. Epub 2015 May 20.
  • Needle D, Lountos GT, Waugh DS, Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity, Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1102-11. doi: 10.1107/S1399004715003521. Epub 2015 Apr 24.
  • Shengjian Li, Yu-He Liang, Jennifer Mariano, Meredith B. Metzger, Daniel K. Stringer, Ventzislava A. Hristova, Jess Li, Paul A. Randazzo, Yien Che Tsai, Xinhua Ji, and Allan M. Weissman, Insights into Ubiquitination from the Unique Clamp-Like Binding of the RING E3 AO7 to the E2 UbcH5B, J Biol Chem. 2015 Oct 16. pii: jbc.M115.685867
  • Lu X1, Liu F1, Durham SE2, Tarasov SG, Walters KJ. A High Affinity hRpn2-Derived Peptide That Displaces Human Rpn13 from Proteasome in 293T Cells. PLoS One. 2015 Oct 14;10(10):e0140518. doi: 10.1371/journal.pone.0140518. eCollection 2015.
  • Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R. GTP-Dependent K-Ras Dimerization. Structure. 2015 Jul 7;23(7):1325-35. doi: 10.1016/j.str.2015.04.019. Epub 2015 Jun 4
  • Nowicka U, Hoffman M, Randles L, Shi X, Khavrutskii L, Stefanisko K, Tarasova NI, Darwin KH, Walters KJ. Mycobacterium tuberculosis copper-regulated protein SocB is an intrinsically disordered protein that folds upon interaction with a synthetic phospholipid bilayer. Proteins. 2015 Dec 9. doi: 10.1002/prot.24970.
  • Chavan TS, Jang H, Khavrutskii L, Abraham SJ, Banerjee A, Freed BC, Johannessen L, Tarasov SG, Gaponenko V, Nussinov R, Tarasova NI. High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site. Biophys J. 2015 Dec 15;109(12):2602-13. doi: 10.1016/j.bpj.2015.09.034
  • Li S, Liang YH, Mariano J, Metzger MB, Stringer DK, Hristova VA, Li J, Randazzo PA, Tsai YC, Ji X, Weissman AM. Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. J Biol Chem. 2015 Dec 18;290(51):30225-39. doi: 10.1074/jbc.M115.685867. Epub 2015 Oct 16.
  • Datta SA, Clark PK, Fan L, Ma B, Harvin DP, Sowder RC 2nd, Nussinov R, Wang YX, Rein A. Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly. J Virol. 2015 Dec 4;90(4):1773-87. doi: 10.1128/JVI.02061-15.


  • Debanjan Biswas,Joseph A. Hrabie, Joseph E. Saavedra, Zhao Cao, Larry K. Keefer, Joseph Ivanic,and Ryan J. Holland, ,Aminolysis of an N‑Diazeniumdiolated Amidine as an Approach to Diazeniumdiolated Ammonia, J. Org. Chem., 2014, 79 (10), pp 4512–4516
  • Anna E. Maciag, Ryan J. Holland, Youseung Kim, Vandana Kumari, Christina E. Luthers, Waheed S. Sehareen, Debanjan Biswas, Nicole L. Morri , Xinhua Ji, Lucy M. Anderson, Joseph E. Saavedra, and Larry K. Keefer, Nitric Oxide (NO) Releasing Poly ADP-ribose Polymerase 1 (PARP-1) Inhibitors Targeted to Glutathione S-Transferase P1-Overexpressing Cancer Cells, J. Med. Chem., 2014, 57 (6), pp 2292–2302
  • Huang T1, Li J, Byrd RA., Solution structure of lysine-free (K0) ubiquitin, Protein Sci. 2014 May;23(5):662-7. doi: 10.1002/pro.2450. Epub 2014 Mar 17.
  • Tianlei Ying, Tina W. Ju, Yanping Wang, Ponraj Prabakaran and Dimiter S. Dimitrov, Interactions of IgG1 CH2 and CH3 domains with FcRn, Front Immunol. 2014 Apr 2;5:146. doi: 10.3389/fimmu.2014.00146. eCollection 2014.
  • Ryan J. Holland, John R. Klose, Jeffrey R. Deschamps, Zhao Cao, Larry K. Keefer and Joseph E. Saavedra, Direct Reaction of Amides with Nitric Oxide To Form Diazeniumdiolates, J. Org. Chem., 2014, 79 (19), pp 9389–9393
  • Shaw GX, Li Y, Shi G, Wu Y, Cherry S, Needle D, Zhang D, Tropea JE, Waugh DS, Yan H, Ji X., Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK–DHPS from the biowarfare agent Francisella tularensis, FEBS J. 2014 Sep;281(18):4123-37. doi: 10.1111/febs.12896. Epub 2014 Jul 23.
  • Sreejith Raran-Kurussi, David S. Waugh, Unrelated Solubility-Enhancing Fusion Partners MBP and NusA Utilize a Similar Mode of Action, Biotechnol Bioeng. 2014 Jun 18. doi: 10.1002/bit.25317
  • Grkovic T, Blees JS, Bayer MM, Colburn NH, Thomas CL, Henrich CJ, Peach ML, McMahon JB, Schmid T, Gustafson KR, Tricyclic guanidine alkaloids from the marine sponge Acanthella cavernosa that stabilize the tumor suppressor PDCD4, Mar Drugs. 2014 Aug 21;12(8):4593-601. doi: 10.3390/md12084593..
  • Zhu Z, Ramakrishnan B, Li J, Wang Y, Feng Y, Prabakaran P, Colantonio S, Dyba MA, Qasba PK, Dimitrov DS, Site-specific antibody-drug conjugation through an engineered glycotransferase and a chemically reactive sugar. MAbs. 2014 Aug 5;6(5)


  • Xianyang Fang, Jinbu Wang, Ina P. O’Carroll, Michelle Mitchell, Xiaobing Zuo, Yi Wang, Ping Yu, Yu Liu, Jason W. Rausch, Marzena A. Dyba, Jørgen Kjems, Charles D. Schwieters, Soenke Seifert, Randall E. Winans, Norman R. Watts, Stephen J. Stahl, Paul T. Wingfield, R. Andrew Byrd, Stuart F.J. Le Grice, Alan Rein, Yun-Xing WangAn Unusual Topological Structure of the HIV-1 Rev Response Element, Cell, Volume 155, Issue 3, 24 October 2013, Pages 594–605
  • Ryan J. Holland, Rika Paulisch, Zhao Cao, Larry K. Keefer, Joseph E. Saavedra, Sonia Donzelli, Enzymatic generation of the NO/HNO-releasing IPA/NO anion at controlled rates in physiological media using β-galactosidase, Nitric Oxide, Volume 35, 30 November 2013, Pages 131–136
  • Tianlei Ying, Weizao Chen, Yang Feng, Yanping Wang, Rui Gong and Dimiter S. Dimitrov, Engineered soluble monomeric IgG1 CH3 domain: generation, mechanisms of function, and implications for design of biological therapeutics. J Biol Chem. 2013 Aug 30;288(35):25154-64. doi: 10.1074/jbc.M113.484154. Epub 2013 Jul 18.
  • Gong R, Wang Y, Ying T, Feng Y, Streaker E, Prabakaran P, Dimitrov DS. N-Terminal Truncation of an Isolated Human IgG1 CH2 Domain Significantly Increases Its Stability and Aggregation Resistance. Mol Pharm. 2013 May 29. [Epub ahead of print]
  • Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA, Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 2013 Sep 11;32(18):2504-16. doi: 10.1038/emboj.2013.174. Epub 2013 Aug 13.
  • Devkota KP, Covell D, Ransom T, McMahon JB, Beutler JA. Growth inhibition of human colon carcinoma cells by sesquiterpenoids and tetralones of Zygogynum calothyrsum. J Nat Prod. 2013 Apr 26;76(4):710-4. doi: 10.1021/np400042q. Epub 2013 Mar 21.
  • Pazgier M, Ericksen B, Ling M, Toth E, Shi J, Li X, Galliher-Beckley A, Lan L, Zou G, Zhan C, Yuan W, Pozharski E, Lu W. Structural and functional analysis of the pro-domain of human cathelicidin, LL-37. Biochemistry. 2013 Mar 5;52(9):1547-58. doi: 10.1021/bi301008r. Epub 2013 Feb 21.
  • Khavrutskii L, Yeh J, Timofeeva O, Tarasov SG, Pritt S, Stefanisko K, Tarasova N. Protein purification-free method of binding affinity determination by microscale thermophoresis. J Vis Exp. 2013 Aug 15;(78). doi: 10.3791/50541.
  • Tewary P, de la Rosa G, Sharma N, Rodriguez LG, Tarasov SG, Howard OM, Shirota H, Steinhagen F, Klinman DM, Yang D, Oppenheim JJ. β-Defensin 2 and 3 promote the uptake of self or CpG DNA, enhance IFN-α production by human plasmacytoid dendritic cells, and promote inflammation. J Immunol. 2013 Jul 15;191(2):865-74. doi: 10.4049/jimmunol.1201648. Epub 2013 Jun 17.


  • Rahul S. Nandurdikar, Anna E. Maciag, Ryan J. Holland, Zhao Cao, Paul J. Shami, Lucy M. Anderson, Larry K. Keefer, Joseph E. Saavedra, Structural modifications modulate stability of glutathione-activated arylated diazeniumdiolate prodrugs. Bioorganic & Medicinal Chemistry 20 (2012) 3094–3099
  • George T. Lountos, Joseph E. Tropea and David S. Waugh, Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system, Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):201-9. Epub 2012 Feb 7
  • Timofeeva OA, Chasovskikh S, Lonskaya I, Tarasova NI, Khavrutskii L, Tarasov SG, Zhang X, Korostyshevskiy VR, Cheema A, Zhang L, Dakshanamurthy S, Brown ML, Dritschilo A., Mechanisms of unphosphorylated STAT3 transcription factor binding to DNA., J Biol Chem. 2012 Apr 20;287(17):14192-200. Epub 2012 Feb 29.
  • Tianlei Ying, Weizao Chen, Rui Gong, Yang Feng and Dimiter S. Dimitrov, Soluble Monomeric IgG1 Fc, J Biol Chem. 2012 Apr 19. [Epub ahead of print]
  • Whitson EL, Sun H, Thomas CL, Henrich CJ, Sayers TJ, McMahon JB, Griesinger C, McKee TC., Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima., J Nat Prod. 2012 Mar 23;75(3):394-9. Epub 2012 Feb 7.
  • Rahul S. Nandurdikara, Anna E. Maciag, Zhao Cao, Larry K. Keefer, Joseph E. Saavedra, Diazeniumdiolated carbamates: A novel class of nitric oxide donors, Bioorg Med Chem. 2012 Mar 15;20(6):2025-9. Epub 2012 Feb 4.
  • Akee RK, Ransom T, Ratnayake R, McMahon JB, Beutler JA., Chlorinated englerins with selective inhibition of renal cancer cell growth, J Nat Prod. 2012 Mar 23;75(3):459-63. Epub 2012 Jan 26.
  • Edson dos A. dos Santos, Paulo C. Prado, Wanderley R. de Carvalho, Ricardo V. de Lima, Adilson Beatriz, Dênis P. de Lima, Ernest Hamel, Marzena A. Dyba and Sergio Albuquerque, Synthesis and Biological Activity of Sulfur Compounds Showing Structural Analogy with Combretastatin A-4 [REF.: 161/12] Qimica Nova, 2012 (in press)
  • Biswas D, Holland RJ, Deschamps JR, Cao Z, Keefer LK, Saavedra JE. O(2)-functionalized methylamine diazeniumdiolates: evidence for e ⇄ z equilibration in an acyclic system. J Org Chem. 2012 Dec 7;77(23):10804-10. doi: 10.1021/jo3020837. Epub 2012 Nov 20. PMID: 23137026 [PubMed - in process]
  • Holland RJ, Maciag AE, Kumar V, Shi L, Saavedra JE, Prud'homme RK, Chakrapani H, Keefer LK. Cross-Linking Protein Glutathionylation Mediated by O(2)-Arylated Bis-Diazeniumdiolate "Double JS-K". Chem Res Toxicol. 2012 Dec 17;25(12):2670-7. doi: 10.1021/tx3003142. Epub 2012 Nov 9. PMID: 23106594 [PubMed - in process]
  • Diyabalanage T, Ratnayake R, Bokesch HR, Ransom TT, Henrich CJ, Beutler JA, McMahon JB, Gustafson KR., Flabelliferins A and B, sesterterpenoids from the South Pacific sponge Carteriospongia flabellifera. J Nat Prod. 2012 Aug 24;75(8):1490-4. doi: 10.1021/np3003518. Epub 2012 Jul 26.
  • Lountos GT, Tropea JE, Waugh DS., Structure of the Trypanosoma cruzi protein tyrosine phosphatase TcPTP1, a potential therapeutic target for Chagas' disease. Mol Biochem Parasitol. 2013 Jan;187(1):1-8. doi: 10.1016/j.molbiopara.2012.10.006. Epub 2012 Nov 5.
  • Shi G, Shaw G, Li Y, Wu Y, Yan H, Ji X. Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: new lead exhibits a distinct binding mode. Bioorg Med Chem. 2012 Jul 15;20(14):4303-9. doi: 10.1016/j.bmc.2012.05.060. Epub 2012 Jun 6
  • Liu S, Chen Y, Li J, Huang T, Tarasov S, King A, Weissman AM, Byrd RA, Das R. Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains. Structure. 2012 Dec 5;20(12):2138-50. doi: 10.1016/j.str.2012.09.020. Epub 2012 Nov 1.
  • Brian P. Austin,József Tözsér, Péter Bagossi, Joseph E. Tropea, David S. Waugh The substrate specificity of Metarhizium anisopliae and Bos Taurus carboxypeptidases A: Insights into their use as tools for the removal of affinity Protein Expr Purif.


  • Siddhartha A. K. Datta1, Frank Heinrich, Sindhu Raghunandan, Susan Krueger, Joseph E. Curtis, Alan Rein and Hirsh Nanda, HIV-1 Gag Extension: Conformational Changes Require Simultaneous Interaction with Membrane and Nucleic Acid, J. Mol. Biol. (2011) 406, 205–214
  • Versiani MA, Diyabalanage T, Ratnayake R, Henrich CJ, Bates SE, McMahon JB, Gustafson KR., Flavonoids from eight tropical plant species that inhibit the multidrug resistance transporter ABCG2., J Nat Prod. 2011 Feb 25;74(2):262-6. Epub 2011 Jan 28.
  • Tanja Grkovica,Emily L. Whitsona, Daniel C. Rabeb, Roberta S. Gardellaa, Donald P. Bottarob, W. Marston Linehanb, James B. McMahona, Kirk R. Gustafson, Tawnya C. McKeea, Identification and evaluation of soft coral diterpenes as inhibitors of HIF-2α induced gene expression, Bioorg Med Chem Lett. 2011 Apr 1;21(7):2113-5. Epub 2011 Feb 23.
  • usan Keay, Piotr Kaczmarek, Chen-Ou Zhang, Kristopher Koch, Zoltan Szekely, Joseph J. Barchi Jr, Christopher MichejdaNormalization of Proliferation and Tight Junction Formation in Bladder Epithelial Cells from Patients with Interstitial Cystitis/Painful Bladder Syndrome by d-Proline and d-Pipecolic Acid Derivatives of Antiproliferative Factor, Chem Biol Drug Des. 2011 Jun;77(6):421-30. doi: 10.1111/j.1747-0285.2011.01108.x. Epub 2011 Apr 27.
  • Tanja Grkovic†, Johanna S. Blees‡§, Nancy H. Colburn‡, Tobias Schmid§, Cheryl L. Thomas†, Curtis J. Henrich†, James B. McMahon†, and Kirk R. Gustafson, Cryptocaryols A–H, α-Pyrone-Containing 1,3-Polyols from Cryptocarya sp. Implicated in Stabilizing the Tumor Suppressor Pdcd4, J Nat Prod. 2011 May 27;74(5):1015-20. Epub 2011 May 3.
  • Siddhartha A.K. Datta, Lakew G. Temeselew, Rachael M. Crist, Ferri Soheilian, Anne Kamata, Jane Mirro, Demetria Harvin, Kunio Nagashima, Raul E. Cachau, and Alan Rein, On the role of the sp1 domain in hiv-1 particle assembly: a molecular switch?, J. Virol. doi:10.1128/JVI.00006-11 (2011)
  • Liv Johannessen], Jarrett Remsberg], Vadim Gaponenko[, Kristie M. Adams], Joseph J.Barchi Jr, Sergey G. Tarasov], Sheng Jiang], Nadya I. Tarasova "Peptide structure stabilization by membrane anchoring and its general applicability for the development of potent cell permeable inhibitors" Chem. and Chem.Biol. 2011 Mar 1. doi: 10.1002/cbic.201000563.
  • Tanigawa S, Wang H, Yang Y, Sharma N, Tarasova N, Ajima R, Yamaguchi TP, Rodriguez LG, Perantoni AO Wnt4 induces nephronic tubules in metanephric mesenchyme by a non-canonical mechanism.. Dev Biol. 2011 Apr 1;352(1):58-69. Epub 2011 Jan 21. PMID: 21256838 [PubMed - in process]
  • Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic acids research. 2011. PMID:21652641 [Journal]
  • Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X. The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA. Proc. Natl. Acad. Sci. U.S.A. 108: 10156-61, 2011. [Journal]
  • Tarasov SG, Gaponenko V, Howard OM, Chen Y, Oppenheim JJ, Dyba MA, Subramaniam S, Lee Y, Michejda C, Tarasova NI.Structural plasticity of a transmembrane peptide allows self-assembly into biologically active nanoparticles. Proc. Natl. Acad. Sci. U.S.A. 108: 9798-803, 2011. [Journal]
  • George T. Lountos , Joseph E. Tropeaand David S. WaughStructure of human dual-specificity phosphatase 27 at 2.38 Å resolution Crystallogr D Biol Crystallogr. 2011 May;67(Pt 5):471-9. Epub 2011 Apr 16.
  • Medhanit Bahta, George T. Lountos, Beverly Dyas, Sung-Eun Kim, Robert G. Ulrich, David S. Waugh, and Terrence R. Burke, Jr Utilization of Nitrophenylphosphates and Oxime-Based Ligation for the Development of Nanomolar Affinity Inhibitors of the Yersinia pestis Outer Protein H (YopH) Phosphatase J. Med. Chem., 2011, 54 (8), pp 2933–2943 DOI: 10.1021/jm200022g Publication Date (Web): March 28, 2011
  • Sung-Eun Kim , Medhanit Bahta , George T. Lountos , Robert G. Ulrich , Terrence R. Burke Jrand David S. Waugh 6Isothiazolidinone (IZD) as a phosphoryl mimetic in inhibitors of the Yersinia pestis protein tyrosine phosphatase YopH Acta Crystallogr D Biol Crystallogr. 2011 Jul;67(Pt 7):639-45. Epub 2011 Jun 11
  • Gong R, Wang Y, Feng Y, Zhao Q, Dimitrov DS., Shortened engineered human antibody CH2 domains: increased stability and binding to the human neonatal Fc receptor., J Biol Chem. 2011 Aug 5;286(31):27288-93. Epub 2011 Jun 13.
  • Whitson EL, Pluchino KM, Hall MD, McMahon JB, McKee TC., New candidaspongiolides, tedanolide analogues that selectively inhibit melanoma cell growth., Org Lett. 2011 Jul 1;13(13):3518-21. Epub 2011 Jun 6.
  • Liu F, Park JE, Qian WJ, Lim D, Gräber M, Berg T, Yaffe MB, Lee KS, Burke TR Jr., Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel., Nat Chem Biol. 2011 Jul 17;7(9):595-601. doi: 10.1038/nchembio.614.
  • Diyabalanage T, Ratnayake R, Wilson JA, Henrich CJ, Beutler JA, Colburn NH, McMahon JB, Gustafson KR., Nothospondin, a new AP-1 inhibitory quassinoid from the Cameroonian plant Nothospondias staudtii., Bioorg Med Chem Lett. 2011 Aug 1;21(15):4397-9. Epub 2011 Jun 17.
  • Popplewell WL, Ratnayake R, Wilson JA, Beutler JA, Colburn NH, Henrich CJ, McMahon JB, McKee TC., Grassypeptolides F and G, cyanobacterial peptides from Lyngbya majuscula., J Nat Prod. 2011 Aug 26;74(8):1686-91. Epub 2011 Aug 1.
  • Koch KR, Zhang CO, Kaczmarek P, Barchi J Jr, Guo L, Shahjee HM, Keay S., The effect of a novel frizzled 8-related antiproliferative factor on in vitro carcinoma and melanoma cell proliferation and invasion., Invest New Drugs. 2011 Sep 20. [Epub ahead of print]
  • George T. Lountosa, Andrew G. Jobsonb, Joseph E. Tropeaa, Christopher R. Selfc, Guangtao Zhangc, Yves Pommierb, Robert H. Shoemakerd, David S. Waugh, Structural characterization of inhibitor complexes with checkpoint kinase 2 (Chk2), a drug target for cancer therapy, J Struct Biol. 2011 Dec;176(3):292-301. Epub 2011 Sep 22.
  • George T. Lountosa, b, Andrew G. Jobsonc, Joseph E. Tropeab, Christopher R. Selfd, Guangtao Zhangd, Yves Pommierc, Robert H. Shoemakere, David S. Waugh, X-ray structures of checkpoint kinase 2 in complex with inhibitors that target its gatekeeper-dependent hydrophobic pocket, FEBS Lett. 2011 Oct 20;585(20):3245-9. Epub 2011 Sep 7.
  • Lee Y, Chen Y, Tarasova NI, Gaponenko V., The structure of monomeric components of self-assembling CXCR4 antagonists determines the architecture of resulting nanostructures, Nanotechnology. 2011 Dec 16;22(50):505101. Epub 2011 Nov 23
  • Genbin Shia, Gary Shawa, Yu-He Lianga, Priadarsini Subburamana, Yue Lib, Yan Wub, Honggao Yanb, Xinhua Ji, Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties, Bioorg Med Chem. 2012 Jan 1;20(1):47-57. Epub 2011 Nov 23
  • Mercer N, Ramakrishnan B, Boeggeman E, Qasba PK., Applications of site-specific labeling to study HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid., PLoS One. 2011;6(10):e26093. Epub 2011 Oct 10.
  • Brian P. Austin, David S. Waugh, Isolation of Metarhizium anisopliae carboxypeptidase A with native disulfide bonds from the cytosol of Escherichia coli BL21(DE3), Protein Expr Purif. 2012 Mar;82(1):116-24. Epub 2011 Dec 14.
  • Bokesch HR, Gardella RS, Rabe DC, Bottaro DP, Linehan WM, McMahon JB, McKee TC., A new hypoxia inducible factor-2 inhibitory pyrrolinone alkaloid from roots and stems of Piper sarmentosum., Chem Pharm Bull (Tokyo). 2011;59(9):1178-9.
  • Shi G, Ji X. New ways to derivatize at position 6 of 7,7-dimethyl-7,8-dihydropterin. Tetrahedron Lett.2011 Nov 16;52(46):6174-6176.












  • Evdokimov AG, Anderson DE, Routzahn KM, Waugh DS. Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of YopM, an essential virulence factor extruded by the plague bacterium Yersinia pestis. Acta Crystallogr. D Biol. Crystallogr. 56: 1676-9, 2000. [Journal]