Publications

 

Recent Publications (2014-2017)

2017

Bai L, Zhou B, Yang CY, Ji J, McEachern D, Przybranowski S, Jiang H, Hu J, Xu F, Zhao Y, Liu L, Fernandez-Salas E, Xu J, Dou Y, Wen B, Sun D, Meagher JL, Stuckey J, Hayes DF, Li S, Ellis MJ, Wang S. Targeted degradation of BET proteins in triple-negative breast cancer. Cancer Research 2017 [Epub ahead of print] DOI: 10.1158/0008-5472.CAN-16-2622.
 
Lopera-Madrid J, Osorio JE, He Y, Xiang Z, Adams LG, Laughlin RC, Mwangi W, Subramanya S, Neilan J, Brake D, Burrage TG, Brown WC, Clavijo A, Bounpheng MA. Safety and immunogenicity of mammalian cell derived and Modified Vaccinia Ankara vectored African swine fever subunit antigens in swine. Veterinary Immunology and Immunopathology. 2017 185:20-33. DOI: 10.1016/j.vetimm.2017.01.004

2016

Akey DL, Terwilliger TC, Smith JL. Efficient merging of data from multiple samples for determination of anomalous substructure. Acta Crystallographica Section D: Structural Biology 2016 73(3): 296-302. DOI: 10.1107/S2059798315021920

Aslam MN, Jepsen KJ, Khoury B, Graf KH, Varani J. Bone structure and function in male C57BL/6 mice: Effects of a high-fat Western-style diet with or without trace minerals. Bone Reports 2016 Dec 5:141-149. Doi: 10.1016/j.bonr.2016.05.002

 
Bergom C, Hauser AD, Rymaszewski A, Gonyo P, Prokop JW, Jennings BC, Lawton AJ, Frei A, Lorimer EL, Aguilera-Barrantes I, Mackinnon AC, Noon K, Fierke CA, Williams CL. The tumor-suppressive small GTPase DiRas1 binds the noncanonical guanine nucleotide exchange factor SmgGDS and antagonizes SmgGDS interactions with oncogenic small GTPases. Journal of Biological Chemistry 2016 March 291(12): 6534 -6545. doi: 10.1074/jbc.M115.696831
 
Boeras I, Song Z, Moran A. Franklin J, Brown WC, Johnson M, Boris-Lawrie K, Heng X. DHX9/RHA binding to the PBS-segment of the genomic RNA during HIV-1 assembly bolsters virion infectivity. J Mol Biol 2016 June 428(11) 2418-2429.
 
Borkin D, Pollock J, Kempinska K, Purohit T, Li X, Wen B, Zhao T, Miao H, Shukla S, He M, Sun D, Cierpicki T, Grembecka J. Property Focused Structure-Based Optimization of Small Molecule Inhibitors of the Protein-Protein Interaction between Menin and Mixed Lineage Leukemia (MLL). J Med Chem 2016 Aug 59(3):892-913. doi: 10.1021/acs.jmedchem.5b01305

Brown WC, Akey DL, Konwerski JR, Tarrasch JT, Skiniotis G, Kuhn RJ, Smith JL. Extended surface for membrane association in Zika virus NS1 structure. Nature Structural and Molecular Biology 2016 23(9):865-867. DOI: 10.1038/nsmb.3268

Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD Jr, Melnick AM. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest 2016 Aug. Epub ahead of print. doi: 10.1172/JCI85795. PMID: 27482887.
 
Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. Journal of Chemical Information and Modeling 2016 June 56(6) 1063-1077. doi 10.1021/acs.jcim.5b00523

Carpenter C, Sorenson RJ, Jin Y, Klossowski S, Cierpicki T, Gnegy M, Showalter HD. Design and synthesis of triarylacrylonitrile analogues of tamoxifen with improved binding selectivity to protein kinase C. Bioorganical and Medicinal Chemistry 2016 24(21):5495-5504.

Cash JN, Davis EM, Tesmer JJG. Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3. Structure 2016 May 24(5)730-740. Doi: 10.1016/j.str.2016.02.022
 
Demars MD, Sheng F, Park SR, Lowell AN, Podust LM, Sherman DH. Biochemical and Structural Characterization of MycCI, a Versatile P450 Biocatalyst from the Mycinamicin Biosynthetic Pathway. ACS Chemical Biology 2016 11(9) 2642-2654.
 
Fick RJ, Kroner GM, Nepal B, Magnani R, Horowitz S, Houtz RL, Scheiner S, Trievel RC. Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9. ACS Chemical Biology 2016 11(3):748-754.
 
Fiers WD, Dodge GJ, Sherman DH, Smith JL, Aldrich CC. Vinylogous dehydration by a polyketide dehydratase domain in curacin biosynthesis. J Am Chem Soc 2016 138(49):16024-16036.
 

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK. D3R grand challenge fo 2015: Evaluation of protein-ligand pose and affinity predictions. Journal of Computer-Aided Molecular Design 2016 Sept 1 30(9)651-668.

 

Gray F, Cho HJ, Shukla S, He S, Harris A, Boytsov B, Jaremko A, Jarermko M, Demeler B, Lawlor ER, Grembecka J, Cierpicki T. BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization. Nature Communications 2016 7:13343.

 
Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, Van Den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL III, Bardwell JCA. Visualizing chaperone-assisted protein folding. Nature Structural and Molecular Biology2016 July 23(7):691-97. doi: 10.1038/nsmb.3237
 
Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-selective analogs of dasatinib reveal insight into kinase inhibitor binding and selectivity. ACS Chem Biol 2016 Feb 19 11(5) 1296- 1304. Doi: 10.1021/acschembio.5b01018
 
Lorenz DA, Garner AL. A click chemistry-based microRNA maturation assay optimized for high-throughput screening. Chemical Communications 2016 52(53): 8267- 8270. doi: 10.1039/c6cc02894b

Maloney FP, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate. Proceedings of the National Academy of Sciences of the United States of America 2016 113(37):10316-10321.

Newmister SA, Gober CM, Romminger S, Yu F, Tripathi A, Parra LLL, Williams RM, Berlinck RGS, Joullie MM, Sherman DH. OxaD: A Versatile Indolic Nitrone Synthase from the Marine-Derived Fungus Penicillium oxalicum F30. Journal of the American Chemical Society 2016 138(35):1176-1184.

Park SR, Tripathi A, Wu J, Schultz PJ, Yim I, McQuade TJ, Yu F, Arevang CJ, Mensah AY, Tamayo-Castillo G, Xi C, Sherman DH. Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway. Nature Communications 2016 Feb 7(10710). doi: 10.1038/ncomms10710
 
Pereira PR, Meagher JL, Winter HC, Goldstein IJ, Paschoalin VM, Silva JT, Stuckey JA. High-resolution crystal structures of Colocasia esculenta tarin lectin. Glycobiology 2016 Aug 24. pii: cww083. [Epub ahead of print]
 
Ramkumar K, Samanta S, Kyani A, Yang S, Tamura S, Ziemke E, Stuckey JA, Li S, Chinnaswamy K, Otake H, Debnath B, Yarovenko V, Sebolt-Leopold JS, Ljungman M, Neamati N. Mechanistic evaluation and transcriptional signature of a glutathione S-transferase omega 1 inhibitor. Nat Commun 2016 Oct 5 7:13084.
 
Ruckthong L, Stuckey JA, Pecoraro VL. Methods for Solving Highly Symmetric De Novo Designed Metalloproteins: Crystallographic Examination of a Novel Three-Stranded Coiled-Coil Structure Containing d-Amino Acids. Methods Enzymol. 2016;580:135-48. doi: 10.1016/bs.mie.2016.05.007. Epub 2016 Jun 23.

Ruckthong L, Zastrow ML, Stuckey JA, Pecoraro VL.  A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins. J Am Chem Soc 2016 Sep 2. [Epub ahead of print]

Shankar S, Pitchiaya S, Malik R, Kothari V, Hosono Y, Yocum AK, Gundlapalli H, White Y, Firestone A, Cao X, Dhanasekaran SM, Stuckey JA, Bollag G, Shannon K, Walter NG, Kumar-Sinha C, Chinnaiyan AM. KRAS Engages AGO2 to Enhance Cellular Transformation. Cell Rep 2016 Feb 16 14(6):1448-61.

Skiba M, Sikkema A, Fiers W, Gerwick WH, Sherman DH, Aldrich CC, Smith JL. Domain organization and active site architecture of a polyketide synthase C-methyltransferase. ACS Chem Biol 2016 11(12):3319-3327.

Stull FW, Bernard, SM, Sapra A, Smith JL, Zuiderweg ERP, Palfey BA. Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase. Biochemistry 2016 55(23):3261.

Tai AW, Vidugiriene J. Measuring activity of phosphoinositide lipid kinases using a bioluminescent ADP-Detecting assay. Methods in Molecular Biology 2016 1360:75-85. Doi: 10.1007/978-1-4939-3073-9_6
 
Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM. Molecular dissection of xyloglucan recognition in a prominent human gut symbiont. mBio 2016 April 7(2): e02134-15. doi: 10.1128/mBio.02134-15.
 
Taylor VG, Bommarito PA, Tesmer JJG. Structure of the regulator of G protein signaling 8 (RGS8)-Gë±q complex: Molecular basis for Gë± selectivity. Journal of Biological Chemistry 2016 March 291(10): 5138-5145.

Terwilliger TC, Bunkozi G, Hung L-W, Zwart PH, Smith JL, Akey DL, Adams PD.Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. Acta Crystallographica Section D: Structural Biology 2016 72(3):346-358. DOI: 10.1107/S2059798315019269

Tesmer JJG. Crystallographic pursuit of a protein-RNA aptamer complex. Methods in Molecular Biology 2016 1380:151-160. Doi: 10.1007/978-1-4939-3197-2_12
 
Tesmer JJG. Hitchhiking on the heptahelical highway: Structure and function of 7TM receptor complexes. Nature Reviews Molecular Cell Biology 2016 July 17(7):439-450. Doi: 10.1038/nrm.2016.36
 
Tripathi A, Choi SS, Sherman DH, Kim ES. Thioesterase domain swapping of a linear polyketide tautomycetin with a macrocyclic polyketide pikromycin in Streptomyces sp. CK4412. Journal of Industrial Microbiology and Biotechnology 2016 August 43(8):1189 – 1193. Doi: 10.1007/s10295-016-1790-2
 
Waldschmidt HV, Homan KT, Cruz-Rodríguez O, Cato MC, Waninger-Saroni J, Larimore KM, Cannavo A, Song J, Cheung JY, Kirchhoff PD, Koch WJ, Tesmer JJG, Larsen SD. Structure-Based Design, Synthesis, and Biological Evaluation of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors. Journal of Medicinal Chemistry 2016 59(8):3793-3807. DOI: 10.1021/acs.jmedchem.5b02000

Wang Y, Virtanen J,  Xue Z, Tesmer JJG,  Zhang Y. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallographica Section D 2016 72:616-628.

Won SJ, Davda D, Labby KJ, Hwang SY, Pricer R, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL 3rd, Stuckey JA, Martin BR. Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). ACS Chem Biol 2016 Dec 16 11(12):3374-3382. Epub 2016 Oct 31.
 
Wijeyesakere SJ, Bedi SK, Huynh D, Raghavan M. The C-terminal acidic region of calreticulin mediates phosphatidylserine binding and apoptotic cell phagocytosis. Journal of Immunology 2016 May 196(9):3896-3909. doi: 10.4049/jimmunol.1502122
 
Yang C-Y, Delproposto J, Chinnaswamy K, Brown WC, Wang S, Stuckey JA, Wang X. Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain. PLoS One 2016 Jan 6 11(1):e0146522. doi: 10.1371/journal.pone.0146522. eCollection 2016. PubMed PMID: 26735493; PubMed Central PMCID: PMC4703388.
 
Yang C-Y, Phillips JG, Stuckey JA, Bai L, Sun Haiying, Delproposto J, Brown WC, Chinnaswamy K. Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors. ACS Med Chem Letter 2016 Sept 14.
 
2015
 
Akey DL, Brown WC, Jose J, Kuhn RJ, Smith JL. Structure-guided insights on the role of NS1 in flavivirus infection. Bioessays 2015 May 37(5):489-94. doi: 10.1002/bies.201400182. Epub 2015 Mar 11. PubMed PMID: 25761098; PubMed Central PMCID: PMC4409125.
 
Almutairi MM, Park SR, Rose S, Hansen DA, Vazquez-Laslop N, Douthwaite S, Sherman DH, Mankin AS. Resistance to ketolide antibiotics by coordinated expression of rRNA methyltransferases in a bacterial producer of natural ketolides. Proceedings of the National Academy of Sciences of the United States of America 2015 October 112(42): 12956-12961. Doi: 10.1073/pnas.1512090112
 
Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O-Methyltransferases. ACS Chem Biol 2015 Feb 26 [Epub ahead of print] PubMed PMID: 25692963.
 
Borkin D, He S, Miao H, Kempinska K, Pollock J, Chase J, Purohit T, Malik B, Zhao T, Wang J, Wen B, Zong H, Jones M, Danet-Desnoyers G, Guzman ML, Talpaz M, Bixby DL, Sun D, Hess JL, Muntean AG, Maillard I, Cierpicki T, Grembecka J. Pharmacologic inhibition of the menin-MLL interaction blocks progression of MLL leukemia in vivo. Cancer Cell 2015 13:589-602.
 
Caldara-Festin G, Jackson DR, Barajas JF, Valentic TR, Patel AB, Aguilar S, Nguyen M, Vo M, Khanna A, Sasaki E, Liu H-W, Tsai S-C, Smith JL. Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases. Proceedings of the National Academy of Sciences of the United States of America 2015 Dec 112(50):E6844- E6851. Doi: 10.1073/pnas.1512976112
 
Bowman BM, Sebolt KA, Hoff BA, Boes JL, Daniels DL, Heist KA, Galbán CJ, Patel RM, Zhang J, Beer DG, Ross BD, Rehemtulla A, Galbán, S. Phospohorylation of FADD by the kinase CK1α promotes KRAS G12D induced lung cancer. Science Signaling 2015 Jan 27 8(361).
 
Chemler JA, Tripathi A, Hansen DA, O'Neil-Johnson M, Williams RB, Starks C, Park SR, Sherman DH. Evolution of Efficient Modular Polyketide Synthases by Homologous Recombination. Journal of the American Chemical Society 2015 July 137(33):10603-10609. doi: 10.1021/jacs.5b04842
Cojohari O, Burrer CM, Peppenelli MA, Abulwerdi FA, Nikolovska-Coleska Z, Chan GC. BH3 Profiling Reveals Selectivity by Herpesviruses for Specific Bcl-2 Proteins To Mediate Survival of Latently Infected Cells. J Virol 2015 May 15 89(10):5739-46. doi: 10.1128/JVI.00236-15. Epub 2015 Mar 4. PubMed PMID: 25740993.
 
Emanuele AA, Garcia GA. Mechanism of Action and Initial, In Vitro SAR of an Inhibitor of the Shigella flexneri Virulence Regulator VirF. PLoS One 2015 Sep 9. doi: 10.1371/journal.pone.0137410. eCollection 2015. PubMed PMID: 26352269; PubMed Central PMCID: PMC4564171.
 
Glukhova A, Hinkovska-Galcheva V, Kelly R, Abe A, Shayman JA, Tesmer JJ. Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase. Nature Communications 2015 Mar 2 6:6250. doi: 10.1038/ncomms7250. PubMed PMID: 25727495; PubMed Central PMCID: PMC4397983.
 
Gray MJ, Li Y, Leichert LI, Xu Z, Jakob U. Does the transcription factor NemR use a regulatory sulfenamide bond to sense bleach? Antioxid Redox Signal 2015 Apr 13 [Epub ahead of print] PubMed PMID: 25867078.
 
Guo EZ, Xu Z. Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains. J Biol Chem 2015 Mar 27 290(13):8396-408. doi: 10.1074/jbc.M114.607903. Epub 2015 Feb 5. PubMed PMID: 25657007; PubMed Central PMCID: PMC4375492.
 
Hansen DA, Koch AA, Sherman DH. Substrate controlled divergence in polyketide synthase catalysis. Journal of the American Chemical Society 2015 March 137(11): 3735-3738. Doi: 10.1021/ja511743n
 
Homan KT, Larimore KM, Elkins JM, Szklarz M, Knapp S, Tesmer JJ. Identification and structure-function analysis of subfamily selective g protein-coupled receptor kinase inhibitors. ACS Chem Biol 2015 Jan 16 10(1):310-9. doi: 10.1021/cb5006323. Epub 2014 Oct 3. PubMed PMID: 25238254; PubMed Central PMCID: PMC4301037.
 
Homan KT, Waldschmidt HV, Glukhova A, Cannavo A, Song J, Cheung JY, Koch WJ, Larsen SD, Tesmer JJ. Crystal Structure of G Protein-coupled Receptor Kinase 5 in Complex with a Rationally Designed Inhibitor. J Biol Chem 2015 Aug 21 290(34):20649-59. doi:10.1074/jbc.M115.647370. Epub 2015 Jun 1. PubMed PMID:26032411; PubMed Central PMCID: PMC4543626.
 
Karatas H, Lee SY, Townsend EC, Cao F, Xu J, Bernard D, Liu L, Dou Y, Wang S. Structure-based design of conformationally constrained cyclic peptidomimetics to target the MLL1-WDR5 protein-protein interaction as inhibitors of the MLL1 methyltransferase activity. Chinese Chemical Letters 2015 April 26(4):455–58.
 
Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models. Acta Crystallogr D Biol Crystallogr 2015 Feb 71(Pt 2):338-43. doi: 10.1107/S1399004714025784. Epub 2015 Jan 23. PubMed PMID: 25664744; PubMed Central PMCID: PMC4321487.
 
Khare D, Hale WA, Tripathi A, Gu L, Sherman DH, Gerwick WH, Hansson K, Smith JL. Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase. Structure 2015 Dec 23(12):2213- 2223. Doi: 10.1016/j.str.2015.09.013
 
Li S, Lowell AN, Yu F, Raveh A, Newmister SA, Bair N, Schaub JM, Williams RM, Sherman DH. Hapalindole/Ambiguine Biogenesis Is Mediated by a Cope Rearrangement, C-C Bond-Forming Cascade. Journal of the American Chemical Society. 2015 Dec 137(49) 15366-15369. DOI: 10.1021/jacs.5b10136
 
Liu L, Bernard D, Wang S. Case Study: Discovery of Inhibitors of the MDM2-p53 Protein-Protein Interaction. Methods Mol Biol 2015 1278:567-85. doi: 10.1007/978-1-4939-2425-7_38. PubMed PMID: 25859977.
 
Lorenz DA, Song JM, Garner AL. High-throughput platform assay technology for the discovery of pre-microrna-selective small molecule probes. Bioconjug Chem 2015 Jan 21 26(1):19-23.
 
Lowell AN, Santoro N, Swaney SM, McQuade TJ, Schultz PJ, Larsen MJ, Sherman DH. Microscale adaptation of in vitro transcription/translation for high-throughput screening of natural product extract libraries. Chemical Biology and Drug Design 2015 Dec 86(6):1331-1338. Doi: 10.1111/cbdd.12614
 
Lund G, Dudkin S, Borkin D, Ni W, Grembecka J, Cierpicki T. Inhibition of CDC25B phosphatase through disruption of protein-protein interaction. ACS Chem Biol 2015 Feb 20 10(2):390-4. doi: 10.1021/cb500883h. Epub 2014 Dec 1. PubMed PMID: 25423142; PubMed Central PMCID: PMC4340349.
 
Morgan CE, Meagher JL, Levengood JD, Delproposto J, Rollins C, Stuckey JA, Tolbert BS. The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein. J Mol Biol 2015 Oct 9 427(20):3241-57. doi: 10.1016/j.jmb.2015.05.009. Epub 2015 May 21. PubMed PMID: 26003924; PubMed Central PMCID: PMC4586317.
 
Narayan A, Jiminez G, Liu P, Negretti S, Zhao W, Gilbert MM, Ramabhadran RO, Yang YF, Furan LR, Li Z, Podust LM, Montgomery J, Houk KN, Sherman DH. Enzymatic hydroxylation of an unactivated methylene C-H bond guided by molecular dynamics simulations. Nature Chemistry 2015 Aug 7(8):653-660.
 
Nikolovska-Coleska Z. Studying protein-protein interactions using surface plasmon resonance. Methods Mol Biol 2015 1278:109-38. doi: 10.1007/978-1-4939-2425-7_7. PubMed PMID: 25859946.
 
Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N,  Dosch J, Van Dort ME, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, Rehemtulla A. The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling. Sci Signal. 2015 Jan 6;8(358):ra1. doi: 10.1126/scisignal.2005379. PubMed PMID: 25564677.
 
Pereira PR, Winter HC, Verícimo MA, Meagher JL, Stuckey JA, Goldstein IJ, Paschoalin VM, Silva JT. Structural analysis and binding properties of isoforms of tarin, the GNA-related lectin from Colocasia esculenta. Biochim Biophys Acta 2015 Oct 23 1854(1):20-30.
 
Peterson LF, Sun H, Liu Y, Potu H, Kandarpa M, Ermann M, Courtney SM, Young M, Showalter HD, Sun D, Jakubowiak A, Malek SN, Talpaz M, Donato NJ. Targeting deubiquitinase activity with a novel small molecule inhibitor as therapy for B-cell malignancies. Blood 2015 Mar 26. pii: blood-2014-10-605584. [Epub ahead of print] PubMed PMID: 25814533.
 
Pinnell N, Yan R., Cho HJ, Keeley T, Murai MJ, Liu Y, Alarcon AS, Qin J, Wang Q, Kuick R, Elenitoba-Johnson KSJ, Maillard I, Samuelson LC, Cierpicki T, Chiang MY. The PIAS-like Coactivator Zmiz1 Is a Direct and Selective Cofactor of Notch1 in T Cell Development and Leukemia. Immunity 2015 Nov 43(5):870-883. Doi: 10.1016/j.immuni.2015.10.007
 
Pollock J, Borkin D, Lund G, Purohit T, Dyguda-Kazimierowicz E, Grembecka J, Cierpicki T. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. Journal of Medicinal Chemistry 2015 Sept 58(18): 7465-7474. Doi: 10.1021/acs.jmedchem.5b00975
 
Riser BL, Barnes JL, Varani J. Balanced regulation of the CCN family of matricellular proteins: a novel approach to the prevention and treatment of fibrosis and cancer. Journal of Cell Communication and Signaling 2015 Dec 9(4) 327-339. Doi: 10.1007/s12079-015-0309-3
 
Rogawski DS, Ndoj J, Cho HJ, Maillard I, Grembecka J, Cierpicki T. Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase. Biochemistry 2015 Sept 54(35): 5401- 5413. Doi: 10.1021/acs.biochem.5b00697
 
Ran X, Zhao Y, Liu L, Bai L, Yang CY, Zhou B, Meagher JL, Chinnaswamy K, Stuckey JA, Wang S. Structure-Based Design of γ-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors. J Med Chem 2015 Jun 25 58(12):4927-39. doi: 10.1021/acs.jmedchem.5b00613. Epub 2015 Jun 16. PubMed PMID: 26080064.
 
Schofield MM, Jain S, Porat D, Dick GJ, Sherman DH. Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET-743. Environmental Microbiology 2015. doi: 10.1111/1462-2920.12908
 
Schuler B.D., Smith J.L. Editorial overview: Biophysical and molecular biological methods: Structure, dynamics, and single molecules. Current Opinion in Structural Biology 2015 October 34: 4-6. doi: 10.1016/j.sbi.2015.09.005
 
Senter T, Gogliotti R, Han C, Locuson CW II, Morrison R, Daniels JS, Cierpicki T, Grembecka J, Lindsley CW, Stauffer SR. Progress towards small molecule inhibitors of the Menin-Mixed Lineage Leukemia (MLL) interaction with in vivo utility. Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US) 2013 Apr 15 [updated 2015 Feb 11].
 
Shultis D, Dodge G, Zhang Y. Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering. Journal of Structural Biology 2015 Aug 191(2)197-206. doi 10.1016/j.jsb.2015.06.009
 
Smith AM, Brown WC, Harms E, Smith JL. Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase. J Biol Chem 2015 Feb 27 290(9):5226-39. doi: 10.1074/jbc.M114.626382. Epub 2015 Jan 7. PubMedPMID: 25568319; PubMed Central PMCID: PMC4342443.
 
Smith JL, Khare D. Recent advances in the structural and mechanistic biology of non-haem Fe(II), 2-oxoglutarate and O2-dependent halogenases. RSC Metallobiology 2015 October 3:401-403. doi: 10.1039/9781782621959-00401
 
Smith RD, Damm-Ganamet KL, Dunbar JB Jr, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J Chem Inf Model 2015 Oct 9. [Epub ahead of print] PubMed PMID: 26419257.
 
Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM. Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity. Cell 2015 Oct 22 163(3):746-58. doi: 10.1016/j.cell.2015.09.056. Epub 2015 Oct 22. PubMed PMID: 26496612; PubMed Central PMCID: PMC4641746.
 
Vild CJ, Li Y, Guo EZ, Liu Y, Xu Z. A novel mechanism of regulating the ATPase VPS4 by its cofactor LIP5 and the endosomal sorting complex required for transport (ESCRT)-III protein CHMP5. J Biol Chem 2015 Mar 13 290(11):7291-303. doi: 10.1074/jbc.M114.616730. Epub 2015 Jan 30. PubMed PMID: 25637630; PubMed Central PMCID: PMC4358147.
 
Wei D, Zhang Q, Schreiber JS, Parsels LA, Abulwerdi FA, Kausar T, Lawrence TS, Sun Y, Nikolovska-Coleska Z, Morgan MA. Targeting mcl-1 for radiosensitization of pancreatic cancers. Transl Oncol 2015 Feb 8(1):47-54. doi: 10.1016/j.tranon.2014.12.004. PubMed PMID: 25749177; PubMed Central PMCID: PMC4350640.
 
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods 2015 Jan 12(1):7-8. doi: 10.1038/nmeth.3213. PubMed PMID: 25549265.
 
Yuan C, Smith WL. A cyclooxygenase-2-dependent prostaglandin E2 biosynthetic system in the Golgi apparatus. J Biol Chem 2015 Feb 27 290(9):5606-20. doi: 10.1074/jbc.M114.632463. Epub 2014 Dec 29. PubMed PMID: 25548276; PubMed Central PMCID: PMC4342474.
 
Zhang P, Chaturvedi CP, Tremblay V, Cramet M, Brunzelle JS, Skiniotis G,
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Zhao Y, Aguilar A, Bernard D, Wang S. Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 Inhibitors) in clinical trials for cancer treatment. J Med Chem 2015 Feb 12 58(3):1038-52. doi: 10.1021/jm501092z. Epub 2014 Nov 14. Review. PubMed PMID: 25396320; PubMed Central PMCID: PMC4329994.
 
2014
 
Aguilar A, Sun W, Liu L, Lu J, McEachern D, Bernard D, Deschamps JR, Wang S. Design of chemically stable, potent, and efficacious MDM2 inhibitors that exploit the retro-mannich ring-opening-cyclization reaction mechanism in spiro-oxindoles. J Med Chem 2014 Dec 26 57(24):10486-98. doi: 10.1021/jm501541j. Epub 2014 Dec 12. PubMed PMID: 25496041; PubMed Central PMCID: PMC4281096.
 
Akey DL, Brown WC, Dutta S, Konwerski J, Jose J, Jurkiw TJ, DelProposto J, Ogata CM, Skiniotis G, Kuhn RJ, Smith JL. Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. Science 2014 Feb 21 343(6173):881-5. doi: 10.1126/science.1247749. Epub 2014 Feb 6. PubMed PMID: 24505133; PubMed Central PMCID: PMC4263348.
 
Akey DL, Brown WC, Konwerski JR, Ogata CM, Smith JL. Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1. Acta Crystallogr D Biol Crystallogr 2014 Oct 70(Pt 10):2719-29. doi: 10.1107/S1399004714017556. Epub 2014 Sep 27. PubMed PMID: 25286855; PubMed Central PMCID: PMC4188011.
 
Abulwerdi FA, Liao C, Mady AS, Gavin J, Shen C, Cierpicki T, Stuckey JA, Showalter HD, Nikolovska-Coleska Z (2014). 3-Substituted-N-(4-hydroxynaphthalen-1-yl)arylsulfonamides as a novel class of selective Mcl-1 inhibitors: structure-based design, synthesis, SAR, and biological evaluation. J Med Chem 2014 May 22 57(10):4111-33. doi: 0.1021/jm500010b. Epub 2014 May 7.
 
Athanassiou-Papaefthymiou M, Shkeir O, Kim D, Divi V, Matossian M, Owen JH, Czerwinski MJ, Papagerakis P, McHugh J, Bradford CR, Carey TE, Wolf GT, Prince ME, Papagerakis S. Evaluation of CD44 variant expression in oral, head and neck squamous cell carcinomas using a triple approach and its clinical significance. Int J Immunopathol Pharmacol 2014 Jul-Sep 27(3):337-49. PubMed PMID: 25280025; PubMed Central PMCID: PMC4266392.
 
Buer BC, Paul B, Das D, Stuckey JA, Marsh EN (2014). Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound. ACS Chem Biol 2014 Nov 21 9(11):2584-93.
 
Guetschow ED, Steyer DJ, Kennedy RT. Subsecond electrophoretic separations from droplet samples for screening of enzyme modulators. Anal Chem 2014 Oct 21 86(20):10373-9. doi: 10.1021/ac502758h. Epub 2014 Oct 2. PubMed PMID: 25233947; PubMed Central PMCID: PMC4204908.
 
Holden VI, Lenio S, Kuick R, Ramakrishnan SK, Shah YM, Bachman MA. Bacterial siderophores that evade or overwhelm lipocalin 2 induce hypoxia inducible factor 1α and proinflammatory cytokine secretion in cultured respiratory epithelial cells. Infect Immun 2014 Sep 82(9):3826-36. doi: 10.1128/IAI.01849-14. Epub 2014 Jun 30. PubMed PMID: 24980968; PubMed Central PMCID: PMC4187820.
 
Holdren GO, Rosenthal DJ, Yang J, Bates AM, Fischer CL, Zhang Y, Brogden NK, Brogden KA. Antimicrobial Activity of Chemokine CXCL10 for Dermal and Oral Microorganisms. Antibiotics (Basel) 2014 Oct 23 3(4):527-539. PubMed PMID: 25859394; PubMed Central PMCID: PMC4387564.
 
Homan KT, Wu E, Cannavo A, Koch WJ, Tesmer JJ. Identification and characterization of amlexanox as a G protein-coupled receptor kinase 5 inhibitor. Molecules 2014 Oct 22 19(10):16937-49. doi: 10.3390/molecules191016937. PubMed PMID: 25340299.
 
Jenkins RJ, Heslip KA, Meagher JL, Stuckey JA, Dotson GD (2014). Structural Basis for the Recognition of Peptide RJPXD33 by Acyltransferases in Lipid A Biosynthesis. J Biol Chem 2014 May 30 289(22):15527-35. doi: 10.1074/jbc.M114.564278. Epub 2014 Apr 16. PubMed PMID: 24742680; PubMed Central PMCID: PMC4140908.
 
Langevin SA, Bowen RA, Reisen WK, Andrade CC, Ramey WN, Maharaj PD, Anishchenko M, Kenney JL, Duggal NK, Romo H, Bera AK, Sanders TA, Bosco-Lauth A,  Smith JL, Kuhn R, Brault AC. Host competence and helicase activity differences exhibited by West Nile viral variants expressing NS3-249 amino acid polymorphisms. PLoS One 2014 Jun 27 9(6):e100802. doi: 10.1371/journal.pone.0100802. eCollection 2014. PubMed PMID: 24971589; PubMed Central PMCID: PMC4074097.
 
Larsen MJ, Larsen SD, Fribley A, Grembecka J, Homan K, Mapp A, Haak A, Nikolovska-Coleska Z, Stuckey JA, Sun D, Sherman DH (2014). The role of HTS in drug discovery at the University of Michigan. Comb Chem High Throughput Screen. 2014 Mar 17(3):210-30. PubMed PMID: 24409957.
 
Lorenz DA, Song JM, Garner AL. High-throughput platform assay technology for the discovery of pre-microrna-selective small molecule probes. Bioconjug Chem 2015 Jan 21 26(1):19-23. doi: 10.1021/bc500544v. Epub 2014 Dec 17. PubMed PMID: 25506628.
 
Lyon AM, Begley JA, Manett TD, Tesmer JJG. Molecular Mechanisms of Phospholipase C [beta]3 Autoinhibition. Structure 2014 22(12): 1844-1854. doi: 10.1016/j.str.2014.10.008
Pal A, Young MA, Donato NJ. Emerging potential of therapeutic targeting of ubiquitin-specific proteases in the treatment of cancer. Cancer Res 2014 Sep 15 74(18):4955-66. doi: 10.1158/0008-5472.CAN-14-1211. Epub 2014 Aug 29. Review.  PubMed PMID: 25172841.
 
Rizvi SM, Salam N, Geng J, Qi Y, Bream JH, Duggal P, Hussain SK, Martinson J, Wolinsky SM, Carrington M, Raghavan M. Distinct assembly profiles of HLA-B molecules. J Immunol 2014 Jun 1 192(11):4967-76. doi: 10.4049/jimmunol.1301670.  Epub 2014 Apr 30. PubMed PMID: 24790147; PubMed Central PMCID: PMC4117407.
 
Sun S, Kennedy RT. Droplet electrospray ionization mass spectrometry for high throughput screening for enzyme inhibitors. Anal Chem 2014 Sep 16 86(18):9309-14. doi: 10.1021/ac502542z. Epub 2014 Aug 26. PubMed PMID: 25137241; PubMed Central PMCID: PMC4165461.
 
Wang S, Sun W, Zhao Y, McEachern D, Meaux I, Barrière C, Stuckey JA, Meagher JL, Bai L, Liu L, Hoffman-Luca CG, Lu J, Shangary S, Yu S, Bernard D, Aguilar A, Dos-Santos O, Besret L, Guerif S, Pannier P, Gorge-Bernat D, Debussche L. SAR405838: an optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression. Cancer Res 2014 Oct 15 74(20):5855-65. doi: 10.1158/0008-5472.CAN-14-0799. Epub 2014 Aug 21. PubMed PMID: 25145672; PubMed Central PMCID: PMC4247201.
 
Wijeyesakere SJ, Richardson RJ, Stuckey JA. Crystal structure of patatin-17 in complex with aged and non-aged organophosphorus compounds. PLoS One 2014 Sep 23 9(9):e108245. doi: 10.1371/journal.pone.0108245. eCollection 2014. PubMed PMID: 25248161; PubMed Central PMCID: PMC4172759.
 
Yang Y, Zhang H, Usharani D, Bu W, Im S, Tarasev M, Rwere F, Pearl NM, Meagher J, Sun C, Stuckey J, Shaik S, Waskell L. Structural and Functional Characterization of a Cytochrome P450 2B4 F429H Mutant with an Axial Thiolate-Histidine Hydrogen Bond. Biochemistry 2014 Aug 12 53(31):5080-91. doi: 10.1021/bi5003794. Epub 2014 Jul 31.