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Structural Biology Publications

  • Maryam Yekefallah, Evan J. van Aalst, Roy A. M. van Beekveld, Isaac R. Eason, Eefjan Breukink, Markus Weingarth, and Benjamin J. Wylie (2024) Cooperative Gating of a K+ Channel by Unmodified Biological Anionic Lipids Viewed by Solid-State NMR Spectroscopy. J. Am. Chem. Soc. 146, 7, 4421–4432.
  • Benjamin J. Wylie, Collin G. Borcik, Reza Amani, Evan J. van Aalst, Maryam Yekefallah, Isaac R. Eason, Carver Rasberry, Roy A.M. van Beekvelld, Markus Weingarth, Chad M. Rienstra, Eefjan Breukink (2024) The KirBac1.1 Inward-Rectifier K+ Channel is Opened Cooperatively by Anionic Lipids. Biophysical Journal, 10.1016/j.bpj.2023.11.1062
  • Zhou T, Wu J, Tang H, Liu D, Jeon BH, Jin W, Wang Y, Zheng Y, Khan A, Han H, Li X (2024) Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer. npj Biofilms and Microbiomes. 10:6, 1-14.
  • Wu H-Y, Zheng Y, Laciak AR, Huang NN, Koszelak-Rosenblum M, Flint AJ, Carr G, Zhu G (2022) Structure and Function of SNM1 Family Nucleases, Adv Exp Med Biol, doi: 10.1007/5584_2022_724.
  • Yekefallah, M., Rasberry, C. A., Van Aalst, E. J., Browning, H. P., Amani, R., Versteeg, D. B., & Wylie, B. J. (2022) Mutational insight into allosteric regulation of kir channel activity. ACS omega, 7(48), 43621-43634.
  • Alghamdi MA, Hussien RA, Zheng Y, Patel HP, Asencion Diez MD, A Iglesias A, Liu D, Ballicora MA (2022) Site-directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci. 31(7):e4376.
  • Borcik, C. G., Eason, I. R., Yekefallah, M., Amani, R., Han, R., Vanderloop, B. H., & Wylie, B. J. (2022) A cholesterol dimer stabilizes the inactivated state of an inward‐rectifier Potassium Channel. Angewandte Chemie International Edition, 61(13), e202112232.
  • Minen RI, Bhayani JA, Hartman MD, Cereijo AE, Zheng Y, Ballicora MA, Iglesias AA, Liu D, Figueroa CM (2022). Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases. Plant Cell Physiol. 63(5):658-670.
  • Stokes ME, Surman MD, Calvo V, Surguladze D, Li A-H, Gasparek J, Betzenhauser M, Zhu G, Du H, Rigby AC, Mulvihill MJ (2022) Optimization of a Novel Mandelamide-Derived Pyrrolopyrimidine Series of PERK Inhibitors, Pharmaceutics, 14(10):2233.
  • Calvo V, Surguladze D, Li AH, Surman MD, Malibhatla S, Bandaru M, Jonnalagadda SK, Adarasandi R, Velmala M, Singireddi DRP, Velpuri M, Nareddy BR, Sastry V, Mandati C, Guguloth R, Siddiqui S, Patil BS, Chad E, Wolfley J, Gasparek J, Feldman K, Betzenhauser M, Wiens B, Koszelak-Rosenblum M, Zhu G, Du H, Rigby AC, Mulvihill MJ. (2021) Discovery of 2-amino-3-amido-5-aryl-pyridines as highly potent, orally bioavailable, and efficacious PERK kinase inhibitors, Bioorg Med Chem Lett, 43:128058.
  • Karim Md F, Liu S, Laciak AR, Volk L, Koszelak-Rosenblum M, Liber MR, Wu M, Curtis R, Huang NN, Carr G, Zhu G. (2020) Structural analysis of the catalytic domain of Artemis endonuclease/SNM1C reveals distinct structural features, J Biol Chem, 295(35):12368-77.
  • Van Aalst, E., Yekefallah, M., Mehta, A. K., Eason, I., & Wylie, B. (2020) Codon harmonization of a kir3. 1-kirbac1.3 chimera for structural study optimization. Biomolecules, 10(3), 430.
  • Jamaleddine, M., Harris, M. S., Liyanage, L., & Cook, G. A. (2020) Expression, purification, and structural analysis of the full-length human integral membrane protein γ-sarcoglycan. Protein Expression and Purification, 167, 105525.
  • Han H, Zheng Y, Zhou T, Liu, P, Li X (2020) Cu (II) nonspecifically binding chromate reductase NfoR promotes Cr (VI) reduction. Environ Microbiol, 23(1), 415-30.
  • O’Neill AG, Beaupre BA, Zheng Y, Liu D, Moran GR (2020) NfoR: Chromate Reductase or Flavin Mononucleotide Reductase? Appl Environ Microbiol., 86(22), e01758-20.
  • Borcik, C. G., Versteeg, D. B., Amani, R., Yekefallah, M., Khan, N. H., & Wylie, B. J. (2020) The lipid activation mechanism of a transmembrane potassium channel. Journal of the American Chemical Society, 142(33), 14102-14116.
  • Amani, R., Borcik, C. G., Khan, N. H., Versteeg, D. B., Yekefallah, M., Do, H. Q., … & Wylie, B. J. (2020) Conformational changes upon gating of KirBac1. 1 into an open-activated state revealed by solid-state NMR and functional assays. Proceedings of the National Academy of Sciences, 117(6), 2938-2947.
  • Shah, K., Lin, X., Queener, S. F., Cody, V., Pace, J., & Gangjee, A. (2018) Targeting species specific amino acid residues: Design, synthesis and biological evaluation of 6-substituted pyrrolo[2,3- d ]pyrimidines as dihydrofolate reductase inhibitors and potential anti-opportunistic infection agents. Bioorganic & Medicinal Chemistry, 26(9), 2640–2650.
  • Luo Q, Yang X, Yu S, Shi H, Wang K, Xiao L, Zhu G, Li T, Li D, Zhang X, Zhou M, Huang Y. (2017) Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG. Nat Struct Mol Biol., 24(5):469-74.
  • Zhu G, Koszelak-Rosenblum M, Connelly SM, Dumont ME, Malkowski MG. (2015) Crystal structure of an integral membrane fatty acid α-hydroxylase, J Biol Chem, 290(50):29820-33.
  • Cody V, Pace J, Namjoshi OA, Gangjee A. (2015) Structure-activity correlations for three pyrido[2,3-d]pyrimidine antifolates binding to human and Pneumocystis carinii dihydrofolate reductase. Acta Crystallogr F Struct Biol Commun. 71(6):799-803.
  • Bauer WJ, Luthra A, Zhu G, Radolf JD, Malkowski MG, Caimano MJ. (2015) Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1, J. Struct Biol., 192(1):48-58.
  • Llaguno MC, Xu H, Shi L, Huang N, Zhang H, Liu Q, Jiang QX. (2014) Chemically functionalized carbon films for single molecule imaging. J Struct Biol. 185(3):405-17.
  • van Staalduinen, L. M., McSorley, F. R., Schiessl, K., Séguin, J., Wyatt, P. B., Hammerschmidt, F., Zechel, D.L. and Jia, Z. (2014) Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates. Proc Natl Acad Sci USA, 111, 5171-5176.
  • Zhu G, Koszelak-Rosenblum M, Malkowski MG. (2013) Crystal structures of α-dioxygenase from Oryza sativa: insights into substrate binding and activation by hydrogen peroxide, Protein Sci., 22(10):1432-8.
  • Cody V, Pace J, Queener SF, Adair OO, Gangjee A. (2013) Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants. Antimicrob Agents Chemother. 57(6):2669-77.
  • Goulah CC, Zhu G, Koszelak-Rosenblum M, Malkowski MG. (2013) The Crystal Structure of alpha-Dioxygenase Provides Insight into Diversity in the Cyclooxygenase-Peroxidase Superfamily, Biochemistry, 52(8): 1364-72.
  • Frampton, M. B., Séguin, J. P., Marquardt, D., Harroun, T. A., & Zelisko, P. M. (2013) Synthesis of polyesters containing disiloxane subunits: Structural characterization, kinetics, and an examination of the thermal tolerance of Novozym-435. Journal of Molecular Catalysis B: Enzymatic, 85, 149-155.
  • Pryor EE Jr, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. (2013) Structure of the integral membrane protein CAAX protease Ste24p, Science, 339(6127): 1600-4.
  • Huang N, Chelliah Y, Taylor C, Yoo SH, Shan YL, Partch C, Green C, Zhang H and Takahashi J. (2012) Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex. Science.337(6091): 189-94.
  • Ge Q, Huang N, R. Wynn M, Li Y, Du X, Miller B, Zhang H and Uyeda K. (2012) Structural characterization of a unique interface between carbohydrate response element binding protein (ChREBP) and 14-3-3β. J. Biol. Chem. 287(50):41914-21
  • Cody V, Pace J, Nawar HF, King-Lyons N, Liang S, Connell TD, Hajishengallis G. (2012) Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding. Acta Crystallogr D Biol Crystallogr. 68(12):1604-12.
  • Cody V, Pace J, Stewart E. (2012) Structural analysis of Pneumocystis carinii dihydrofolate reductase complexed with NADPH and 2,4-diamino-6-[2-(5-carboxypent-1-yn-1-yl)-5-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine. Acta Crystallogr Sect F Struct Biol Cryst Commun. 68(4):418-23.
  • Ye X, Huang N, Liu Y, Paroo Z, Chen S, Huerta C, Li P, Chen S, Liu Q, Zhang H. (2011) Crystal Structure of C3PO and its endoribonuclease activity in human RISC activation. Nat. Struct. Mol. Biol. 18: 650-657.
  • Luthra A, Zhu G, Desrosiers DC, Eggers CH, Mulay V, Anand A, McArthur FA, Romano FB, Caimano MJ, Heuck AP, Malkowski MG, Radolf JD. (2011) The transition from closed to open conformation of Treponema pallidum outer membrane-associated lipoprotein TP0453 involves membrane sensing and integration by two amphipathic helices, J Biol Chem, 286(48):41656-68.
  • Cody V, Pace J, Nowak J. (2011) Structural analysis of human dihydrofolate reductase as a binary complex with the potent and selective inhibitor 2,4-diamino-6-{2′-O-(3-carboxypropyl)oxydibenz[b,f]-azepin-5-yl}methylpteridine reveals an unusual binding mode. Acta Crystallogr D Biol Crystallogr. 2011, 67(10):875-80.
  • Cody V, Pace J, Piraino J, Queener SF. (2011) Crystallographic analysis reveals a novel second binding site for trimethoprim in active site double mutants of human dihydrofolate reductase. J Struct Biol. 176(1):52-9.
  • Cody V, Pace J. (2011) Structural analysis of Pneumocystis carinii and human DHFR complexes with NADPH and a series of five potent 6-[5′-(ω-carboxyalkoxy)benzyl]pyrido[2,3-d]pyrimidine derivatives. Acta Crystallogr D Biol Crystallogr. 67(1):1-7.
  • Huang N, Kolhatkar R, Eyobo Y, Sorci L, Osterman A, MacKerell A, Zhang H. (2010) Structures of bacterial NaMN adenylyltransferase in complex with inhibitors: implication for structure based drug design and improvement. J. Med. Chem. 53(14):5229-39.
  • Bardaweel S, Pace J, Chou TF, Cody V Wagner CR. Probing the Impact of the echinT C-Terminal Domain on Structure and Catalysis. Journal of Molecular Biology. 2010, 404 (4): 627-638.
  • Cody V, Piraino J, Pace J, Li W, Gangjee A. (2010) Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ternary complexes with NADPH and human dihydrofolate reductase. Acta Crystallogr D Biol Crystallogr. 66(12):1271-7.
  • Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H. (2009) Structure and Function of an ADP-Ribose-Dependent Transcriptional Regulator of NAD Metabolism. Structure 17(7):939-51.
  • Koszelak-Rosenblum M, Krol A, Mozumdar N, Wunsch K, Ferin A, Cook E, Veatch CK, Nagel R, Luft JR, Detitta GT, Malkowski MG, (2009) Determination and application of empirically derived detergent phase boundaries to effectively crystallize membrane proteins, Protein Sci., 18(9), 1828-39.
  • Zhang W, Wang L, Liu Y, Xu J, Zhu G, Cang H, Li X, Bartlam M, Hensley K, Li G, Rao Z, Zhang XC. (2009) Structure of human lanthionine synthetase C-like protein 1 and its interaction with Eps8 and glutathione, Genes Dev., 23(12): 1387-92.
  • Liu X, Xu L, Liu Y, Tong X, Zhu G, Zhang X, Li X, Rao Z. (2009) Crystal Structure of the Hexamer of Human Heat Shock Factor Binding Protein 1, Proteins, 75(1): 1-11.
  • Sorci L, Pan Y, Eyobo Y, Rodionova I, Huang N, Kurnasov O, Zhong S, MacKerell AD Jr, Zhang H, Osterman AL. (2009) Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol. 16(8):849-61
  • Gangjee A, Li W, Lin L, Zeng Y, Ihnat M, Warnke LA, Green DW, Cody V, Pace J, Queener SF. (2009) Design, synthesis, and X-ray crystal structures of 2,4-diaminofuro[2,3-d]pyrimidines as multireceptor tyrosine kinase and dihydrofolate reductase inhibitors. Bioorg Med Chem. 17(20):7324-36.
  • Huang N, Sorci L, Zhang X, Brautigan C, Raffaelli N, Magni G, Grishin N, Osterman A, and Zhang H. (2008) Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure. 16(2):196-209
  • Cody V, Pace J, Rosowsky A. (2008) Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2′-hydroxydibenz[b,f]azepin-5-yl)methylpteridine. Acta Crystallogr D Biol Crystallogr. 64(9):977-84.
  • Zhang R, Zhu G, Zhang W, Cao S, Ou X, Li X, Bartlam M, Xu Y, Zhang XC. (2008) Crystal Structure of a Carbonyl Reductase from Candida Parapsilosis with anti-Prelog Stereospecificity, Protein Sci., 17(8): 1412-23.
  • Chen J, Li W, Wang M, Zhu G, Liu D, Sun F, Hao N, Li X, Rao Z, Zhang XC. (2008) Crystal Structure and Mutagenic Analysis of GDOsp, a Gentisate 1,2-Dioxygenase from Silicibacter Pomeroyi, Protein Sci., 17(8): 1362-73.
  • Snell EH, Luft JR, Potter SA, Lauricella AM, Gulde SM, Malkowski MG, Koszelak-Rosenblum M, Said MI, Smith JL, Veatch CK, Collins RJ, Franks G, Thayer M, Cumbaa C, Jurisica I, Detitta GT (2008) Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images Acta Crystallogr D Biol Crystallogr, 64(Pt 11), 1123-30.
  • Zhu G, Chen J, Liu J, Brunzelle JS, Huang B, Wakeham N, Terzyan S, Li X, Li G, Rao Z, Zhang XC. (2007) Structure of APPL1 BAR-PH domain and characterization of its interaction with Rab5, EMBO J., 26(14): 3484-93.
  • Zhu G, Zhai P, Liu J, Terzyan S, Li G, Zhang XC. (2004) Structural basis of Rab5-Rabaptin5 interaction in endocytosis, Nat Struct Mol Biol., 11(10):975-83.
  • Zhu G, Zhai P, He X, Wakeham N, Rodgers K, Li G, Tang J, Zhang XC. (2004) Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5, EMBO J., 23(20):3909-17.
  • Terzyan S, Zhu G, Li G, Zhang XC. (2004) Refinement of the structure of human Rab5a GTPase domain at 1.05Å resolution, Acta Crystallogr D, 60(1), 54-60.
  • Zhu G, Zhai P, He X, Terzyan S, Zhang R, Joachimiak A, Tang J, Zhang X. (2003) Crystal Structure of human GGA1 GAT Domain, Biochemistry, 42(21), 6392-9.
  • Zhu G, He, X., Zhai P, Terzyan S, Tang J, Zhang X. (2003) Crystal Structure of GGA2 VHS Domain and Its Implication in Plasticity in the Ligand Binding Pocket, FEBS Letters, 537(1-3), 171-6.
  • Zhu G, Liu J, Terzyan S, Zhai P, Li G, Zhang X. (2003) High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop, J Biol Chem, 278(4), 2452-60.
  • He X, Zhu G, Koelsch G, Rodgers KK, Zhang XC, Tang J. (2003) Biochemical and structural characterization of the interaction of memapsin 2 (beta-secretase) cytosolic domain with the VHS domain of GGA proteins, Biochemistry, 42(42), 12174-80.
  • Wu G, Huang Q, Zhu G, Qian M, Tang Y. (2003) Crystal Structure of Beta-Trypsin Complex with Amylamine in Cyclohexane, Acta Chimica Sinica, 61, 1393-1398.
  • Zhu G, Huang Q, Qian M, Tang Y. (2001) Crystal structure of alpha-momorcharin in 80% acetonitrile-water mixture, Biochim Biophys Acta, 1548(1), 152-158.
  • Zhu G, Huang Q, Zhu Y, Li Y, Chi C, Tang Y. (2001) X-ray study on an artificial mung bean inhibitor complex with bovine beta-trypsin in neat cyclohexane, Biochim Biophys Acta, 1546(1), 98-106.
  • Zhu G, Huang Q, Wang Z, Qian M, Jia Y, Tang Y. (1998) X-ray studies on two forms of bovine beta-trypsin crystals in neat cyclohexane, Biochim Biophys Acta, 1429(1), 142-150.
  • Wang Z, Zhu G, Huang Q, Qian M, Shao M, Jia Y, Tang Y. (1998) X-ray studies on cross-linked lysozyme crystals in acetonitrile-water mixture, Biochim Biophys Acta, 1384(2), 335-344.

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