MacCHESS User Publications

Complete lists of publications for CHESS on line

2018

2018

2017

  1. Alamo L., Ware J.S., Pinto A., Gillilan R.E., Seidman J.G., Seidman C.E., Padrón R. "Effects of myosin variants on interacting-heads motif explain distinct hypertrophic and dilated cardiomyopathy phenotypes," Elife eLife 2017;6:e24634, 2017.
  2. Bhatt A., Mahon B.P., Cruzeiro V.W., Cornelio B., Laronze-Cochard M., Ceruso M., Sapi J., Rance G., Khlobystov A.N., Fontana A., Roitberg A., Supuran C.T., McKenna R. "Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity," Chem Bio Chem 18(2), 213-222, 2017.
  3. Bingaman J.L., Zhang S., Stevens D.R., Yennawar N.H., Hammes-Schiffer S., Bevilacqua P.C., "The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme," Nature Chemical Biology 13(4), 439-445, 2017.
  4. Comandur R., Olson E.D. and Musier-Forsyth K. "Conservation of tRNA mimicry in the 5'-untranslated region of distinct HIV-1 subtypes". Published by Cold Spring Harbor Laboratory Press for the RNA Society, RNA, 2017.
  5. Gibbs E.B., Lu F., Portz B., Fisher M.J., Medellin B.P., Laremore T.N., Zhang Y.J., Gilmour D.S. & Showalter S.A. "Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain". Nature Communications 8, Article number: 15233, doi:10.1038/ncomms15233, 2017.
  6. Günther S., Deredge D., Bowers A.L., Luchini A., Bonsor D.A. Beadenkopf R., Liotta L., Wintrode P.L., Sundberg E.J. "Family Cytokines Use Distinct Molecular Mechanisms to Signal through Their Shared Co-receptor". Immunity, v. 47, 3, 510-523, e4, 2017.
  7. Gupta K., Sharp R., Yuan J.B., Li H. and Van Duyne G.D. "Coiled-coil interactions mediate serine integrase directionality". Nucleic Acids Research, Vol. 45, No. 12, 7339–7353, 2017.
  8. Hettle A., Fillo A., Abe K., Massel P., Pluvinage B., Langelaan D.N., Smith S.P. and Boraston A.B. "Properties of a family 56 carbohydrate-binding module and its role in the recognition and hydrolysis of ß-1,3-glucan". JBC, doi: 10.1074/jbc.M117.806711, 2017.
  9. Hopkins. J.B., Gillilan, R.E., Skou, S. "BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis." J. Appl. Cryst. , 50, 2017.
  10. Jayanthi S, Koppolu B.P., Nguyen K.G., mith S.G., Felber B.K., Kumar T.K.S.& Zaharoff D.A. "Modulation of Interleukin-12 activity in the presence of heparin". Scientific Reports 7, Article number: 5360 doi:10.1038/s41598-017-05382-1, 2017.
  11. Lan TY, Wierman JL, Tate MW, Philipp HT, Elser V, Gruner SM, "Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns", Journal of Applied Crystallography 50(4), 985-993 (2017).
  12. Leamy K.A., Yennawar N.H., and Bevilacqua P.C. "Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization". Biochemistry, 2017, 56 (27), 3422–3433, DOI: 10.1021/acs.biochem.7b00325, 2017.
  13. Lemon D.J., Yang X., Srivastava P., Luk Y-Y. & Garza A.G."Polymertropism of rod-shaped bacteria: movement along aligned polysaccharide fibers". Scientific Reports 7, Article number: 7643, doi:10.1038/s41598-017-07486-0, 2017.
  14. Lynch M.J., Levenson R., Kim E.A., Sircar R., Blair D.F., Dahlquist F.W., Crane B.R. "Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar MotorOriginal". Structure, v. 25, (2), 317-328, 2017.
  15. Maffioli SA. Zhang Y., Degen D., Carzaniga T. Del Gatto G., Serina S., Monciardini P,. Mazzetti C., Guglierame P., Candiani G., Chiriac A.I., Facchetti G., Kaltofen P., Sah H-G., Dehò G., Donadio S., Ebright R.H. "Antibacterial "Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase". Cell, V. 169, Issue 7, 1240-1248, e23, 2017.
  16. Malhotra K., Modak A., Nangia S., Daman T.H., Gunse U., Robinson V.L., Mokranjac D., May E.R. and Alder N.N. "Cardiolipin mediates membrane and channel interactions of the mitochondrial TIM23 protein import complex receptor Tim50". Science Advances, Vol. 3, no. 9, e1700532, DOI: 10.1126/sciadv.1700532, 2017.
  17. Mboge M.Y., Mahon B.P., Lamas N., Socorro L., Carta F., Supuran C.T., Frost S.C., McKenna R. "Structure activity study of carbonic anhydrase IX: Selective inhibition with ureido-substituted benzenesulfonamides". European Journal of Medicinal Chemistry, v. 132, 184-191, 2017.
  18. Meisburger S.P., Ando N., "Correlated Motions from Crystallography beyond Diffraction," Accounts of Chemical Research 50(3), 580-583, 2017.
  19. Molodtsov, V., Scharf, N.T., Stefan, M.A., Garcia, G.A. and Murakami, K.S. "Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis". Molecular Microbiology. doi:10.1111/mmi.13606, 2017.
  20. Muñoz-Escobar J., Matta-Camacho E., Cho C, Kozlov G., Gehring K. "Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase". Structure, v. 25, 5, 719–729, e3. 2017.
  21. Murakami K.S., Shin, Y., Turnbough C.L., Jr., and Molodtsov V. "X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway." PNAS U S A 114, 8211-8216, 2017
  22. Nguyen K., Li J., Puthenveeti R., Lin X., Poe M.M., Hsiao C-H.C., Vinogradova O. and Wiemer A.J. "The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region". FASEB J., doi: 10.1096/fj.201601370RR, 2017,
  23. O'Donnell JP., Cooley R.B., Kelly C.M., Miller K., Sondermann H. "Timing and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin Original research article." Structure, In press, Available online 9 June 2017
  24. Oudouhou F., Casu B., Puemi A.S.D., Sygusch J., Baron C., "Analysis of Novel Interactions between Components of the Selenocysteine Biosynthesis Pathway, SEPHS1, SEPHS2, SEPSECS, and SECp43," Biochemistry 56(17), 2261-2270, 2017.
  25. Park W.M., Bedewy M., Berggren K.K. & Keating A.E. "Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils". Scientific Reports 7, Article number: 10577 doi:10.1038/s41598-017-10918-6, 2017
  26. Plumridge A, Meisburger S.P, Andresen K, Pollack L, "The impact of base stacking on the conformations and electrostatics of single-stranded DNA," Nucleic Acids Research 45(7), 3932-3943 (2017).
  27. Plumridge A., Meisburger S.P., Pollack L., "Visualizing single-stranded nucleic acids in solution," Nucleic Acids Research 45(9), 2017.
  28. Portz B., Lu F., Gibbs E.B., Mayfield J.E., Mehaffey M.R., Zhang Y.J., Brodbelt J.S., Showalter S.A. & Gilmour D.S. "Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain". Nature Communications 8, Article number: 15231, doi:10.1038/ncomms15231, 2017.
  29. Pudasaini A., Shim J.S., Song Y.H., Shi H., Kiba T., Somers D.E., Imaizumi T., and Zoltowski B.D. "Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis". eLife, 6: e21646. 2017.
  30. Roig-Solvas B., Makowski L. "Calculation of the cross-sectional shape of a fibril from equatorial scattering". Ths paper is written in celebration of the occasion of Donald L.D. Caspar’s 90th Birthday. Journal of Structural Biology, 2017.
  31. Wong K., Perpich J.D., Kozlov G., Cygler M., Kwaik Y.A., Gehring K. "Structural Mimicry by a Bacterial F Box Effector Hijacks the Host Ubiquitin-Proteasome SystemOriginal". Structure, v. 25, (2), 376-383, 2017.
  32. Zhang H., Kozlov G., Li X., Wu H., Gulerez I. & Gehring K. "PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3". Scientific Reports 7, Article number: 48, doi:10.1038/s41598-017-00147-2, 2017.

Ph.D. Theses

  1. Wierman, J.L. "Exploration of Methods for Serial Microcrystallography at Storage Ring X-ray Sources" Ph.D. Thesis, Cornell University, Adviser: Sol M. Gruner (2017)

2016

  1. Alamo L, Qi D, Wriggers W, Antonio, Zhu J, Bilbao A, Gillilan RE, Hu S, Padron R. "Conserved intramolecular interactions maintain myosin interacting-heads motifs explaining tarantula muscle super-relaxed state structural basis." Journal of Molecular Biology (2016).
  2. Ando N, Li H, Brignole EJ, Thompson S, McLaughlin MI, Page JE, Asturias FJ, Stubbe J, and Drennan CL. "Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer". Biochemistry, 55 (2), pp 373–381, (2016).
  3. Bauman JD, Harrison JJEK, Arnold E. "Rapid experimental SAD phasing and hot-spot identification with halogenated fragments." IUCrJ 3(1), 51-60 (2016).
  4. Bhambure R, Gillespie CM, Phillips M, Graalfs H, Lenhoff AM. "Ionic strength-dependent changes in tentacular ion exchangers with variable ligand density. I. Structural properties". Journal of Chromatography A, Volume 1463, 9 September 2016, Pages 90-101, ISSN 0021-9673, (2016).
  5. Bhatt, A., Mahon, B. P., Cruzeiro, V. W. D., Cornelio, B., Laronze-Cochard, M., Ceruso, M., Sapi, J., Rance, G. A., Khlobystov, A. N., Fontana, A., Roitberg, A., Supuran, C. T. and McKenna, R. "Structure–Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity". ChemBioChem. doi:10.1002/cbic.201600513 (2016).
  6. Bhardwaj A, Sankhala RS, Olia AS, Brooke D, Casjens SR, Taylor DJ, Prevelige PE Jr, Cingolani G. "Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions." The Journal of Biological Chemistry 291, 215-226 (2016).
  7. Boyaci H, Shah T, Hurley A, Kokona B, Li Z, Ventocilla C, Jeffrey PD, Semmelhack MF, Fairman R, Bassler BL, Hughson FM. "Structure, Regulation, and Inhibition of the Quorum-Sensing Signal Integrator LuxO". PLOC, (2016).
  8. Mahon BP, Bhatt A, Socorro L, Driscoll JM, Okoh C, Lomelino CL, Mboge MY, Kurian JJ, Tu C, Agbandje-McKenna M, Frost SC, and McKenna R. "The Structure of Carbonic Anhydrase IX Is Adapted for Low-pH Catalysis". Biochemistry, 55 (33), 4642-4653 (2016).
  9. Cho S, Dickey SW, Urban S. "Crystal Structures and Inhibition Kinetics Reveal a Two-Stage Catalytic Mechanism with Drug Design Implications for Rhomboid Proteolysis." Molecular Cell 61(3), 329-340 (2016).
  10. Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR. "Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock". EMBO Journal, 35, 1707-1719,(2016)
  11. Cooley RB, O’Donnell JP and Sondermann H. “Coincidence detection and bi-directional transmembrane signaling control a bacterial second messenger receptor.” eLife 2016;5:e21848, (2016).
  12. Corcos AR, Villanueva O, Walroth RC, Sharma SK, Bacsa J, Lancaster KM, MacBeth CE, Berry JF, "Oxygen Activation by Co(II) and a Redox Non-Innocent Ligand: Spectroscopic Characterization of a Radical–Co(II)–Superoxide Complex with Divergent Catalytic Reactivity," Journal of the American Chemical Society 138(6), 1796-1799 (2016).
  13. Dahlstrom KM, Giglio KM, Sondermann H and O'Toole GA "The Inhibitory Site of a Diguanylate Cyclase Is a Necessary Element for Interaction and Signaling with an Effector Protein". J. Bacteriol. v. 198 no. 11, 1595-1603, (2016).
  14. Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, and Arnold E. "Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis—Binding of Foscarnet". ACS Chem. Biol. (2016).
  15. Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, and Marcotrigiano J. "Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I". PNAS, vol. 113 no. 3 pp. 596–601, (2016).
  16. Eisemann T, McCauley M, Langelier M-F, Gupta K, Roy S, Van Duyne GD, Pascal JM. "Tankyrase-1 Ankyrin Repeats Form an Adaptable Binding Platform for Targets of ADP-Ribose Modification". Structure, 24, 1–14, (2016).
  17. Ericson DL, Yin X, Scalia A, Samara YN, Stearns R, Vlahos H, Ellson R, Sweet RM, Soares AS. "Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase". Journal of Laboratory Automation, v. 21 no. 1, pp. 107-114, (2016).
  18. Fenwick MK, Philmus B, Begley TP, and Ealick SE. "Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis". Biochemistry, 55 (19), pp 2748–2759, (2016).
  19. Fenwick MK and Ealick SE. "Crystal Structures of the Iron–Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate". Biochemistry, 55 (30), 4135-4139, (2016).
  20. Gibbs EB and Showalter SA. "Quantification of Compactness and Local Order in the Ensemble of the Intrinsically Disordered Protein FCP1". J. Phys. Chem. B, 120 (34), pp 8960–8969, (2016).
  21. Gorelik A, Illes K, Superti-Furga G, Nagar B, "Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-Like Phosphodiesterase SMPDL3A," The Journal of Biological Chemistry (2016).
  22. Henderson RC, Gao F, Jayanthi S, Kight A, Sharma P, Goforth RL, Heyes CD, Henry RL, Thallapuranam Krishnaswamy Suresh Kumar. "Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle", Biophysical Journal, Volume 111, Issue 6, 1151-1162, (2016)
  23. Hopkins JB and Thorne RE, "Quantifying radiation damage in biomolecular small-angle X-ray scattering", J Appl Crystallogr, 49(3), 880-890 (2016).
  24. Huang LY, Patel A, Ng R, Miller EB, Halder S, McKenna R, Asokan A, and Agbandje-McKenna M. "Characterization of the Adeno-Associated Virus 1 and 6 Sialic Acid Binding Site". Journal of Virology, (2016)
  25. Huang Q, Gruner SM, Kim CU, Mao Y, Wu X, Szebenyi DM. "Reduction of lattice disorder in protein crystals by high-pressure cryocooling," J Appl Crystallogr. 49(1), 149-157 (2016).
  26. Huang Q, Szebenyi DME, "Improving diffraction resolution using a new dehydration method." Acta Crystallographica Section F 72(2), 152-159 (2016).
  27. Karasawa A., Kawate T. "Structural basis for subtype-specific inhibition of the P2X7 receptor". eLife, 2016.
  28. Kim CU, Song HJ, Avvaru BS, Gruner SM, Park SY, and McKenna R. "Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals." PNAS, v. 113 no. 19, pp. 5257–5262, (2016).
  29. Li Y, Erickson JW, Stalnecker CA, Katt WP, Huang Q, Cerione RA, Ramachandran S, "Mechanistic Basis of Glutaminase Activation: A Key Enzyme that Promotes Glutamine Metabolism in Cancer Cells", J Bio Chem (2016).
  30. Lomelino CL, Mahon BP, McKenna R, Carta F, Supuran CT. "Kinetic and X-ray crystallographic investigations on carbonic anhydrase isoforms I, II, IX and XII of a thioureido analog of SLC-0111". Bioorganic & Medicinal Chemistry, v 24, 5, pp. 976–981, (2016).
  31. Lucido MJ, Orlando BJ, Vecchio AJ, Malkowski MG. "Crystal structure of aspirin-acetylated human cyclooxygenase-2: Insight into the formation of products with reversed stereochemistry." Biochemistry including biophysical chemistry and molecular biology 55(8), 1226-1238 (2016).
  32. Lukk T, Gillilan RE, Szebenyi DM, Zipfel WR. "A visible-light-excited fluorescence method for imaging protein crystals without added dyes." J Appl Crystallogr 49, 234-240 (2016).
  33. Mahon BP, Kurian JJ, Lomelino CL, Smith IR, Socorro L, Bennett A, Hendon AM, Chipman P, Savin DA, Agbandje-McKenna M and McKenna R. "Microbatch Mixing: “Shaken not Stirred”, a Method for Macromolecular Microcrystal Production for Serial Crystallography". Crystal Growth & Design, 16 (11), 6214-6221, (2016).
  34. Matsuyama BY, Krasteva P, Baraquet C, Harwood CS, Sondermann H, Navarro MVAS. "Mechanistic insights into c-di-GMP–dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa". PNAS, v. 113, 2, (2016).
  35. McDermott LA , Iyer P, Vernetti L, Rimer S, Sun J, Boby M, Yang T, Fioravanti M, O’Neill J, Wang L, Drakes D, Katt W, Huang Q, Cerione R. "Design and evaluation of novel glutaminase inhibitors." Bioorganic & Medicinal Chemistry (2016).
  36. Meisburger SP, Taylor AB, Khan CA, Zhang S, Fitzpatrick PF, and Ando A. "Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering". J. Am. Chem. Soc., 138 (20), pp. 6506–6516, (2016).
  37. Miller MT, Tuske S, Das K, DeStefano JJ, Arnold E. "Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer." Protein Sci. 25, 46-55 (2016).
  38. Mori S, Simkhada D, Zhang H, Erb MS, Zhang Y, Williams H, Fedoseyenko D, Russell WK, Kim D, Fleer N, Ealick SE, and Watanabe CMH. "Polyketide Ring Expansion Mediated by a Thioesterase, Chain Elongation and Cyclization Domain, in Azinomycin Biosynthesis: Characterization of AziB and AziG". Biochemistry, 55 (4), pp 704–714, (2016).
  39. Oot RA, Kane PM, Berry EA & Wilkens S. "Crystal structure of yeast V1-ATPase in the autoinhibited state". EMBO Journal, 35, 1694-1706, (2016).
  40. Pabit SA, Katz AM, Tolokh AS, Drozdetski A, Baker N, Onufriev AV, and Pollack L. "Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations". J. Chem. Phys. 144, 205102 (2016).
  41. Payne T, Yee E, Dzikovski B, Crane B, "Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c." Biochemistry 55(34), 4807-4822 (2016).
  42. Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy PM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M and Arnold E. "A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain". J. Biolog. Chem., v. 291, NO. 45, pp. 23569 –23577, (2016)..
  43. Pinard MA, Kurian J., Aggarwal M, Agbandje-McKenna M. and McKenna R. "Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3". Acta Crystallographica Section F, Volume 72, Part 7, 573-577 (2016).
  44. Postel S, Deredge D, Bonsor DA, Yu X, Diederichs K. Helmsing S, Vromen A, Friedler A, Hust M, Egelman EH, Beckett D, Wintrode PL, Sundberg EJ. "Bacterial flagellar capping proteins adopt diverse oligomeric states". eLife 2016;5:e18857
  45. Pradhan L, Gopal S, Li S, Ashur S, Suryanarayanan S, Kasahara H, and Nam HJ. "Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5". Biochemistry, 55 (12), pp 1702–1710, (2016)
  46. Reimer JM, Aloise MN, Harrison PM, Schmeing TM, "Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase," Nature 529, 239-242 (2016).
  47. Richardson BC, Halaby SL, Gustafson MA, Fromme JC. "The Sec7 N-terminal regulatory domains facilitate membrane-proximal activation of the Arf1 GTPase". eLIFE (2016).
  48. Rustiguel, J. K., Soares, R. O. S., Meisburger, S. P., Davis, K. M., Malzbender, K. L., Ando, N., Dias-Baruffi, M., & Nonato, M. C. “Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication” Sci. Rep. 6, 33633. (2016)
  49. Sarowar S, Hu J, Werneburg GT, Thanassi DG, Li H. "The Escherichia coli P and type 1 pilus assembly chaperones PapD and FimC are monomeric in solution". J. Bacteriol., (2016).
  50. Schormann, N., Zhukovskaya, N., Bedwell, G., Nuth, M., Gillilan, R., Prevelige, P. E., Ricciardi, R. P., Banerjee, S. and Chattopadhyay, D. "Poxvirus uracil-DNA glycosylase—An unusual member of the family I uracil-DNA glycosylases." Protein Science, 25: 2113–2131. doi:10.1002/pro.3058, (2016).
  51. Singh G, Zhang J, Ma Y, Cerione RA, Antonyak MA, "The different conformational states of Tissue Transglutaminase have opposing affects on cell viability". The Journal of Biological Chemistry (2016).
  52. Trempe J.-F, Šašková KG, Sivá M, Ratcliffe CDH, Veverka V, Hoegl A, Ménade M, Feng X, Shenker S, Svoboda M, Kožíšek M, Konvalinka J, Gehring K. "Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family". Sci. Rep. 6, 33671, (2016).
  53. Wierman J, Lan TY, Tate M, Philipp H, Elser V, and Gruner S. "Protein Crystal Structure from Non-oriented, Single-axis Sparse X-ray Data." IUCrJ 3: 43-50 (2016).
  54. Xiong Z-X, Huang J., Poda G., Pomès R., Privé G.G. "Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis". J. Mol. Biology, In Press, (2016).
  55. Xu C, Kozlov G, Wong K, Gehring K, Cygler M. "Crystal Structure of the Salmonella Typhimurium Effector GtgE". PLoS ONE 11(12): e0166643. doi:10.1371/journal. pone.0166643 (2016).
  56. Zhang H, Chang Y-C,, Huang Q, Brennan ML, Wu J. "Structural and Functional Analysis of a Talin Triple-Domain Module Suggests an Alternative Talin Autoinhibitory Configuration". Structure, v. 24, 5, pp. 721–729, (2016).

Ph.D. Theses

  1. Hopkins J., "Development Of Low Temperature Biological Small Angle X-Ray Scattering, Cryosaxs, And Study Of Ice Formation In Aqueous Solutions" Ph.D. Thesis, Cornell University, Advisor: Robert Thorne, (2016).
  2. Howell SC., "Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering," Ph.D. Thesis, The George Washington University, Advisor: Xiangyun Qiu (2016).

Videos

  1. CLASSE atCornell, "BioSAXS Essentials 6 Workshop, May 2016", YouTube, Web. 24 Aug. 2016.

2015

  1. Acerbo AS, Cook MJ, Gillilan RE, "Upgrade of MacCHESS facility for X-ray scattering of biological macromolecules in solution". J Synchrotron Radiat., PMID: 25537607 22(1), 180-6 (2015)
  2. Aggarwal M, Chua TK, Pinard MA, Szebenyi DM, McKenna R, "Carbon Dioxide "Trapped" in a ß-Carbonic Anhydrase," Biochemistry 54(43), 6631-6638 (2015)
  3. Ayyer K, Philipp HT, Tate MW, . Wierman JL, Elser V and Gruner S M. "Determination of crystallographic intensities from sparse data." IUCrJ 2:29-34 (2015)
  4. Balzarini J, Das K, Bernatchez J, Martinez S, Ngure M, Keane S, Ford A, Maguire N, Mullins N, John J, Kim Y, Dehaen W, Woorde J, Liekens S, Naesens L, Gotte M, Maguire A, Arnold E, "Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics," PNAS 112(11) (2015)
  5. Barnett GV, Razinkov VI, Kerwin BA, Laue TM, Woodka AH, Butler PD, Perevozchikova T, Roberts CJ, "Specific-ion effects on the aggregation mechanisms and protein-protein interactions for anti-streptavidin immunoglobulin gamma-1," J Phys Chem B 119(18), 5793-804 (2015)
  6. Boock JT, King BC, Taw M, Conrado RJ, Siu K-H, Stark J, Walker LP, Gibson DM, DeLisa MP, "Repurposing a bacterial quality control mechanism to enhance production of a fungal endocellulase". Journal of Molecular Biology (2015)
  7. Boone C, Rasi V, McKenna R. "Structural and catalytic effects of proline substitution and surface loop deletion in the extended active site of human carbonic anhydrase II". FEBS Journal, v 282, 8, 1445–1457, (2015)
  8. Carta F, Mannelli LDC, Pinard M, Ghelardini C, Scozzafava A, McKenna R, Supuran CT. "A class of sulfonamide carbonic anhydrase inhibitors with neuropathic pain modulating effects". Bioorganic & Medicinal Chemistry, v 23, 8, 1828–1840, (2015)
  9. Criswell A, Mooers BHM, "Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering". Methods Mol Biol. 1240, 165-89 (2015)
  10. Couoh-Cardel S, Milgrom E and Wilkens S. "Affinity Purification and Structural Features of the Yeast Vacuolar ATPase Vo Membrane Sector". The Journal of Biological Chemistry, 290, 27959-27971, (2015)
  11. Freed DM, Alvarado D, & Lemmon MA. "Ligand regulation of a constitutively dimeric EGF receptor". Nature Communications, 6, Article number: 7380, (2015)
  12. Dahlstrom KM, Giglio KM, Collins AJ, Sondermann H, O’Toole GA. "Contribution of Physical Interactions to Signaling Specificity between a Diguanylate Cyclase and Its Effector". mBio vol. 6 no. 6, (2015)
  13. Díaz-Torres NA, Mahon BP, Boone CD, Pinard MA, Tu C, Ng R, Agbandje-McKenna M, Silverman D, Scott K and McKenna R. "Structural and biophysical characterization of the a-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2: insights into engineering thermostable enzymes for CO2 sequestration". Acta Crystallographica Section D, v 71, 8, 1745-1756, (2015)
  14. Garg A, Lukk T, Kumar V, Choi JY, Augagneur Y, Voelker DR, Nair S, Mamoun CB, "Structure, Function and Inhibition of the Phosphoethanolamine Methyltransferases of the Human Malaria Parasites Plasmodium vivax and Plasmodium knowlesi", Scientific Reports 5 (2015).
  15. Gilman MSA, Moin SM, Mas V, Chen M, Patel NK, Kramer K, Zhu Q, Kabeche SC, Kumar A, Palomo C, Beaumont T, Baxa U, Ulbrandt ND, Melero JA, Graham BS, McLellan JS. "Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein". PLoS Pathogens Issue, Vol. 11(7), (2015)
  16. Greene DG, Modla S, Wagner NJ, Sandler SI, Lenhoff AM. "Local Crystalline Structure in an Amorphous Protein Dense Phase". Biophysical Journal, v 109, 8, pp 1716–1723, (2015)
  17. Greenswag AR, Muok A, Li X, Crane BR. "Conformational Transitions that Enable Histidine Kinase Autophosphorylation and Receptor Array Integration". Journal of Molecular Biology, v 427, 24, 3890–3907, (2015)
  18. Greenswag AR, Li X, Borbat PP, Samanta D, Watts KJ, Freed JH, and Crane BR. "Preformed Soluble Chemoreceptor Trimers That Mimic Cellular Assembly States and Activate CheA Autophosphorylation". Biochemistry, 54 (22), pp 3454–3468, (2015)
  19. Gruner S, Lattman E, "Biostructural Science Inspired by Next-Generation X-Ray Sources", Annual Rev. Biophysics 44:33-51. (2015)
  20. Guo F, Zhou W, Li P, Mao Z, Yennawar NH, French JB, and Huang TJ. "Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves". Small, v 11, Issue 23, pp 2733–2737, (2015)
  21. Gupta K, Martin R, Sharp R, Sarachan KL, Ninan NS and Van Duyne GD. "Oligomeric Properties of Survival Motor Neuron·Gemin2 Complexes". The Journal of Biological Chemistry 290, 20185-20199, (2015)
  22. Haldera S, Vlieta KV, Smith JK, Duong TTP, McKenna R, Wilson JM, Agbandje-McKenna M. "Structure of neurotropic adeno-associated virus AAVrh.8". Journal of Structural Biology, v 192, 1, pp 21–36, (2015)
  23. Hauk G, Bowman GD. "Formation of a Trimeric Xpo1-Ran[GTP]-Ded1 Exportin Complex Modulates ATPase and Helicase Activities of Ded1". PLOS, (2015)
  24. Hopkins JB, Katz AM, Meisburger SP, Warkentin MA, Thorne RE, Pollack L, "A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS". Applied Crystallography Online 48(1), 227-237 (2015)
  25. Hsu F, Hu F, Mao Y, "Spatiotemporal control of phosphatidylinositol 4-phosphate by Sac2 regulates endocytic recycling," J Cell Biol 209(1), 97-110 (2015)
  26. Huang Q, Gruner SM, Kim CU, Mao Y , Wu X, and Szebenyi DME. "Reduction of lattice disorder in protein crystals by high pressure cryocooling". J. Appl. Crystallography (In press) (2015)
  27. Keedy D A, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM,Lemke H, Gonzalez A, Sauter NK, Cohen AE, Van den Bedem H, Thorne RE, Fraser JS. "Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography". eLife, 10.7554, (2015)
  28. Kim CU, Tate MW, and Gruner SM. "Glass-to-cryogenic liquid transitions in water solutions examined by crack-healing". Proc. Natl. Acad. Sci. USA 112:11765-11770 (2015)
  29. Kucerka N, Oosten B, Pan J, Heverle F, Harroun T, Katsaras J, "Molecular Structures of Fluid Phosphatidylethanolamine Bilayers Obtained from Simulation-to-Experiment Comparisons and Experimental Scattering Density Profiles," The Journal of Physical Chemistry B 119(5), 1947-1956 (2015)
  30. Kumar AK, Kumar RSS, Yennawar NH, Yennawar HP, and Ferry JG. "Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans". Biochemistry, 54 (19), pp 3122–3128, (2015)
  31. Loh S, Ha J-H, Mitrea D, "Domain Swapping Modules", (2015)
  32. Lokhandwala J, Hopkins HC, Rodriguez-Iglesias A, Dattenböck C, Schmoll M, Zoltowski BD. "Structural Biochemistry of a Fungal LOV Domain Photoreceptor Reveals an Evolutionarily Conserved Pathway Integrating Light and Oxidative Stress". Structure, v 23, 1, 116–125, (2015)
  33. Luo X, Wasilko DJ, Liu Y, Sun J, Wu X, Luo ZQ, Mao Y. "Structure of the Legionella Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome". PLOS, (2015)
  34. Madasu Y, Yang C, Boczkowska M, Bethoney KA, Zwolak A, Rebowski G, Svitkina T, Dominguez R, "PICK1 is implicated in organelle motility in an Arp2/3 complex-independent manner," Mol Biol Cell. 26(7), 1308-22 (2015)
  35. Meisburger SP, Pabit SA, Pollack L, "Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements", Biophys J. 108(12), 2886-95 (2015)
  36. Mizrachi D, Chen Y, Liu J, Peng HM, Ke A, Pollack L, Turner RJ, Auchus RJ & DeLisa MP. "Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy". Nature Communications, 6, Article number:6826, (2015)
  37. Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS, "X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein," J Med Chem 58(7), 3156-71 (2015)
  38. Moravcevic K, Alvarado D, Schmitz KR, Kenniston JA, Mendrola JM, Ferguson KM, Lemmon MA "Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site", Structure 23(2), 352-363 (2015)
  39. Moustafa IM, Uchida A, Wang Y, Yennawar N, Cameron CE, "Structural models of mammalian mitochondrial transcription factor B2," Biochim Biophys Acta 1849(8), 987-1002 (2015)
  40. Moustafa IM, Gohara DW, Uchida A, Yennawar N, and Cameron CE. "Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?". Viruses, 7(11), 5962-5986, (2015)
  41. Muñoz-Escobar J, Matta-Camacho E, Kozlov G and Gehring K. "The MLLE Domain of the Ubiquitin Ligase UBR5 Binds to Its Catalytic Domain to Regulate Substrate Binding". The Journal of Biological Chemistry, 290, 22841-22850, (2015)
  42. Organtini LJ, Allison AB, Lukk T, Parrish CR, Hafenstein S, "Global displacement of canine parvovirus by a host-adapted variant: A structural comparison between pandemic viruses with distinct host ranges," J Virol. 89(3), 1909-12 (2015).
  43. Orlando BJ, Lucido MJ, Malkowski MG. "The structure of ibuprofen bound to cyclooxygenase-2". Journal of Structural Biology, v 189, 1, pp 62–66, (2015)
  44. Pinard MA, Aggarwal M, Mahon BP, Tuc C, and McKenna R. "A sucrose-binding site provides a lead towards an isoform-specific inhibitor of the cancer-associated enzyme carbonic anhydrase IX". Acta Crystallographica Section F, v 71, 10, pp 1352-1358, (2015)
  45. Pinard MA, Lotlikar SR, Boone CD, Vullo D, Supuran CT, Patrauchan MA, McKenna R. "Structure and inhibition studies of a type II beta-carbonic anhydrase psCA3 from Pseudomonas aeruginosa". Bioorganic & Medicinal Chemistry, v 23, 15, pp 4831–4838, (2015)
  46. Price IR, Gaballa A, Ding F, Helmann JD, Ke A. "Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches". Molecular Cell, v 57, 6, pp 1110–1123, (2015)
  47. Ranaivoson FM, Liu Q, Martini F, Bergami F, Von Daake S, Li S, LeeD, Demeler B, Hendrickson WA, Comoletti D. "Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development". Structure, v 23, 9, pp 1665–1677, (2015)
  48. Shinsky SA and Cosgrove MS. "Unique Role of the WD-40 Repeat Protein 5 (WDR5) Subunit within the Mixed Lineage Leukemia 3 (MLL3) Histone Methyltransferase Complex". The Journal of Biological Chemistry 290, 25819-25833, (2015)
  49. Sircar R, Borbat PP, Lynch MJ, Bhatnagar J, Beyersdorf MS, Halkides CJ, Freed JH, Crane BR. "Assembly States of FliM and FliG within the Flagellar Switch Complex". Journal of Molecular Biology, v 427, 4, 867–886, *2015)
  50. Tang S, Henne MW, Borbat PP, Buchkovich NJ, Freed JH, Mao Y, Fromme CJ, Emr SD. "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments". eLIFE, (2015)
  51. Teng Y, Jing H, Aramsangtienchai P, He B, Khan S, Hu J, Lin H, Hao Q, "Efficient Demyristoylase Activity of SIRT2 Revealed by Kinetic and Structural Studies", Scientific Reports 5 (2015)
  52. Tondnevis F, Gillilan R, Bloom L, McKenna R, "Solution study of the Escherichia coli DNA polymerase III clamp loader reveals the location of the dynamic ?? heterodimer," Structural Dynamics 2(054701), (2015)
  53. Wang O, Vogan EM, Nocka LM, Rosen CE, Zorn JA, Harrison SC, John Kuriyan. "Autoinhibition of Bruton's tyrosine kinase (Btk) and activation by soluble inositol hexakisphosphate". eLife 2015;4:e06074, (2015)
  54. Wong K, Kozlov G, Zhang Y and Gehring K. "Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism". The Journal of Biological Chemistry 290, 24727-24737, (2015)
  55. Yang Y, Ye Q, Jia Z and Côté GP. "Characterization of the Catalytic and Nucleotide Binding Properties of the a-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A". The Journal of Biological Chemistry, 290, 23935-23946, (2015)

Ph.D. Theses

  1. Barnett G, "Mechanistic insights into the role of protein interactions on the aggregation behavior of anti-streptavidin immunoglobulin gamma-1," Ph.D. Thesis, University of Delaware, Advisor: Christopher J Roberts (2015).
  2. Boock JT, "Expanding the capabilities of a bacterial quality control mechanism for engineering enzymes", Ph.D. Thesis, Cornell University, Advisor: Matthew P DeLisa (2015).
  3. Paradise P, "In-situ diffraction studies of rate dependence of twinning, phase transformation, and slip in shape memory alloys", Ph.D. Thesis, Colorado School of Mines, Advisor: Aaron P Stebner (2015).
  4. Pinard MA, "Structure, catalytic mechanism and inhibition of a type II beta carbonic anhydrase psCA3 from Pseudomonas aeruginosa", Ph.D. Thesis, University of Florida, Advisor: Robert McKenna (2015).

 

Videos

  1. WebsEdgeEducation, "Cornell High Energy Synchrotron Source," YouTube, Web. 27 Feb. 2015," YouTube, Web. 24 Aug. 2016.

2014

  1. Bastos-Aristizabal S, Kozlov G, Gehring K, "Structure of the substrate-binding b' domain of the Protein Disulfide Isomerase-Like protein of the Testis", Sci Rep., doi: 10.1038/srep04464., PMID: 24662985 4, 4464 (2014).
  2. Bastos-Aristizabal S, Kozlov G, Gehring K, "Structural insight into the dimerization of human protein disulfide isomerase," Protein Sci. 23(5), 618-26 (2014).
  3. Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernández-Tornero C, Kulbachinskiy A, Murakami KS, "Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme," J Biol Chem 289(35), 24549-59 (2014).
  4. Bhardwaj A, Casjens SR, Cingolani G, "Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography," Acta Crystallogr D Biol Crystallogr 70(2), 342-53 (2014).
  5. Bollini M, Frey KM, Cisneros JA, Spasov KA, Das K, Bauman JD, Arnold E, Anderson KS, Jorgensen WL, "Extension into the entrance channel of HIV-1 reverse transcriptase-crystallography and enhanced solubility," Bioorg Med Chem Lett 23(18), 5209-12 (2014).
  6. Boscia AL, Treece BW, Mohammadyani D, Klein-Seetharaman J, Braun AR, Wassenaar TA, Klösgen B, Tristram-Nagle S, "X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes", Chem Phys Lipids., doi: 10.1016/j.chemphyslip.2013.12.010 178, 1-10 (2014).
  7. Chatterjee D, Cooley R B, Boyd CD, Mehl R A, O'Toole G A, Sondermann H, "Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP." Elife (2014).
  8. Das K, Martinez S E, Bandwar R P, Arnold E, "Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage." Nucleic Acids Res 42(12), 8125-37 (2014).
  9. Degen D, Feng Y, Zhang Y, Ebright K Y, Ebright Y W, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright R H, "Transcription inhibition by the depsipeptide antibiotic salinamide A." Elife 3 (2014).
  10. Gruner, S M, "Expanding the femtosecond crystallography toolkit." PNAS U S A 111(48), 16986-7 (2014).
  11. Gupta K, Contreras L M, Smith D, Qu G, Huang T, Spruce L A, Seeholzer S H, Belfort M, Van Duyne G D, "Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering." Nucleic Acids Res., doi: 10.1093/nar/gku140 42(8), 5347-5360 (2014).
  12. Heim K P, Crowley P J, Long J R, Kailasan S, McKenna R, Brady L J, "An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1." Proc Natl Acad Sci U S A 111(44), 15746-51 (2014).
  13. Heymann M, Opthalage A, Wierman J L, Akella S, Szebenyi D M, Gruner S M, Fraden S, "Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction." IUCrJ 1(5), 349-60 (2014).
  14. Hsu F, Luo X, Qiu J, Teng Y B, Jin J, Smolka M B, Luo Z Q, Mao Y, "The Legionella effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling." Proc Natl Acad Sci U S A. 111(29), 10538-10543 (2014).
  15. Huo Y, Nam K H, Ding F, Lee H, Wu L, Xiao Y, Farchione M D Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A, "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation." Nat Struct Mol Biol. (2014).
  16. Jun S H, Hirata A, Kanai T, Santangelo T J, Imanaka T, Murakami K S, "The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration." Nat Commun 5, 5132 (2014).
  17. Kang HJ, Paterson NG, Kim CU, Middleditch M, Chang C, Ton-That H, Baker EN, "A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly", Acta Cryst., D 70, 1190-1201 (2014).
  18. Kozlov G, Vinaik R, Gehring K, "Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli", Acta Crystallogr Sect F Struct Biol Cryst Commun., doi: 10.1107/S1744309113010841, PMID: 23695562 69(Pt 5), 499-502 (2014).
  19. Lima E, Chushkin Y, van der Linden P, Kim CU, Zontone F, Carpentier P, Gruner SM, Pernot P, "Cryogenic x-ray diffraction microscopy utilizing high-pressure cryopreservation," Phys Rev E Stat Nonlin Soft Matter Phys., PMID: 25375529 90(4-1), 042713 (2014).
  20. Liu CT, Layfield JP, Stewart RJ 3rd, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ, "Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase," J Am Chem Soc 136(29), 10349-60 (2014).
  21. Martinez M, Ahmed AH, Loh AP, Oswald RE, "Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: implications for drug development," Biochemistry 53(23), 3790-5 (2014).
  22. Merz GE, Borbat PP, Pratt AJ, Getzoff ED, Freed JH, Crane BR, "Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states," Biophys J 107(7), 1669-74 (2014).
  23. Mikals K, Nam HJ, Van Vliet K, Vandenberghe LH, Mays LE, McKenna R, Wilson JM, Agbandje-McKenna M, "The structure of AAVrh32.33, a novel gene delivery vector," J Struct Biol 186(2), 308-17 (2014).
  24. Organtini LJ, Allison AB, Lukk T, Parrish CR, Hafenstein S, "Global displacement of canine parvovirus by a host-adapted variant: A structural comparison between pandemic viruses with distinct host ranges," J Virol., PMID: 25410876 (2014).
  25. Organtini LJ, Makhov AM, Conway JF, Hafenstein S, Carson SD, "Kinetic and structural analysis of coxsackievirus B3 receptor interactions and formation of the A-particle," J Virol. 88(10), 5755-65 (2014).
  26. Orlando BJ, Lucido MJ, Malkowski MG, "The structure of ibuprofen bound to cyclooxygenase-2," J Struct Biol 189(1), 62-6 (2014).
  27. Paczkowski JE, Fromme JC, "Structural basis for membrane binding and remodeling by the exomer secretory vesicle cargo adaptor," Dev Cell 30(5), 610-24 (2014).
  28. Patel D, Bauman JD, Arnold E, "Advantages of crystallographic fragment screening: Functional and mechanistic insights from a powerful platform for efficient drug discovery," Prog Biophys Mol Biol 116(2-3), 92-100 (2014).
  29. Pradhan L, Gopal S, Nam H-J, "Crystallization and preliminary X-ray analysis of the cardiac transcription factor complex of NKX2.5 and TBX5 with DNA", Acta Cryst., F 70, 592-595 (2014).
  30. Ptak CP, Hsieh CL, Weiland GA, Oswald RE, "Role of stoichiometry in the dimer-stabilizing effect of AMPA receptor allosteric modulators", ACS Chem Biol., doi: 10.1021/cb4007166 9(1), 128-33 (2014).
  31. Sagong HY, Bauman JD, Patel D, Das K, Arnold E, LaVoie EJ, "Phenyl substituted 4-hydroxypyridazin-3(2H)-ones and 5-hydroxypyrimidin-4(3H)-ones: inhibitors of influenza A endonuclease," J Med Chem. 57(19), 8086-98 (2014).
  32. Saliba M, Tan KW, Sai H, Moore DT, Scott T, Zhang W, Estroff LA, Wiesner U, Snaith HJ, "Influence of Thermal Processing Protocol upon the Crystallization and Photovoltaic Performance of Organic–Inorganic Lead Trihalide Perovskites", J. Phys. Chem. C, Article ASAP DOI: 10.1021/jp500717w (2014).
  33. Sasaki E, Zhang X, Sun HG, Lu MY, Liu TL, Ou A, Li JY, Chen YH, Ealick SE, Liu HW, "Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis," Nature 510(7505), 427-31 (2014).
  34. Skou M, Skou S, Jensen TG, Vestergaard B, Gillilan RE, "In situ microfluidic dialysis for biological small-angle X-ray scattering," J Appl Crystallogr 47(4), 1355-1366 (2014).
  35. Skou S, Gillilan RE, Ando N, "Synchrotron-based small-angle X-ray scattering of proteins in solution," Nat Protoc 9(7), 1727-39 (2014).
  36. Wedekind J, Liberman J, Jenkin J, Salim M, "Metal Dependence of Ligand Binding and Heavy-Atom Derivatization of Evolutionarily Distinct PreQ 1 Riboswitches," Chemical Biology of Nucleic Acids (2014).
  37. Weiskoff AM, Fromme JC, "Distinct N-terminal regions of the exomer secretory vesicle cargo Chs3 regulate its trafficking itinerary," Front Cell Dev Biol 2(47) (2014).
  38. Yearley EJ, Godfrin PD, Perevozchikova T, Zhang H, Falus P, Porcar L, Nagao M, Curtis JE, Gawande P, Tain R, Zarraga IE, Wagner NJ, Liu Y, "Observation of Small Cluster Formation in Concentrated Monoclonal Antibody Solutions and Its Implications to Solution Viscosity", Biophysical Journal 106(8), 1763-1770 (2014).
  39. Zhang S, Liua X, Barreto-Ortiz SF, Yu Y, Ginn BP, DeSantis NA, Hutton DL, Grayson WL, Cui FZ, Korgel BA, Gerecht S, Mao HQ, "Creating polymer hydrogel microfibres with internal alignment via electrical and mechanical stretching", Biomaterials 35(10), 3243–3251 (2014).
  40. Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH, "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides," Elife (2014).

 

Ph.D. Theses

  1. Gee KO, "Characterization of transcriptional activators in the fungal circadian clock," Ph.D. Thesis, Cornell University, Advisor: Brian R. Crane (2014).
  2. Heymann M, "Microfluidic tools to investigate protein crystallization," Ph.D. Thesis, Brandeis University, Advisor: Seth Fraden (2014).
  3. Kopp MC, "Structural studies of sulfur transfer in thiocarboxylate-dependent methionine biosynthesis," Ph.D. Thesis, Cornell University Advisor: Steven Ealick (2014).
  4. Liberman JA, "Structural and Functional Analysis of Gene Regulatory PreQ 1 Riboswitches," Ph.D. Thesis, University of Rochester, Advisor: Joseph E. Wedekind (2014).
  5. Payne TM, "Crystallographic and spectroscopic studies on the complex of Cytochrome c Peroxidase and Cytochrome c," Ph.D. Thesis, Cornell University, Advisor: Brian Crane (2014).
  6. Toulabi LB, "Identification and structural characterization of a Legionella Phosphoinositide phosphatase," Ph.D. Thesis, Cornell University, Advisor: Yuxin Mao (2014).

 

Videos

  1. WebsEdgeEducation, "MacCHESS, Cornell University - Advancing the Research Goals...," YouTube, Web. 15 Feb. 2014.

2013

  1. Govindasamy L., Dimattia M. A., Gurda B. L., Halder S., McKenna R., Chiorini J. A., Muzyczka N., Zolotukhin S., and Agbandje-McKenna M. Structural insights into Adeno-associated virus serotype 5. J. Virol., doi: 10.1128/JVI.00867-13, 2013
  2. Halder S., Nam H. J., Govindasamy L., Vogel M., Dinsart C., Salomé N., McKenna R., and Agbandje-McKenna M. Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Empty Capsids. J. Virol. 87(9), 5128-5140, 2013
  3. Joseph D. Bauman, Disha Patel, Steven F. Baker, R. S. K. Vijayan, Amy Xiang, Ajit K. Parhi, Luis Martinez-Sobrido, Edmond J. LaVoie, Kalyan Das, and Eddy Arnold. Crystallographic fragment screening and structure-based optimization yields a new class of Infuenza endonuclease inhibitors. ACS, http://pubs.acs.org/doi/full/10.1021/cb400400j, 2013
  4. Bauman J. D., Patel D., Dharia Chhaya., Fromer M. W., Ahmed S., Frenkel Y., Vijayan R. S. K., Eck J. T., Ho W. C., Das K., Shatkin A. J., and Arnold E. Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening. J. Med. Chem., Article ASAP DOI: 10.1021/jm301271j, 2013
  5. Liu C., Hanoian P., French J., Pringle T., Hammes-Schiffer S., Benkovic S. Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. PMID: 23733948, PMCID: PMC3690862, 2013
  6. De Bari H. and Berry E. A. Structure of Vibrio cholerae Ribosome Hibernation Promoting Factor. Acta F, 69, 228-236, 2013
  7. Zhou Y., Johnson J., Cerione R., and Erickson J. Prenylation and Membrane Localization of Cdc42 Are Essential for Activation by DOCK7. Biochemistry, 52(25), 4354-4363, 2013
  8. O`Neall-Hennessey E., Reshetnikova L., Kumar S., Robinson H., Szent-Gyorgyi A. G., Cohen C. Purification, crystallization and preliminary X-ray crystallographic analysis of squid heavy meromyosin. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 69, 248-252, 2013
  9. Conrad K. S., Bilwes A. M., Crane B. R. Light-Induced Subunit Dissociation by a Light−Oxygen−Voltage Domain Photoreceptor from Rhodobacter sphaeroides. Biochemistry 52, 378−391, 2013
  10. Airola M. V., Sukomon N., Samanta D., Borbat P. P., Freed J. H., Watts K. J., and Crane B. R. HAMP Domain Conformers That Propagate Opposite Signals in Bacterial Chemoreceptors, PLOS Biology, 11, 1-13, 2013
  11. Airola M. V., Huh D., Sukomon N., Widom J., Sircar R., Borbat P. P., Freed J. H., Watts K. J., Crane B. R. Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling, JMB, PMID: 23274111, PMCID: PMC3577987 425, 886-901, 2013
  12. Sircar R., Greenswag A. R., Bilwes A. M., Gonzalez-Bonet G., Crane B. R. Structure and activity of the flagellar rotor protein FliY: A member of the CheC phosphatase family. JBC, PMID: 23532838, 1-18, 2013
  13. Madasu Y., Suarez C., Kast D. J., Kovar D. R., Dominguez R. Rickettsia Sca2 has evolved formin-like activity through a different molecular mechanism. PNAS USA, PMID: 23818602, PMCID: PMC3718132 110(29), E2677-86 doi: 10.1073/pnas.1307235110, 2013
  14. E. C. Minnihan, N. Ando, E. J. Brignole, L. Olshansky, J. Chittuluru, F. J. Asturias, C. L. Drennan, D. G. Nocera, and J. Stubbe. Generation of a stable, aminotyrosyl radical-induced α2β2 complex of Escherichia coli class Ia ribonucleotide reductase. PNAS, 110: 3835-3840, 2013
  15. Angela V. Toms, Anagha Deshpande, Randall McNally, Youngjee Jeong, Julia M. Rogers, Sol M. Gruner, Chae Un Kim, Scott B. Ficarro, Jarrod A. Marto, Martin Sattler, James D. Griffin, Michael J. Eck. Structure of a pseudokinase domain switch that controls activation of Jak kinases, Nature Structural & Molecular Biology, Adv. Online Pub., 2013
  16. Richardson B. C. and Fromme J. C. The Exomer Cargo Adaptor Features a Flexible Hinge Domain. Structure 21(3), 486-492, 2013
  17. Vinaik R., Kozlov G., Gehring K. Structure of the non-catalytic domain of the protein disulfide isomerase-related protein (PDIR) reveals function in protein binding. PLoS ONE 8, 2013
  18. Kozlov G., Vinaik R., and Gehring K. Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli. Acta Cryst. F69(5), 499-502, 2013
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2012

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2011

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