Argonne National Laboratory

GM/CA @ APS

Staff Publications

Department of Energy Office of Science
GM/CA @ APS Sponsors:
National Institute of General Medical Sciences (NIGMS) and National Cancer Institute (NCI) of the National Institutes of Health (NIH)
 
 

    2016

  1. "Dynamic X-ray diffraction sampling for protein crystal positioning",
    Scarborough, N. M., Godaliyadda, G. M., Ye, D. H., Kissick, D. J., Zhang, S., Newman, J. A., Sheedlo, M. J., Chowdhury, A. U., Fischetti, R. F., Das, C., Buzzard, G. T., Bouman, C. A., and Simpson, G. J.
    J Synchrotron Radiat (2016) 24, 188-195.
     
  2. "Extremum seeking x-ray position feedback using power line harmonic leakage as the perturbation",
    Zohar, S., Kissick, D. J., Venugopalan, N., Ogata, C. M., Makarov, O., Stepanov, S., and Fischetti, R. F.
    Phys. Rev. Spec. Top. Accel. Beams (2016) , 092801-092807.
     
  3. "Rotation of X-ray polarization in the glitches of a silicon crystal monochromator",
    Sutter, J. P., Boada, R., Bowron, D. T., Stepanov, S. A., and Diaz-Moreno, S.
    J Appl Crystallogr (2016) 49, 1209-1222.
     
  4. "Rapid in situ X-ray position stabilization via extremum seeking feedback",
    Zohar, S., Venugopalan, N., Kissick, D., Becker, M., Xu, S., Makarov, O., Stepanov, S., Ogata, C., Sanishvili, R., and Fischetti, R. F.
    J Synchrotron Radiat (2016) 23, 443-447.
     
  5. "Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging",
    Newman, J. A., Zhang, S., Sullivan, S. Z., Dow, X. Y., Becker, M., Sheedlo, M. J., Stepanov, S., Carlsen, M. S., Everly, R. M., Das, C., Fischetti, R. F., and Simpson, G. J.
    J Synchrotron Radiat (2016) 23, 959-965.
     
  6. "Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy",
    Mei, Y., Su, M., Sanishvili, R., Chakravarthy, S., Colbert, C. L., and Sinha, S. C.
    Biochemistry (2016) 55, 4239-4253.
     
  7. "Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy",
    Mei, Y., Ramanathan, A., Glover, K., Stanley, C., Sanishvili, R., Chakravarthy, S., Yang, Z., Colbert, C. L., and Sinha, S. C.
    Biochemistry (2016) 55, 1945-1958.
     
  8. "The impact of alterations in lignin deposition on cellulose organization of the plant cell wall",
    Liu, J., Kim, J. I., Cusumano, J. C., Chapple, C., Venugopalan, N., Fischetti, R. F., and Makowski, L.
    Biotechnol Biofuels (2016) 9, 126.
     
  9. "Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue",
    Liu, J., Costantino, I., Venugopalan, N., Fischetti, R. F., Hyman, B. T., Frosch, M. P., Gomez-Isla, T., and Makowski, L.
    Scientific reports (2016) 6, 33079.
     
  10. "Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation",
    Lechtenberg, B. C., Rajput, A., Sanishvili, R., Dobaczewska, M. K., Ware, C. F., Mace, P. D., and Riedl, S. J.
    Nature (2016) 529, 546-550.
     
  11. "Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O-demethylase crystals by the microseeding method",
    Harada, A., Sato, Y., Kamimura, N., Venugopalan, N., Masai, E., and Senda, T.
    Acta crystallographica. Section F, Structural biology communications (2016) 72, 897-902.
     
  12. "A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals",
    Broecker, J., Klingel, V., Ou, W. L., Balo, A. R., Kissick, D. J., Ogata, C. M., Kuo, A. L., and Ernst, O. P.
    Crystal Growth & Design (2016) 16, 6318-6326.
     
  13. 2015

  14. "Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography",
    Nichols, D. A., Hargis, J. C., Sanishvili, R., Jaishankar, P., Defrees, K., Smith, E. W., Wang, K. K., Prati, F., Renslo, A. R., Woodcock, H. L., and Chen, Y.
    Am Chem Soc (2015) 137, 8086-8095.
     
  15. "A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions",
    Murray, T. D., Lyubimov, A. Y., Ogata, C. M., Vo, H., Uervirojnangkoorn, M., Brunger, A. T., and Berger, J. M.
    Acta Crystallogr D Biol Crystallogr (2015) 71, 1987-1997.
     
  16. "Mechanism of Inactivation of gamma-Aminobutyric Acid Aminotransferase by (1S,3S)-3-Amino-4-difluoromethylene-1-cyclopentanoic Acid (CPP-115)",
    Lee, H., Doud, E. H., Wu, R., Sanishvili, R., Juncosa, J. I., Liu, D., Kelleher, N. L., and Silverman, R. B.,
    J Am Chem Soc (2015) 137, 2628-2640.
     
  17. "Design and Mechanism of Tetrahydrothiophene-Based gamma-Aminobutyric Acid Aminotransferase Inactivators",
    Le, H. V., Hawker, D. D., Wu, R., Doud, E., Widom, J., Sanishvili, R., Liu, D., Kelleher, N. L., and Silverman, R. B.,
    J Am Chem Soc (2015) 137, 4525-4533.
     
  18. "Imaging local electric fields produced upon synchrotron X-ray exposure",
    Dettmar, C. M., Newman, J. A., Toth, S. J., Becker, M., Fischetti, R. F., and Simpson, G. J.,
    Proc Natl Acad Sci USA (2015) 112, 696-701.
     
  19. 2014

  20. "Targeting gamma-Herpesvirus 68 Bcl-2-mediated Down-regulation of Autophagy",
    Su, M., Mei, Y., Sanishvili, R., Levine, B., Colbert, C. L., and Sinha, S.,
    J Biol Chem (2014) 289, 8029-8040.
     
  21. "Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in beamline control system",
    Pothineni, S. B., Venugopalan, N., Ogata, C. M., Hilgart, M. C., Stepanov, S., Sanishvili, R., Becker, M., Winter, G., Sauter, N. K., Smith, J. L., and Fischetti, R. F.,
    J Appl Crystallogr (2014) 47, 1992-1999.
     
  22. "Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2",
    Poor, C. B., Wegner, S. V., Li, H., Dlouhy, A. C., Schuermann, J. P., Sanishvili, R., Hinshaw, J. R., Riggs-Gelasco, P. J., Outten, C. E., and He, C.,
    Proc Natl Acad Sci USA (2014) 111, 4043-4048.
     
  23. "The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile",
    Martinez, S., Wu, R., Sanishvili, R., Liu, D., and Holz, R.,
    J Am Chem Soc (2014) 136, 1186-1189.
     
  24. "Multiscale deconstruction of molecular architecture in corn stover",
    Inouye, H., Zhang, Y., Yang, L., Venugopalan, N., Fischetti, R. F., Gleber, S. C., Vogt, S., Fowle, W., Makowski, B., Tucker, M., Ciesielski, P., Donohoe, B., Matthews, J., Himmel, M. E., and Makowski, L.,
    Scientific reports (2014) 4, 3756.
     
  25. "Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1",
    Akey, D. L., Brown, W. C., Konwerski, J. R., Ogata, C. M., and Smith, J. L.,
    Acta Crystallogr D Biol Crystallogr (2014) 70, 2719-2729.
     
  26. "Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system",
    Akey, D. L., Brown, W. C., Dutta, S., Konwerski, J., Jose, J., Jurkiw, T. J., DelProposto, J., Ogata, C. M., Skiniotis, G., Kuhn, R. J., and Smith, J. L.,
    Science (2014) 343, 881-885.
     
  27. 2013

  28. "Performance of the compact visual beam imaging system on the GM/CA BM beamline at the APS",
    Xu S., Ogata C., Makarov O., Corcoran S., Ferguson D., and Fischetti R.F.,
    J. Phys.: Conf. Ser. (2013) 425, 012016.
     
  29. "JBluIce-EPICS: a fast and flexible open-source beamline control system for macromolecular crystallography",
    Stepanov S.A., Hilgart M., Makarov O., Pothineni S.B., Yoder D., Ogata C., Sanishvili R., Venugopalan N., Smith J.L., and Fischetti R.F.,
    J. Phys.: Conf. Ser. (2013) 425, 012019.
     
  30. "Cybersecurity, massive data processing, community interaction, and other developments at WWW-based computational X-ray Server",
    Stepanov S.A.,
    J. Phys.: Conf. Ser. (2013) 425, 162006.
     
  31. "Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline",
    Madden J.T., Toth S.J., Dettmar C.M., Newman J.A., Oglesbee R.A., Hedderich H.G., Everly R.M., Becker M., Ronau J.A., Buchanan S.K., Cherezov V., Morrow M.E., Xu S., Ferguson D., Makarov O., Das C., Fischetti R., and Simpson G.J.,
    J Synchrotron Radiat (2013) 20, 531-540.
     
  32. "Tissue specific specialization of the nanoscale architecture of Arabidopsis",
    Liu, J., Inouye, H., Venugopalan, N., Fischetti, R. F., Gleber, S. C., Vogt, S., Cusumano, J. C., Kim, J. I., Chapple, C., and Makowski, L.,
    J Struct Biol (2013) 184, 103-114.
  33. "Towards protein-crystal centering using second-harmonic generation (SHG) microscopy",
    Kissick D.J., Dettmar C.M., Becker M., Mulichak A.M., Cherezov V., Ginell S.L., Battaile K.P., Keefe L.J., Fischetti R.F., and Simpson G.J.,
    Acta Crystallogr. D Biol. Crystallogr. (2013) 69, 843-851.
     
  34. "Predicted optical performance of the GM/CA@APS micro-focus beamline",
    Fischetti R.F., Yoder D., Xu S., Makarov O., Ogata C., and Smith J.L.,
    J. Phys.: Conf. Ser. (2013) 425, 012006.
     
  35. 2012

  36. "Exploration of synchrotron Mössbauer microscopy with micrometer resolution: forward and a new backscattering modality on natural samples",
    Yan L., Zhao J., Toellner T.S., Divan R., Xu S., Cai Z., Boesenberg J.S., Friedrich J.M., Cramer S.P., and Alp E.E.,
    J. Synchrotron Radiat. (2012) 19, 814-820.
     
  37. "Direct observation of dynamics of thermal expansion using pump-probe high-energy-resolution x-ray diffraction",
    Stoupin S., March A.M., Wen H., Walko D.A., Li Y., Dufresne E.M., Stepanov S.A., Kim K.-J., Shvyd’ko Yu.V., Blank V.D., and Terentyev S.A.,
    Phys. Rev. B (2012) 86, 054301(5).
     
  38. "Micro-crystallography comes of age",
    Smith J.L., Fischetti R.F., and Yamamoto M.,
    Curr. Opin. Struct. Biol. (2012) 22, 602-612.
     
  39. "Multi-wavelength anomalous diffraction using medium-angle X-ray solution scattering (MADMAX)",
    Makowski L., Bardhan J., Gore D., Rodi D.J., and Fischetti R.F.,
    Biophys J. (2012) 102, 927-933.
     
  40. "Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA",
    Hayashi T., Senda M., Morohashi H., Higashi H., Horio M., Kashiba Y., Nagase L., Sasaya D., Shimizu T., Venugopalan N., Kumeta H., Noda N. N., Inagaki F., Senda T., and Hatakeyama, M.,
    Cell Host & Microbe (2012) 12, 20-33.
     
  41. 2011

  42. "PID feedback control of monochromator thermal stabilization",
    Yoder D.W., Makarov O., Corcoran S., and Fischetti R.F.,
    Nucl. Instum. Meth. Phys. Res. A (2011) 649, 107-108.
     
  43. "Mini-beam collimator applications at the Advanced Photon Source",
    Xu S., Keefe L.J., Mulichak A., Yan L., Alp E.E., Zhao J., and Fischetti R.F.,
    Nucl. Instum. Meth. Phys. Res. A (2011) 649, 104-106.
     
  44. "Alignment Protocol for Effective use of Hard X-ray Quad collimator for micro-crystallography",
    Xu S., Nagarajan V., Sanishvili R., and Fischetti R.F.,
    Proc. SPIE (2011) 8125, 81250X1-81250X8.
     
  45. "Simulation and optimization of a sub-micron beam for macromolecular crystallography using SHADOW and XOP at GM/CA CAT at the APS",
    Liu Z., Xu S., Yoder D., and Fischetti R.F.,
    Proc. SPIE (2011) 8129, 81290E1-81290E8.
     
  46. "Crystal Structure of a Zinc-dependent D-Serine Dehydratase from Chicken Kidney",
    Tanaka H., Senda M., Venugopalan N., Yamamoto A., Senda T., Ishida T., and Horiike K.,
    J. Biol. Chem. (2011) 286, 27548-27558.
     
  47. "Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals",
    Hilgart M.C., Sanishvili R., Ogata C.M., Becker M., Venugopalan N., Stepanov S., Makarov O., Smith J.L., and Fischetti R.F.,
    J. Synchrotron Radiat. (2011) 18, 717-722.
     
  48. "Fast fluorescence techniques for crystallography beamlines",
    Stepanov S., Hilgart M., Yoder D.W., Makarov O., Becker M., Sanishvili R., Ogata C.M., Venugopalan N., Aragão D., Caffrey M., Smith J.L., and Fischetti R.F.,
    J. Appl. Crystallogr. (2011) 44, 772-778.
     
  49. "Control system for the 2nd generation Berkeley automounters (BAM2) at GM/CA-CAT macromolecular crystallography beamlines",
    Makarov O., Hilgart M., Ogata C., Pothineni S., and Cork C.,
    Nucl Instrum. & Methods Phys. Res. A (2011) 649, 87-90.
     
  50. "Radiation damage in protein crystals is reduced with a micron-sized X-ray beam",
    Sanishvili R., Yoder D.W., Pothineni S.B., Rosenbaum G., Xu S., Vogt S., Stepanov S., Makarov O.A., Corcoran S., Benn R., Nagarajan V., Smith J.L., and Fischetti R.F.,
    Proc. Natl. Acad. Sci. USA. (2011) 108, 6127-6132.
     
  51. "JBluIce-EPICS control system for macromolecular crystallography",
    Stepanov S., Makarov O., Hilgart M., Pothineni S.B., Urakhchin A., Devarapalli S, Yoder D, Becker M, Ogata C, Sanishvili R, Venugopalan N., Smith J.L., and Fischetti R.F.,
    Acta Crystallogr. D Biol. Crystallogr. (2011) 67, 176-188.
     
  52. "Structure, signaling mechanism and regulation of the natriuretic peptide receptor guanylate cyclase",
    Misono K.S., Philo J.S., Arakawa T., Ogata C.M., Qiu Y., Ogawa H., and Young H.S.,
    FEBS J. (2011) 278, 1818-1829.
     
  53. "X-Ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles",
    Makowski L., Gore D., Mandava S., Minh D., Park S., Rodi D.J., and Fischetti R.F.,
    Biopolymers (2011) 95, 531-542.
     
  54. "WAXS studies of the structural diversity of hemoglobin in solution",
    Makowski L., Bardhan J., Gore D., Lal J., Mandava S., Park S., Rodi D.J., Ho N.T., Ho C., and Fischetti R.F.,
    J. Mol. Biol. (2011) 408, 909-921.
     
  55. 2010

  56. "Design and manufacture of mini-beam collimators for macromolecular crystallography at the GM/CA-CAT at APS",
    Xu S., Nagarajan V., and Fischetti R.F.,
    Diamond Light Source Proc. (2010) 1, 1-4.
     
  57. "One-Micron Beams for Macromolecular Crystallography at GM/CA-CAT",
    Yoder D.W., Sanishvili R., Vogt S., Xu S., Makarov O., Benn R., Corcoran S., and Fischetti, R.F.,
    AIP Conf. Proc. (2010) 1234, 419-422.
     
  58. "Micro-Crystallography Developments at GM/CA-CAT at the APS",
    Xu S., Makarov O., Benn R., Yoder D.W., Stepanov S., Becker M., Corcoran S., Hilgart M., Nagarajan V., Ogata C.M., Pothineni S., Sanishvili R., Smith J.L., and Fischetti R.F.,
    AIP Conf. Proc. (2010) 1234, 905-908.
     
  59. "In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex",
    Jensen L.M., Sanishvili R., Davidson V.L., and Wilmot C.M.,
    Science (2010) 327, 1392-1394.
     
  60. "Characterization of the secondary binding sites of Maclura pomifera agglutinin by glycan array and crystallographic analyses",
    Huang J., Xu Z., Wang D., Ogata C.M., Palczewski K., Lee X., and Young N.M.,
    Glycobiology (2010) 20, 1643-1653.
     
  61. 2009

  62. "Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 μm size X-ray synchrotron beam",
    Cherezov V., Hanson M.A., Griffith M.T., Hilgart M.C., Sanishvili R., Nagarajan V., Stepanov S., Fischetti R.F., Kuhn P., and Stevens R.C.,
    J. Royal Soc. Interface (2009) 6, S587-S597.
     
  63. "Mini-beam collimator enables microcrystallography experiments on standard beamlines",
    Fischetti R.F., Xu S., Yoder D.W., Becker M., Nagarajan V., Sanishvili R., Hilgart M.C., Stepanov S., Makarov O., and Smith J.L.,
    J. Synchrotron Radiat. (2009) 16, 217-225.
     
  64. "Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli",
    Brown G., Singer A., Lunin V.V., Proudfoot M., Skarina T., Flick R., Kochinyan S., Sanishvili R., Joachimiak A., Edwards A.M., Savchenko A., and Yakunin, A.F.,
    J. Biol. Chem. (2009) 284, 3784-3792.
     
  65. 2008

  66. "A 7μm mini-beam improves diffraction data from small or imperfect crystals of macromolecules",
    Sanishvili R., Nagarajan V., Yoder D., Becker M., Xu S., Corcoran S., Akey D.L., Smith J.L., and Fischetti R.F.,
    Acta Crystallogr D Biol. Crystallogr. (2008) 64, 425-435.
     
  67. "Characterization of protein fold by wide-angle X-ray solution scattering",
    Makowski L., Rodi D.J., Mandava S., Devarapalli S., and Fischetti R.F.,
    J. Mol. Biol. (2008 383, 731-744.
     
  68. "Fitting dynamical X-ray diffraction data over the World Wide Web",
    Stepanov S. and Forrest R.,
    J. Appl. Crystallogr., (2008) 41 958-962.
     
  69. "Automated X-ray Focusing Using Kirkpatrick-Baez Bimorph Mirrors",
    Yoder D.W., Stepanov S., Signorato R. and Fischetti R.F.,
    MEDSI/Pan American SRI 2008 Meeting Proceeding (2008).
    Note: this manuscript was peer reviewed and accepted, but the plans to publish the Proceeding were not realized.
    You can read the paper
    here.

     
  70. 2007

  71. "EPICS controlled sample mounting robots at the GM/CA CAT",
    Makarov O.A., Benn R., Corcoran S., Devarapalli S., Fischetti R., Hilgart M., Smith W.W., Stepanov S., and Xu S.,
    Nucl Instrum. & Methods Phys. Res. A (2007) 582, 156-158.
     
  72. "Optical Performance of the GM/CA-CAT canted undulator beamlines for protein crystallography",
    Fischetti R.F., Yoder D.W., Xu S., Stepanov S., Makarov O., Benn R., Corcoran S., Diete W., Schwoerer-Boehing M., Signorato R., Schroeder L., Berman L., Viccaro P.J., and Smith J.L.,
    AIP Conf. Proc. (2007) 879, 754-757.
     
  73. "Design and performance of the compact YAG imaging system for diagnostics at GMCA beamlines at APS",
    Xu S.L., Fischetti R.F., Benn R., and Corcoran S.,
    AIP Conf. Proc. (2007) 879, 1403-1406.
     
  74. "Design and performance of a compact collimator on GM/CA-CAT at the Advanced Photon Source",
    Xu S. and Fischetti R.F.,
    Proc. SPIE (2007) 6665, 66650X1-66650X8.
     
  75. "Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli",
    Savchenko A., Proudfoot M., Skarina T., Singer A., Litvinova O., Sanishvili R., Brown G., Chirgadze N., and Yakunin A.F.,
    J. Mol. Biol. (2007) 374, 1091-1103.
     
  76. "Crystal structure of the human beta2 adrenergic G-protein-coupled receptor",
    Rasmussen S.G., Choi H.J., Rosenbaum D.M., Kobilka T.S., Thian F.S., Edwards P.C., Burghammer M., Ratnala V.R., Sanishvili R., Fischetti R.F., Schertler G.F., Weis W.I., and Kobilka B.K.,
    Nature (2007) 450, 383-387.
     
  77. "Transformation of X-ray Server from a set of WWW-accessed programs into WWW-based library for remote calls from X-ray data analysis software",
    Stepanov S.,
    Thin Solid films (2007) 515, 5700-5703.
     
  78. 2006

  79. "A new approach to wide-angle dynamical X-ray diffraction by deformed crystals",
    Podorov S., Faleev N., Pavlov K., Paganin D., Stepanov S., and Foerster E.,
    J. Appl. Crystallogr., (2006) 39,652-655.
     
  80. 2004

  81. "A ray-tracing study of the dependence of focal properties on surface figure error for a Kirkpatrick-Baez (K-B) mirror system",
    Xu S. and Fischetti R.F.,
    Synchrotron Radiation Instrumentation (2004) 705, 776-779.
     
  82. "X-ray server: an online resource for simulations of X-ray diffraction and scattering",
    Stepanov S.,
    Proc. SPIE (2004) 5536, 16-26.
     
  83. "How to make X-ray simulation software working of WWW: A simple recipe based on seven years of experience",
    Stepanov S.,
    Proc. SPIE (2004) 5536, 165-170.
     

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