Zbyszek Otwinowski

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc Diffraction data analysis in the presence of radiation damage
    Dominika Borek
    University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Acta Crystallogr D Biol Crystallogr 66:426-36. 2010
  2. ncbi request reprint Multiparametric scaling of diffraction intensities
    Zbyszek Otwinowski
    Department of Biochemistry, University of Texas, Southwestern Medical Center at Dallas, TX 75390 9038, USA
    Acta Crystallogr A 59:228-34. 2003
  3. pmc Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins
    Daisy W Leung
    Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:689-92. 2010
  4. pmc Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates
    Pavlina Rezacova
    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Mol Microbiol 69:895-910. 2008
  5. pmc The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assembly
    Pavlina Rezacova
    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390 8816, USA
    Proteins 69:679-82. 2007
  6. pmc WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes
    Da Jia
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 107:10442-7. 2010
  7. ncbi request reprint The many faces of radiation-induced changes
    Dominika Borek
    Department of Biochemistry, University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    J Synchrotron Radiat 14:24-33. 2007
  8. pmc Structure of the human cohesin inhibitor Wapl
    Zhuqing Ouyang
    Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 110:11355-60. 2013
  9. pmc Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor
    Mischa Machius
    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Mol Biol 373:681-94. 2007
  10. ncbi request reprint The crystallographic fast Fourier transform. III. Centred lattices
    Małgorzata Rowicka
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 59:183-92. 2003

Research Grants

  1. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2009
  2. Ab Initio Phasing of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2007
  3. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2006
  4. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2005
  5. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2003
  6. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2003
  7. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2010
  8. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 1999
  9. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 1999
  10. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2000

Collaborators

Detail Information

Publications28

  1. pmc Diffraction data analysis in the presence of radiation damage
    Dominika Borek
    University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Acta Crystallogr D Biol Crystallogr 66:426-36. 2010
    ....
  2. ncbi request reprint Multiparametric scaling of diffraction intensities
    Zbyszek Otwinowski
    Department of Biochemistry, University of Texas, Southwestern Medical Center at Dallas, TX 75390 9038, USA
    Acta Crystallogr A 59:228-34. 2003
    ..This scaling model can be extended to include additional corrections for various instrumental and data-collection problems...
  3. pmc Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins
    Daisy W Leung
    Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:689-92. 2010
    ..Diffraction data were collected using synchrotron sources at the Advanced Light Source and the Advanced Photon Source...
  4. pmc Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates
    Pavlina Rezacova
    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Mol Microbiol 69:895-910. 2008
    ..Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion...
  5. pmc The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assembly
    Pavlina Rezacova
    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390 8816, USA
    Proteins 69:679-82. 2007
  6. pmc WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes
    Da Jia
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 107:10442-7. 2010
    ..Strumpellin is mutated in the human disease hereditary spastic paraplegia, and its link to WASH suggests that misregulation of actin dynamics on endosomes may play a role in this disorder...
  7. ncbi request reprint The many faces of radiation-induced changes
    Dominika Borek
    Department of Biochemistry, University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    J Synchrotron Radiat 14:24-33. 2007
    ..The influence of temperature and crystal composition on different characteristics of radiation damage is analyzed. The observed effects are discussed in terms of their impact on data processing and phasing procedures...
  8. pmc Structure of the human cohesin inhibitor Wapl
    Zhuqing Ouyang
    Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 110:11355-60. 2013
    ..Thus, Wapl-N forms extensive interactions with Pds5 and Scc1-SA2. Wapl-C interacts with other cohesin subunits and possibly unknown effectors to trigger cohesin release from chromatin. ..
  9. pmc Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor
    Mischa Machius
    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Mol Biol 373:681-94. 2007
    ..pallidum. We thus rename Tp0655 as TpPotD. The ramifications of TpPotD as a polyamine-binding protein to the parasitic strategy of T. pallidum are discussed...
  10. ncbi request reprint The crystallographic fast Fourier transform. III. Centred lattices
    Małgorzata Rowicka
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 59:183-92. 2003
    ..The requirements on the grid size and how they interact with the choice of algorithms are also discussed in detail...
  11. ncbi request reprint The crystallographic fast Fourier transform. Recursive symmetry reduction
    Andrzej Kudlicki
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 8816, USA
    Acta Crystallogr A 63:465-80. 2007
    ..The maximally efficient FFT for such grids has been described in previous papers by the same authors. The interaction between the grid size factorization and the symmetry operators and its influence on the algorithm design are discussed...
  12. ncbi request reprint The crystallographic fast Fourier transform. II. One-step symmetry reduction
    Małgorzata Rowicka
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 59:172-82. 2003
    ..Acta Cryst A59, 183-192; Rowicka, Kudlicki & Otwinowski (2003), in preparation], where more complicated groups will be considered...
  13. ncbi request reprint Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase
    Maojun Yang
    Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Mol Cell 23:377-87. 2006
    ..This spatially separated, multivalent nucleosome binding mode may apply to other chromatin-modifying enzymes that generally contain multiple nucleosome binding modules...
  14. pmc Secondary structure of Huntingtin amino-terminal region
    Mee Whi Kim
    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
    Structure 17:1205-12. 2009
    ..We further propose that the pathogenic polyQ expansion in the Htt protein increases the length of the random coil, which promotes aggregation and facilitates abnormal interactions with other proteins in cells...
  15. pmc Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus
    Pavlina Rezacova
    Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390 8816, USA
    Proteins 70:311-9. 2008
    ..65 A and reveals the role of conserved acidic residues in Mg2+ ion coordination. The structural similarities to other Toprim domain containing proteins and potential function and substrates of APC35832 are discussed in this article...
  16. ncbi request reprint Measurement errors and their consequences in protein crystallography
    Dominika Borek
    Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Acta Crystallogr D Biol Crystallogr 59:2031-8. 2003
    ..The sources and types of experimental errors are described and methods of minimizing their impact are discussed. Practical calculations of sigma estimates in DENZO and SCALEPACK are presented...
  17. pmc Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35
    Daisy W Leung
    Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
    Nat Struct Mol Biol 17:165-72. 2010
    ..These results suggest that simultaneous recognition of dsRNA backbone and blunt ends provides a mechanism by which Ebola VP35 antagonizes host dsRNA sensors and immune responses...
  18. pmc High-resolution timing of cell cycle-regulated gene expression
    Maga Rowicka
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 104:16892-7. 2007
    ..Our results reveal distinct subphases of the cell cycle undetectable by morphological observation, as well as the precise timeline of macromolecular complex assembly during key cell cycle events...
  19. ncbi request reprint Coordinate transformations in modern crystallographic computing
    Malgorzata Rowicka
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 60:542-9. 2004
    ..A review of 4 x 4-matrix notation and of tensor formalism focused on crystallographic applications is presented. A discussion of examples shows how this notation simplifies tasks encountered in crystallographic computing...
  20. pmc Identification of patterns in diffraction intensities affected by radiation exposure
    Dominika Borek
    Department of Biophysics, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    J Synchrotron Radiat 20:37-48. 2013
    ..This model is typically sufficient to explain radiation-induced effects observed in diffraction intensities. This analysis will guide the parameterization of the model, enabling its use in subsequent crystallographic calculations...
  21. pmc Structure and control of the actin regulatory WAVE complex
    Zhucheng Chen
    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
    Nature 468:533-8. 2010
    ..The spatial proximity of the Rac binding site and the large basic surface of the WRC suggests how the GTPase and phospholipids could cooperatively recruit the complex to membranes...
  22. ncbi request reprint The crystallographic fast Fourier transform. IV. FFT-asymmetric units in the reciprocal space
    Andrzej Kudlicki
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 60:146-52. 2004
    ..Modifications needed to adapt the results to data with Hermitian symmetry will be described in our forthcoming article [Kudlicki, Rowicka & Otwinowski (2004), in preparation]...
  23. ncbi request reprint SCEPTRANS: an online tool for analyzing periodic transcription in yeast
    Andrzej Kudlicki
    University of Texas Southwestern Medical Center, Department of Biochemistry, Dallas, TX 75390 8816, USA
    Bioinformatics 23:1559-61. 2007
    ..AVAILABILITY: Available online at http://sceptrans.org/..
  24. ncbi request reprint The crystallographic fast Fourier transform. I. p3 symmetry
    Małgorzata Rowicka
    Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Acta Crystallogr A 58:574-9. 2002
    ..The algorithm has been tested and benchmarked against FFT on the unit cell, revealing the expected increase in speed. This is a non-trivial example of a more general approach developed recently by the authors...
  25. ncbi request reprint The structural genomics experimental pipeline: insights from global target lists
    Nicholas O'Toole
    Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
    Proteins 56:201-10. 2004
    ....
  26. pmc From nonpeptide toward noncarbon protease inhibitors: metallacarboranes as specific and potent inhibitors of HIV protease
    Petr Cigler
    Institutes of Organic Chemistry and Biochemistry and Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
    Proc Natl Acad Sci U S A 102:15394-9. 2005
    ..This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition...
  27. pmc Expression, purification and X-ray crystallographic analysis of thioredoxin from Streptomyces coelicolor
    Petra Stefankova
    Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH 1, 842 15 Bratislava, Slovak Republic
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:164-8. 2005
    ..The protein reveals a thioredoxin-like fold with a typical CXXC active site. The crystal exhibits the symmetry of space group P2(1)2(1)2, with unit-cell parameters a = 43.6, b = 71.8, c = 33.2 A...
  28. ncbi request reprint HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes
    Wladek Minor
    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
    Acta Crystallogr D Biol Crystallogr 62:859-66. 2006
    ..The current development is oriented towards very fast structure solution in order to provide feedback during the diffraction experiment. Work is also proceeding towards improving the quality of phasing calculation and model building...

Research Grants18

  1. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2009
    ..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..
  2. Ab Initio Phasing of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2007
    ..In terms of understanding the molecular biology, the highest expected impact is in structure determination of complex molecular assemblies. ..
  3. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2006
    ..The research and its implementation will increase the accuracy and reliability of 3-dimensional macromolecular structures, and will streamline the structure determination process. ..
  4. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2005
    ..The research and its implementation will increase the accuracy and reliability of 3-dimensional macromolecular structures, and will streamline the structure determination process. ..
  5. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2003
    ..The research and its implementation will increase the accuracy and reliability of 3-dimensional macromolecular structures, and will streamline the structure determination process. ..
  6. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2003
    ..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..
  7. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2010
    ..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..
  8. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 1999
    ..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..
  9. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 1999
    ....
  10. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2000
    ..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..
  11. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2004
    ..The research and its implementation will increase the accuracy and reliability of 3-dimensional macromolecular structures, and will streamline the structure determination process. ..
  12. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2001
    ..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..
  13. The Crystallography of Macromolecules
    Zbyszek Otwinowski; Fiscal Year: 2007
    ..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..
  14. X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES
    Zbyszek Otwinowski; Fiscal Year: 2002
    ..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..