Research Topics
Genomes and Genes | Zbyszek OtwinowskiSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Publications
Multiparametric scaling of diffraction intensitiesZbyszek 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...
Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteinsDaisy 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...- 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 intermediatesPavlina 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... - WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexesDa 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... - The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assemblyPavlina Rezacova
Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390 8816, USA
Proteins 69:679-82. 2007 - The crystallographic fast Fourier transform. III. Centred latticesMałgorzata 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... - The crystallographic fast Fourier transform. II. One-step symmetry reductionMałgorzata 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... - The crystallographic fast Fourier transform. Recursive symmetry reductionAndrzej 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... - High-resolution timing of cell cycle-regulated gene expressionMaga 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... - The many faces of radiation-induced changesDominika 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... - Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35Daisy 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... - Coordinate transformations in modern crystallographic computingMalgorzata 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... - Measurement errors and their consequences in protein crystallographyDominika 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... - Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilusPavlina 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... - SCEPTRANS: an online tool for analyzing periodic transcription in yeastAndrzej 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/.. - Structure and control of the actin regulatory WAVE complexZhucheng 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... - The crystallographic fast Fourier transform. IV. FFT-asymmetric units in the reciprocal spaceAndrzej 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]... - Secondary structure of Huntingtin amino-terminal regionMee 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... - The crystallographic fast Fourier transform. I. p3 symmetryMałgorzata 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... - Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptorMischa 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... - HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutesWladek 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... - From nonpeptide toward noncarbon protease inhibitors: metallacarboranes as specific and potent inhibitors of HIV proteasePetr 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... - The structural genomics experimental pipeline: insights from global target listsMarek Grabowski
Department of Biochemistry, McGill University, , , Canada
Proteins 56:201-10. 2004.... - Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylaseMaojun 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... - Expression, purification and X-ray crystallographic analysis of thioredoxin from Streptomyces coelicolorPetra 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...
Research Grants
- The Crystallography of MacromoleculesZbyszek Otwinowski; Fiscal Year: 2009..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..
- The Crystallography of MacromoleculesZbyszek Otwinowski; Fiscal Year: 2007..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..
- Ab Initio Phasing of MacromoleculesZbyszek Otwinowski; Fiscal Year: 2007..In terms of understanding the molecular biology, the highest expected impact is in structure determination of complex molecular assemblies. ..
- The Crystallography of MacromoleculesZbyszek 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. ..
- X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESZbyszek Otwinowski; Fiscal Year: 2003..The third area for development will be in standardizing optimal data collection strategies and data archiving. ..
- X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESZbyszek Otwinowski; Fiscal Year: 1999....
- The Crystallography of MacromoleculesZbyszek Otwinowski; Fiscal Year: 2010..The developed algorithms and methods will be implemented in the HKL2000 suite, widely used by the crystallographic community. ..