Research Topics
Species | Zygmunt DerewendaSummaryAffiliation: University of Virginia Country: USA Publications
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Publications
On wine, chirality and crystallographyZygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908 0736, USA
Acta Crystallogr A 64:246-58. 2008..But one central inanimate character was there at all times - an inconspicuous somewhat obscure organic compound found in wine: tartaric acid. This is the story of its contribution to science...
On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEFMeiying Zheng
Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 800736, Charlottesville, Virginia, 22908 0736, USA
BMC Struct Biol 9:36. 2009..These GEFs include p115, LARG and PDZRhoGEF (PRG)...- PAF-acetylhydrolasesZ S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia, P O Box 10011, Charlottesville, VA 22906 0011, USA
Biochim Biophys Acta 1441:229-36. 1999..Recent crystallographic studies shed new light on the complex structure-function relationships in PAF-AHs... - Advances in Protein Crystallography - fourth annual meetingZygmunt Derewenda
University of Virginia School of Medicine, Department of Molecular Physiology and Biological Physics, PO Box 800736, Charlottesville, VA 22908-0836, USA
IDrugs 10:256-8. 2007 - The use of recombinant methods and molecular engineering in protein crystallizationZygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
Methods 34:354-63. 2004..This review discusses recent advances in the field and describes a number of examples of diverse protein engineering techniques used in crystallographic investigations... - Rational protein crystallization by mutational surface engineeringZygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
Structure 12:529-35. 2004..Several recent examples of this new methodology suggest that the method has the potential to become a routine tool in protein crystallography... - Entropy and surface engineering in protein crystallizationZygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 229008 0736, USA
Acta Crystallogr D Biol Crystallogr 62:116-24. 2006.... - It's all in the crystals…Zygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908 0793, USA
Acta Crystallogr D Biol Crystallogr 67:243-8. 2011..Here, one such established strategy, surface-entropy reduction (SER), is discussed, including its successes, limitations and possible future developments... - Application of protein engineering to enhance crystallizability and improve crystal propertiesZygmunt S Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 66:604-15. 2010..This article presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application... - The impact of Lys-->Arg surface mutations on the crystallization of the globular domain of RhoGDIJan Czepas
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
Acta Crystallogr D Biol Crystallogr 60:275-80. 2004..0 A the resolution of the diffraction of the wild-type crystal. Major crystal contacts in the new lattice were created by the mutated epitope... - The role of entropy and polarity in intermolecular contacts in protein crystalsMarcin Cieslik
Department of Molecular Physiology and Biological Physics and the PSI2 Integrated Center for Structure Function Innovation, University of Virginia, Charlottesville, VA 22908, USA
Acta Crystallogr D Biol Crystallogr 65:500-9. 2009..It is also shown that crystal contacts with larger buried surfaces containing eight or more amino acids have cores that are depleted of polar amino acids... - Structure of the Bacillus subtilis OhrB hydroperoxide-resistance protein in a fully oxidized stateDavid R Cooper
Department of Molecular Physiology and Biological Physics, University of Virginia and the PSI2 Integrated Center for Structure Function Innovation Charlottesville, Virginia 22908, USA
Acta Crystallogr D Biol Crystallogr 63:1269-73. 2007..However, the stereochemistry of the disulfides is unorthodox and strained, suggesting that they are sensitive to reducing agents. A deep solvent-accessible gorge reaching Cys55 may represent the access route for the reductant... - The impact of Glu-->Ala and Glu-->Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 A resolutionAgnieszka Mateja
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
Acta Crystallogr D Biol Crystallogr 58:1983-91. 2002.... - Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolutionIzabela Janda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 60:1101-7. 2004..8 angstroms resolution. The protein is a canonical alpha/beta hydrolase, with an active site that is accessible to solvent... - Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domainsMeiying Zheng
Department of Molecular Physiology and Biological Physics, Integrated Center for Structure Function Innovation, University of Virginia, Charlottesville, VA 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 65:356-65. 2009..Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors... - Structure of a constitutively activated RhoA mutant (Q63L) at 1.55 A resolutionKenton Longenecker
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Acta Crystallogr D Biol Crystallogr 59:876-80. 2003..The data support the notion that differences observed between the mutants in vivo are likely to arise from altered affinities for RhoGDI and not from direct structural differences... - Preliminary crystallographic analysis of the complex of the human GTPase RhoA with the DH/PH tandem of PDZ-RhoGEFArkadiusz Oleksy
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
Acta Crystallogr D Biol Crystallogr 60:740-2. 2004..The nucleotide-free DH/PH-RhoA complex was purified by gel filtration and crystallized. The crystals belong to space group P2(1), with unit-cell parameters a = 88.6, b = 119.0, c = 91.5 A, beta = 114.7 degrees... - The binding of the PDZ tandem of syntenin to target proteinsJolanta Grembecka
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736, USA
Biochemistry 45:3674-83. 2006.... - The structure of the FERM domain of merlin, the neurofibromatosis type 2 gene productBeom Sik Kang
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 58:381-91. 2002..The structure allows a better rationalization of the impact of selected disease-causing mutations on the integrity of the protein... - The crystal structure of RhoA in complex with the DH/PH fragment of PDZRhoGEF, an activator of the Ca(2+) sensitization pathway in smooth muscleUrszula Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Structure 12:1955-65. 2004..The DH domain makes several specific interactions with RhoA residues not conserved among other Rho family members, suggesting the molecular basis for the observed specificity... - The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanismIzabela Janda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Structure 12:1901-7. 2004..coli protein, although there is no domain swapping. The Zn2+ binding domain is clearly resolved showing the details of the tetrahedral coordination of Zn2+ by four thiolates. We propose a structure-based activation pathway for Hsp33... - The DC-module of doublecortin: dynamics, domain boundaries, and functional implicationsTomasz Cierpicki
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908 0736, USA
Proteins 64:874-82. 2006.... - Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif Urszula Derewenda
Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908 0736, USA
Biochemistry 48:8664-71. 2009..Functional assays confirmed that the protein displays a level of isomerase activity that might be biologically significant. We propose a mechanism by which the members of this family catalyze isomerization using the CXC catalytic site... - Protein crystallization by surface entropy reduction: optimization of the SER strategyDavid R Cooper
Department of Molecular Physiology and Biological Physics and Integrated Center for Structure Function Innovation, University of Virginia, Charlottesville, Virginia 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 63:636-45. 2007..Taken together, these results suggest a powerful crystallization strategy that combines surface engineering with efficient screening using standard and alternate reservoir solutions... - The structure of the N-terminal domain of the product of the lissencephaly gene Lis1 and its functional implicationsMyung Hee Kim
Department of Molecular Physiology and Biological Physics and Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
Structure 12:987-98. 2004..The structure explains the molecular basis of a low severity form of lissencephaly... - The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallographyBeom Sik Kang
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 0736, USA
J Mol Biol 338:483-93. 2004..Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C-H...O type are clearly visible between the beta-strands. The study sets a new standard for high-resolution protein crystallography... - The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteinsYancho Devedjiev
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908 0736, USA
J Mol Biol 343:395-406. 2004..The atomic model of the complex was refined using data to 2.3 A resolution and revealed a unique H-bonding pattern that constitutes the molecular basis of specificity for the HMP moiety of thiamin... - The structure of the coiled-coil domain of Ndel1 and the basis of its interaction with Lis1, the causal protein of Miller-Dieker lissencephalyUrszula Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Structure 15:1467-81. 2007.... - PDZ tandem of human syntenin: crystal structure and functional propertiesBeom Sik Kang
Department of Molecular Physiology and Biological Physics and The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
Structure 11:459-68. 2003..The independent binding of merlin by PDZ1 and syndecan-4 by PDZ2 provides direct evidence for the coupling of syndecan-mediated signaling to actin regulation by merlin... - Probing the supramodular architecture of a multidomain protein: the structure of syntenin in solutionTomasz Cierpicki
Department of Molecular Physiology, and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
Structure 13:319-27. 2005.... - The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoATomasz Cierpicki
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, 22908, USA
Protein Sci 18:2067-79. 2009..The complex is readily and rapidly dissociated in the presence of both GDP and GTP nucleotides, with no evidence of intermediate ternary complexes... - The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamilyDavid R Cooper
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 66:219-24. 2010..The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms... - B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymesJakub Bielnicki
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908 0736, USA
Proteins 62:144-51. 2006..The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology... - Purification and crystallization of the N-terminal domain from the human doublecortin-like kinaseMyung Hee Kim
Department of Molecular Physiology and Biological Physics and The Cancer Center, University of Virginia, PO Box 800736, Charlottesville, Virginia 22908 0736, USA
Acta Crystallogr D Biol Crystallogr 59:502-5. 2003..33 A, beta = 101.3 degrees. Crystals of SeMet-substituted N-DCLK (Leu120Met) were also obtained, but they exhibit the symmetry of space group P2(1), with unit-cell parameters a = 38.81, b = 29.43, c = 40.1 A, beta = 115.7 degrees... - The DCX-domain tandems of doublecortin and doublecortin-like kinaseMyung Hee Kim
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908 0736, USA
Nat Struct Biol 10:324-33. 2003..In functional assays, the N-terminal DCX domain of doublecortin binds only to assembled microtubules, whereas the C-terminal domain binds to both microtubules and unpolymerized tubulin... - Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigmBeom Sik Kang
Department of Molecular Physiology and Biological Physics, The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
Structure 11:845-53. 2003..These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism... - The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plagueUrszula Derewenda
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Structure 12:301-6. 2004.... - Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD proteinT W Martin
Department of Molecular Physiology and Biological Physics, University of Virginia, Health Sciences System, Charlottesville 22908, USA
Structure 10:933-42. 2002..The location of the binding site is identical to the ones in evolutionarily related enzymes, suggesting that the protein may have been recruited from a different metabolic pathway... - Toward rational protein crystallization: A Web server for the design of crystallizable protein variantsLukasz Goldschmidt
Howard Hughes Medical Institute, University of California, Los Angeles DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
Protein Sci 16:1569-76. 2007..In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER... - Degenerate specificity of PDZ domains from RhoA-specific nucleotide exchange factors PDZRhoGEF and LARGKatarzyna Smietana
Faculty of Biotechnology, Laboratory of Protein Engineering, University of Wrocław, Wrocław, Poland
Acta Biochim Pol 55:269-80. 2008.... - Coupling PAF signaling to dynein regulation: structure of LIS1 in complex with PAF-acetylhydrolaseCataldo Tarricone
Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy
Neuron 44:809-21. 2004..Our data suggest that the LIS1 molecule undergoes major conformational rearrangement when switching from a complex with the acetylhydrolase to the one with Ndel1... - Bivalent peptides as models for multimeric targets of PDZ domainsMarcin Paduch
Faculty of Biotechnology, Department of Protein Engineering, University of Wrocław, Tamka 2, 54 137 Wrocław, Poland
Chembiochem 8:443-52. 2007..This is consistent with the notion that multimerization of both receptors and PDZ-containing proteins might constitute an important regulatory mechanism... - The molecular basis of RhoA specificity in the guanine nucleotide exchange factor PDZ-RhoGEFArkadiusz Oleksy
Institute of Biochemistry and Molecular Biology, University of Wroclaw, 50-137 Wroclaw, Poland
J Biol Chem 281:32891-7. 2006..The key selectivity determinants are dominated by polar contacts involving residues unique to RhoA. We find that selectivity for RhoA versus Cdc42 is defined by a small number of interactions... - The dimerization mechanism of LIS1 and its implication for proteins containing the LisH motifAgnieszka Mateja
Laboratory of Protein Engineering, Institute of Biochemistry and Molecular Biology, University of Wroclaw, Tamka 2, 50 137 Wroclaw, Poland
J Mol Biol 357:621-31. 2006..The observed lability of the coiled-coil fragment in LIS1 is most likely of functional importance... - The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolaseMyung Hee Kim
Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejon 305 600, Korea
Proc Natl Acad Sci U S A 102:17606-11. 2005..We present experimental evidence that AHL-lactonase is a metalloenzyme containing two zinc ions involved in catalysis, and we propose a catalytic mechanism for bacterial metallo-AHL-lactonases...
Research Grants
- Preparing high resolution membrane protein crystalsZygmunt Derewenda; Fiscal Year: 2005..abstract_text> ..
- Molecular Mechanisms of Neuronal MigrationsZygmunt S Derewenda; Fiscal Year: 2010..A comparison of results based on the Xenopus assays with the pull-down assays using mouse brain extracts will provide us with a unique database for Nud-protein interactions and invaluable insight into their function. ..
- Rapid protein crystallization by surface mutagenesisZygmunt Derewenda; Fiscal Year: 2004..Funds are requested to further test the general applicability and success rate of this method, and to apply the method to a subset of targets selected for the Structural Genomic Initiative. ..
- Molecular Mechanisms of Neuronal MigrationZygmunt Derewenda; Fiscal Year: 2005..We will also attempt to crystallize complexes of Lisi and DCX with downstream signaling partners. ..
- MECHANISMS OF LIPID-MEDIATED SIGNAL TRANSDUCTIONZygmunt Derewenda; Fiscal Year: 2001....
- Molecular Mechanisms of Neuronal MigrationsZygmunt Derewenda; Fiscal Year: 2009..A comparison of results based on the Xenopus assays with the pull-down assays using mouse brain extracts will provide us with a unique database for Nud-protein interactions and invaluable insight into their function. ..