Zygmunt  S.  Derewenda
Degree(s): PhD
Graduate School: University of Lodz, Poland
Primary Appointment: Professor, Molecular Physiology and Biological Physics

Research Interests:
Mechanisms of Intracellular Signal Transduction; X-ray Crystallography
 

Contact Information   Office Address: PO Box 800736, Jordan Hall, 4211a,   

Office Phone: +1 434-243-6842, Lab Phone +1 434-982-3151,

Fax: +1 434-982-1616

Email Address: zsd4n@virginia.edu

Research Description

Our primary interest is in the mechanisms by which protein molecules accomplish their diverse biological tasks. Crystallography and molecular biology are the primary tools with which we probe into the structure-function relationships in complex proteins. There are two major themes in our work: structural biology of cytoskeletal regulation and the mechanism of hydrolytic enzymes, such as esterases and thioesterases.

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Structural Biology of Rho-GTPase mediated signal transduction The laboratory is involved in comprehensive studies of structure-function relationships in proteins implicated in cell regulation by the Rho GTPases. We determined the crystal structure of RhoA in complex with GDP, only the second Rho GTPase to have its structure elucidated back in 1997. Subsequently we determined the molecular basis of RhoA interactions with the predominant isoform of the guanine nucleotide exchange factor (RhoGDI). We have also defined some aspects of the molecular roots of specificity in a focal adhesion associated GTPase activating protein (GAP). Our current studies focus on the structure and function of the guanine nucleotide exchange factors and similar multidomain molecules. Recently we have determined the X-ray structure of the RGSL domain of PDZRhoGEF. Our collaborators on this project are: Drs. A.P. Somlyo, A.V. Somlyo, J.T.Parsons (UVA) and S. Gutkind (NIH). The project is currently supported by the NHLBI (NIH)

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Structure and Function in Merlin - the Neurofibromatosis Type II Gene Product. ERM (ezrin-radixin-moesin) family of proteins are implicated in the regulation of cytoskeleton, and are thought to interact with RhoGDI (see above). Merlin, the product of the causal gene for neurofibromatosis type II, is also a member of this family. We have recently determined the structure of the N-terminal domain (N-ERMAD) of merlin at 1.8A resolution - the most accurate study to date of any member of the ERM family - and we are pursuing further aspects of structure-function relationship in this protein. Among them, we are interested in the interactions of merlin with syntenin, a protein containing a tandem of PDZ domains, and RhoGDI, which ties the project to the Rho-signaling pathways. Collaborators: Dr. Jacek Otlewski, Wroclaw University, Poland & UVA; Current support for this project is from the Congressionally Directed Medical Research Program of the DOD.

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Structure, Function and Biology of the Proteins Involved in Neuronal Migration. One of the most active areas of research in neurosciences is neuronal migration. Because the phenomenon involves active control of the cytoskeleton, the biology is related to the general area of Rho-mediated cell regulation. PAFAH(Ib) - PAF acetylhydrolase Ib - is an oligomeric complex made up of two catalytic subunits (denoted a1 and a2) and two copies of a regulatory protein LIS1, the product of a causal gene for a genetic disorder known as the Miller-Dieker lissencephaly. Through a multifaceted, interdisciplinary study we have probed the structure-function relationships in the catalytic a subunits and we have determined several structures of homo- and heterodimers. We have also probed the catalytic function of the enzyme and the roots of substrate specificity using site directed mutagenesis. However, our current work focuses on the marker for migrating neurons - doublecortin. This is a novel MAP (microtubule associated protein), and we have both NMR and X-ray structures of specific domains, as well as data showing the mechanismof microtubule bundling by doublecortin. Collaborating laboratories: Dr. John Bushweller, UVA; Dr. Chris Walsh, Harvard Medical Schools, Dr. Jacek Otlewski, Wroclaw University, Poland & UVA. Current support for this project is from the NINDS (NIH)

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METHODOLOGICAL PROJECTS Structural biology would not be where it is today without the revolution in methodologies, especially without the new computing methods in crystallography, advent of synchrotron radiation two decades ago, and the tools of molecular biology. We have been at the forefront of many of these development over the course of the last years, and we continue to dedicate our efforts to the perfection of selected crystallographic techniques.

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Crystallization by Rational Surface Mutagenesis. We believe that modifying the protein sample is a better way to ensure success in crystallization, than attempting to diversify the precipitating conditions into tens of thousands of drops. We have shown that this approach gave very good results in the model system of RhoGDI, and we applied the concept to a novel structure of the RGSL domain from PDZ_containing RhoGEF. We are currently extending this approach to other proteins. Collaborating laboratories: Dr. Zbigniew Dauter, NCI, NSLS; Dr. Jacek Otlewski, Wroclaw University, Poland & UVA. Current support for this project is from the NIGMS (NIH)

Publications

The N-terminal coiled-coil of Ndel1 is a regulated scaffold that recruits LIS1 to dynein. Zyłkiewicz E, Kijańska M, Choi WC, Derewenda U, Derewenda ZS, Stukenberg PT. J Cell Biol. 2011 Feb 7;192(3):433-45. Epub 2011 Jan 31. PMID: 21282465

Application of protein engineering to enhance crystallizability and improve crystal properties. Derewenda ZS.Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):604-15. Epub 2010 Apr 21. PMID: 20445236

The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Mar 1;66(Pt 3):219-24. Epub 2010 Feb 23. PMCID: PMC2833023

The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA. Cierpicki T, Bielnicki J, Zheng M, Gruszczyk J, Kasterka M, Petoukhov M, Zhang A, Fernandez EJ, Svergun DI, Derewenda U, Bushweller JH, Derewenda ZS. Protein Sci. 2009 Oct;18(10):2067-79. PMCID: PMC2786971

Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif . Derewenda U, Boczek T, Gorres KL, Yu M, Hung LW, Cooper D, Joachimiak A, Raines RT, Derewenda ZS. Biochemistry. 2009 Sep 15;48(36):8664-71. PMCID: PMC2739605

On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF. Zheng M, Cierpicki T, Momotani K, Artamonov MV, Derewenda U, Bushweller JH, Somlyo AV, Derewenda ZS. BMC Struct Biol. 2009 May 21;9:36. PMCID: PMC2695464

The role of entropy and polarity in intermolecular contacts in protein crystals. Cieślik M, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):500-9. Epub 2009 Apr 18. PMCID: PMC2672819

Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Zheng M, Cooper DR, Grossoehme NE, Yu M, Hung LW, Cieslik M, Derewenda U, Lesley SA, Wilson IA, Giedroc DP, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):356-65. Epub 2009 Mar 19. PMCID: PMC2659884

Dissecting the thermodynamics of GAP-RhoA interactions. Jelen F, Lachowicz P, Apostoluk W, Mateja A, Derewenda ZS, Otlewski J. J Struct Biol. 2009 Jan;165(1):10-8. Epub 2008 Oct 2. PMCID: PMC2656442

Degenerate specificity of PDZ domains from RhoA-specific nucleotide exchange factors PDZRhoGEF and LARG. Smietana K, Kasztura M, Paduch M, Derewenda U, Derewenda ZS, Otlewski J. Acta Biochim Pol. 2008;55(2):269-80. Epub 2008 Jun 7. PMID:18542831

On wine, chirality and crystallography. Derewenda ZS. Acta Crystallogr A. 2008 Jan;64(Pt 1):246-58. Epub 2007 Dec 21. PMID: 18156689

Structure of the Bacillus subtilis OhrB hydroperoxide-resistance protein in a fully oxidized state. Cooper DR, Surendranath Y, Devedjiev Y, Bielnicki J, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1269-73. Epub 2007 Nov 16. PMID:18084074

The structure of the coiled-coil domain of Ndel1 and the basis of its interaction with Lis1, the causal protein of Miller-Dieker lissencephaly. Derewenda U, Tarricone C, Choi WC, Cooper DR, Lukasik S, Perrina F, Tripathy A, Kim MH, Cafiso DS, Musacchio A, Derewenda ZS. Structure. 2007 Nov;15(11):1467-81. PMID: 17997972

Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. Protein Sci. 2007 Aug;16(8):1569-76. PMCID: PMC2203352

Protein crystallization by surface entropy reduction: optimization of the SER strategy. Cooper DR, Boczek T, Grelewska K, Pinkowska M, Sikorska M, Zawadzki M, Derewenda Z. Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):636-45. Epub 2007 Apr 21. PMID: 17452789

Advances in Protein Crystallography - fourth annual meeting. Derewenda Z. IDrugs. 2007 Apr;10(4):256-8. No abstract available. PMID: 17390248

Bivalent peptides as models for multimeric targets of PDZ domains. Paduch M, Biernat M, Stefanowicz P, Derewenda ZS, Szewczuk Z, Otlewski J. Chembiochem. 2007 Mar 5;8(4):443-52. PMID: 17279591

The molecular basis of RhoA specificity in the guanine nucleotide exchange factor PDZ-RhoGEF. Oleksy A, Opaliński Ł, Derewenda U, Derewenda ZS, Otlewski J. J Biol Chem. 2006 Oct 27;281(43):32891-7. Epub 2006 Sep 5. PMID:16954208

The DC-module of doublecortin: dynamics, domain boundaries, and functional implications. Cierpicki T, Kim MH, Cooper DR, Derewenda U, Bushweller JH, Derewenda ZS. Proteins. 2006 Sep 1;64(4):874-82. PMID: 16835924

The binding of the PDZ tandem of syntenin to target proteins. Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS. Biochemistry. 2006 Mar 21;45(11):3674-83. PMID: 16533050

The dimerization mechanism of LIS1 and its implication for proteins containing the LisH motif. Mateja A, Cierpicki T, Paduch M, Derewenda ZS, Otlewski J. J Mol Biol. 2006 Mar 24;357(2):621-31. Epub 2006 Jan 19. PMID: 16445939

Entropy and surface engineering in protein crystallization. Derewenda ZS, Vekilov PG. Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):116-24. Epub 2005 Dec 14. Review. PMID: 16369101

The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Kim MH, Choi WC, Kang HO, Lee JS, Kang BS, Kim KJ, Derewenda ZS, Oh TK, Lee CH, Lee JK. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17606-11. Epub 2005 Nov 28. PMCID: PMC1295591

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS. Proteins. 2006 Jan 1;62(1):144-51. PMCID: PMC2792008

Probing the supramodular architecture of a multidomain protein: the structure of syntenin in solution. Cierpicki T, Bushweller JH, Derewenda ZS. Structure. 2005 Feb;13(2):319-27. PMID:15698575

Coupling PAF signaling to dynein regulation: structure of LIS1 in complex with PAF-acetylhydrolase. Tarricone C, Perrina F, Monzani S, Massimiliano L, Kim MH, Derewenda ZS, Knapp S, Tsai LH, Musacchio A. Neuron. 2004 Dec 2;44(5):809-21. PMID:15572112

The crystal structure of RhoA in complex with the DH/PH fragment of PDZRhoGEF, an activator of the Ca(2+) sensitization pathway in smooth muscle. Derewenda U, Oleksy A, Stevenson AS, Korczynska J, Dauter Z, Somlyo AP, Otlewski J, Somlyo AV, Derewenda ZS. Structure. 2004 Nov;12(11):1955-65. PMID:15530360

The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism. Janda I, Devedjiev Y, Derewenda U, Dauter Z, Bielnicki J, Cooper DR, Graf PC, Joachimiak A, Jakob U, Derewenda ZS. Structure. 2004 Oct;12(10):1901-7. PMID:15458638

The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins. Devedjiev Y, Surendranath Y, Derewenda U, Gabrys A, Cooper DR, Zhang RG, Lezondra L, Joachimiak A, Derewenda ZS. J Mol Biol. 2004 Oct 15;343(2):395-406. PMCID: PMC2792028

The use of recombinant methods and molecular engineering in protein crystallization. Derewenda ZS. Methods. 2004 Nov;34(3):354-63. Review. PMID:15325653

The structure of the N-terminal domain of the product of the lissencephaly gene Lis1 and its functional implications. Kim MH, Cooper DR, Oleksy A, Devedjiev Y, Derewenda U, Reiner O, Otlewski J, Derewenda ZS.Structure. 2004 Jun;12(6):987-98. PMID: 15274919

Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution. Janda I, Devedjiev Y, Cooper D, Chruszcz M, Derewenda U, Gabrys A, Minor W, Joachimiak A, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1101-7. Epub 2004 May 21. PMCID: PMC2792027

The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography. Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS. J Mol Biol. 2004 Apr 30;338(3):483-93. Erratum in: J Mol Biol. 2004 Jun 25;340(1):191. PMID: 15081807

Rational protein crystallization by mutational surface engineering. Derewenda ZS. Structure. 2004 Apr;12(4):529-35. PMID:15062076

Preliminary crystallographic analysis of the complex of the human GTPase RhoA with the DH/PH tandem of PDZ-RhoGEF. Oleksy A, Barton H, Devedjiev Y, Purdy M, Derewenda U, Otlewski J, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2004 Apr;60(Pt 4):740-2. Epub 2004 Mar 23. PMID: 15039571

The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague. Derewenda U, Mateja A, Devedjiev Y, Routzahn KM, Evdokimov AG, Derewenda ZS, Waugh DS. Structure. 2004 Feb;12(2):301-6. PMID:14962390

The impact of Lys-->Arg surface mutations on the crystallization of the globular domain of RhoGDI. Czepas J, Devedjiev Y, Krowarsch D, Derewenda U, Otlewski J, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):275-80. Epub 2004 Jan 23. PMID: 14747703

Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS. Structure. 2003 Jul;11(7):845-53. PMID: 12842047

Structure of a constitutively activated RhoA mutant (Q63L) at 1.55 A resolution. Longenecker K, Read P, Lin SK, Somlyo AP, Nakamoto RK, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):876-80. Epub 2003 Apr 25. PMID:12777804

The DCX-domain tandems of doublecortin and doublecortin-like kinase. Kim MH, Cierpicki T, Derewenda U, Krowarsch D, Feng Y, Devedjiev Y, Dauter Z, Walsh CA, Otlewski J, Bushweller JH, Derewenda ZS. Nat Struct Biol. 2003 May;10(5):324-33. PMID:12692530

PDZ tandem of human syntenin: crystal structure and functional properties. Kang BS, Cooper DR, Jelen F, Devedjiev Y, Derewenda U, Dauter Z, Otlewski J, Derewenda ZS. Structure. 2003 Apr;11(4):459-68. PMID: 12679023

Purification and crystallization of the N-terminal domain from the human doublecortin-like kinase. Kim MH, Derewenda U, Devedjiev Y, Dauter Z, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2003 Mar;59(Pt 3):502-5. Epub 2003 Feb 21. PMID:12595708

Assignment of 1H, 13C and 15N resonances of the N-terminal microtubule-binding domain of human doublecortin. Cierpicki T, Kim MH, Otlewski J, Derewenda ZS, Bushweller JH. J Biomol NMR. 2003 Jan;25(1):81-2. No abstract available. PMID:12567003

The impact of Glu-->Ala and Glu-->Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 A resolution. Mateja A, Devedjiev Y, Krowarsch D, Longenecker K, Dauter Z, Otlewski J, Derewenda ZS.Acta Crystallogr D Biol Crystallogr. 2002 Dec;58(Pt 12):1983-91. Epub 2002 Nov 23. PMID: 12454455

Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein. Martin TW, Dauter Z, Devedjiev Y, Sheffield P, Jelen F, He M, Sherman DH, Otlewski J, Derewenda ZS, Derewenda U. Structure. 2002 Jul;10(7):933-42. PMID: 12121648

The crystal structure of a major dust mite allergen Der p 2, and its biological implications. Derewenda U, Li J, Derewenda Z, Dauter Z, Mueller GA, Rule GS, Benjamin DC. J Mol Biol. 2002 Apr 19;318(1):189-97. PMID: 12054778

The structure of the FERM domain of merlin, the neurofibromatosis type 2 gene product. Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):381-91. Epub 2002 Feb 21. PMID:11856822

Preparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib. Sheffield PJ, McMullen TW, Li J, Ho YS, Garrard SM, Derewenda U, Derewenda ZS. Protein Eng. 2001 Jul;14(7):513-9. PMID:11522926

Structure of the RGS-like domain from PDZ-RhoGEF: linking heterotrimeric g protein-coupled signaling to Rho GTPases. Longenecker KL, Lewis ME, Chikumi H, Gutkind JS, Derewenda ZS. Structure. 2001 Jul 3;9(7):559-69. PMID:11470431

Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Longenecker KL, Garrard SM, Sheffield PJ, Derewenda ZS. Acta Crystallogr D Biol Crystallogr. 2001 May;57(Pt 5):679-88. Epub 2001 Apr 24. PMID:11320308

Expression, purification, and crystallization of the RGS-like domain from the Rho nucleotide exchange factor, PDZ-RhoGEF, using the surface entropy reduction approach. Garrard SM, Longenecker KL, Lewis ME, Sheffield PJ, Derewenda ZS. Protein Expr Purif. 2001 Apr;21(3):412-6. PMID: 11281715

The functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib). McMullen TW, Li J, Sheffield PJ, Aoki J, Martin TW, Arai H, Inoue K, Derewenda ZS. Protein Eng. 2000 Dec;13(12):865-71. PMID:11239086

Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. Devedjiev Y, Dauter Z, Kuznetsov SR, Jones TL, Derewenda ZS. Structure. 2000 Nov 15;8(11):1137-46. PMID: 11080636

Structure of the BH domain from graf and its implications for Rho GTPase recognition. Longenecker KL, Zhang B, Derewenda U, Sheffield PJ, Dauter Z, Parsons JT, Zheng Y, Derewenda ZS. J Biol Chem. 2000 Dec 8;275(49):38605-10. PMID: 10982819

Substrate specificity in glycoside hydrolase family 10. Structural and kinetic analysis of the Streptomyces lividans xylanase 10A. Ducros V, Charnock SJ, Derewenda U, Derewenda ZS, Dauter Z, Dupont C, Shareck F, Morosoli R, Kluepfel D, Davies GJ. J Biol Chem. 2000 Jul 28;275(30):23020-6. PMID:10930426

Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme. Li J, Derewenda U, Dauter Z, Smith S, Derewenda ZS. Nat Struct Biol. 2000 Jul;7(7):555-9. PMID:10876240

Homologs of the alpha- and beta-subunits of mammalian brain platelet-activating factor acetylhydrolase Ib in the Drosophila melanogaster genome. Sheffield PJ, Garrard S, Caspi M, Aoki J, Arai H, Derewenda U, Inoue K, Suter B, Reiner O, Derewenda ZS. Proteins. 2000 Apr 1;39(1):1-8. PMID:1073792