Dr. Markus Perbandt University of Hamburg University Medical Center Eppendorf Laboratory for Structural Biology of Infection and Inflammation c/o DESY, Build. 22a Notkestr. 85 - 20146 Hamburg, Germany Phone: 040 / 8998 - 4745, Fax: - 4747 E-Mail: perbandt(at)chemie.uni-hamburg.de Curriculum: Study of Biochemistry/Molecular Biology at the University of Hamburg (Diploma Thesis 1995);  Dissertation (1999) at the Institute of Biochemistry of the Freien Universität Berlin (Prof. V.A. Erdmann); Postdoc at the University Medical Center Hamburg-Eppendorf, Center for Experimental Medizine, Prof. Dr. Dr. Ch. Betzel (1999-2000);  Postdoc at the Massachusetts Institute of Technology, Boston, USA, Prof. Dr. A. Rich (2000); Senior scientist at the Institute of Biochemistry and Molecular Biology of the University of Hamburg, Prof. Dr. Dr. Ch. Betzel (2001-2007); Senior scientist  at the Institute of Biochemistry of the University of Lübeck, Prof. Dr. Dr. R. Hilgenfeld (2007-2009); Senior Scientist at the Institute of Biochemistry and Molecular Biology of the University of Hamburg, Prof. Dr. Dr. Ch. Betzel (since 2009) Membership in Scientific Organizations: German Society for Biochemistry and Molecular Biology (GMB), German Society for Crystallography (DGK), American Society for Biochemistry and Molecular Biology (ASBMB), German Society for Parasitology (DGP). Functions: Coordinator of the syndicate Hamburg-Lübeck for experimental research at the beamline X13 (EMBL/HASYLAB), Member of the HASYLAB User Committee (2005-2008), Member of the scientific committee at DESY (2006-2008); Educational Coordinator of the graduate school "Structure and Dynamics in Infection- SDI" Cooperations: University of Münster (Prof. E. Liebau), Freie Universität Berlin (Prof. V.A. Erdmann), Christian-Albrechts-University of Kiel (Prof. S. Rose-John, Prof. J. Grötzinger) All India Institute of Medical Sciences (Prof. T.P. Singh), University of Rome/Italy (Prof. G. Ricci)

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Research Topics

Structure-based drug and ligand design - Main focus eucaryotic parasits -

Structure based drug design originates from the central assumption that the inhibitors or ligands bind to a molecular target. The prerequisite for a strong binding is an extensive structural and chemical complementary between the target and the ligand. The structure-based drug design is therefore the search of a small molecule that fits perfectly into the binding pocket of the target protein.

For the development of specific inhibitors or drugs against certain illnesses or infections, it is of particular importance to characterize the complex at high resolution. In order to reach this, the bio molecules are crystallized and are examined by X-ray structural analysis. Based on these results the structure-function relationship can be described very precisely.

Inhibitors or drugs must be very specific against the molecular targets to avoid potential side effects with other proteins. This fact is of great importance especially for the development of specific drugs against viruses, bacteria or parasites, because finally the micro organism should be killed and not the human being. Of course, the structure-based drug design finds its application not only in medicine. Structural biology can also achieve valuable services for the development of high affinity peptides against bio molecules to modulate the binding affinity. [more]

Publications

Complete directory of all publications (more then 50 reviewed publications)

2008

D. Georgieva, A. Kardas, F. Buck, M. Perbandt, and Ch. Betzel. Isolation, crystallization and preliminary X-ray diffraction analysis of L-amino-acid oxidase from Vipera ammodytes ammodytes venom. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 964:918-921 (2008)

E. Liebau, J. Höppner, M. Mühlmeister, C. Burmeister, K. Lüersen, M. Perbandt, C. Schmetz, D. Büttner and N. Brattig. The secretory omega-class glutathione transferase OvGST3 from the human pathogenic parasite Onchocerca volvulus. FEBS J. 5, 3438-3453 (2008)

P. Sharma, N. Singh, M. Sinha, S. Sharma, M. Perbandt, C. Betzel, P. Kaur, A. Srinivasan, and T.P. Singh. Crystal structure of the peptidoglycan recognition protein at 1.8 A resolution reveals dual strategy to combat infection through two independent functional homodimers. J. Mol. Biol. 378:921-930 (2008)

M. Perbandt, J. Höppner, C. Burmeister, K. Lüersen, C. Betzel, and E. Liebau. Structure of the extracellular Prostaglandin D Synthase from the human pathogenic parasite Onchocerca volvulus. J. Mol. Biol. 377, 501-511 (2008)

C. Förster, A. Zerressen-Harte, J.P. Fürste, M. Perbandt, C. Betzel, and V.A. Erdmann. Comparative X-ray structure analysis of human and Escherichia coli tRNA(Gly) acceptor stem microhelices. Biochem. Biophys. Res. Commun. 368: 1002-1006 (2008)

C. Förster, M. Mankowska, J.P. Fürste, M. Perbandt, C. Betzel, and V.A. Erdmann. Crystal structure of a human tRNA(Gly) microhelix at 1.2A resolution. Biochem. Biophys. Res. Commun. 368:996-1001 (2008)

2007

C. Forster, A.B. Brauer, D. Lehmann, T. Borowski, S. Brode, J.P. Fürste, M. Perbandt, C. Betzel, and V.A. Erdmann. Cocrystallizing natural RNA with its unnatural mirror image: biochemical and preliminary X-ray diffraction analysis of a 5S rRNA A-helix racemate. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63:839-843 (2007)

C. Forster, A.B. Brauer, M. Perbandt, D. Lehmann, J.P. Furste, C. Betzel, V.A. Erdmann Crystal structure of an Escherichia coli tRNA(Gly) microhelix at 2.0A resolution. Biochem. Biophys. Res. Commun. 363:621-625 (2007).

S. Bolik, M. Rubhausen, S. Binder, B. Schulz, M. Perbandt, N. Genov, V.A. Erdmann, S. Klussmann, C. Betzel. First experimental evidence for the preferential stabilization of the natural D- over the nonnatural L-configuration in nucleic acids. RNA 11:1877-1880 (2007)

C. Forster, K. Szkaradkiewicz, M. Perbandt, A.B. Brauer, T. Borowski, J.P. Furste, C. Betzel, V.A. Erdmann. Human tRNA(Gly) acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 A resolution. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63:858-861 (2007)

C. Forster, A.B. Brauer, D Lehmann, T. Borowski, S. Brode, J.P. Furste, M. Perbandt, C. Betzel, V.A. Erdmann. Cocrystallizing natural RNA with its unnatural mirror image: biochemical and preliminary X-ray diffraction analysis of a 5S rRNA A-helix racemate. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63:839-843 (2007)

C. Forster, A.B. Brauer, M. Perbandt, D. Lehmann, J.P. Furste, C. Betzel, V.A. Erdmann. Crystal structure of an Escherichia coli tRNA(Gly) microhelix at 2.0A resolution. Biochem. Biophys. Res. Commun. 363:621-625 (2007)

M. Perbandt, O. Bruns, M. Vallazza, T. Lamla, C. Betzel, VA. Erdmann. High resolution structure of streptavidin in complex with a novel high affinity peptide tag mimicking the biotin binding motif. Proteins: Structure, Function and Genetics. 67:1147-1153 (2007)

M. Sherawat, P. Kaur, M. Perbandt, C. Betzel, WA. Slusarchyk, GS. Bisacchi, C. Chang, BL. Jacobson, HM. Einspahr, TP. Singh. Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution. Acta Crystallogr. D Biol. Crystallogr. 63:500-507 (2007)

J.H. Hehemann, L. Redecke, M. Perbandt, R. Saborowski, C. Betzel. Crystallization and preliminary X-ray diffraction studies of trypsin-like proteases from the gastric fluid of the marine crab Cancer pagurus. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 63:242-245 (2007)

C. Forster, M. Perbandt, A.B. Brauer, S. Brode, J.P Furste, C. Betzel, VA. Erdmann. Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNA(Gly) acceptor-stem microhelix. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 63:46-48 (2007)

2006

N. Singh, T. Jabeen, A. Pal, S. Sharma, M. Perbandt, C. Betzel, TP. Singh. Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding. Proteins: Structure Function and Bioinformatics 64:89-100 (2006)

W.R. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, L.J. deLucas, C. Betzel, V.A. Erdmann. The first crystal structure of an RNA racemate. Acta Crystallogr. D Biol. Crystallogr. 62:659-664 (2006)

C. Forster, N. Krauss, A.B. Brauer, K. Szkaradkiewicz, S. Brode, K. Hennig, J.P Furste, M. Perbandt, C. Betzel, V.A. Erdmann. Crystallization and preliminary X-ray diffraction analysis of a tRNASer acceptor-stem microhelix. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 62:559-561 (2006)

C. Forster, A.B. Brauer, S. Brode, K.S. Schmidt, M. Perbandt, A. Meyer, W.R. Rypniewski, C. Betzel, J. Kurreck, J.P Furste, V.A. Erdmann. Comparative crystallization and preliminary X-ray diffraction studies of locked nucleic acid and RNA stems of a tenascin C-binding aptamer. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 62:665-668 (2006)

2005

R. Czaja, M. Perbandt, C. Betzel, U. Hahn. Purine activity of RNase T1RV is further improved by substitution of Trp59 by tyrosine. Biochem. Biophys. Res. Commun. 336:882-889 (2005)

S. Bilgrami, S. Yadav, P. Kaur, S. Sharma, M. Perbandt, C. Betzel, T.P. Singh. Crystal Structure of the Disintegrin Heterodimer from Saw-Scaled Viper (Echis carinatus) at 1.9 A Resolution. Biochemistry  44(33):11058-11066 (2005)

E. Liebau, F. De Maria, C. Burmeister, M. Perbandt, P. Turella, G. Antonini, G. Federici, F. Giansanti, L. Stella, M. Lo Bello, A.M. Caccuri, G. Ricci. Cooperativity and pseudo-cooperativity in the glutathione S-transferase from Plasmodium falciparum. J. Biol. Chem. 280:26121-26128 (2005)

T. Jabeen, S. Sharma, N. Singh, R. K. Singh, P. Kaur, M. Perbandt, Ch. Betzel, A. Srinivasan and T. P. Singh. Crystal structure of a calcium - induced dimer of two isoforms of cobra phospholipase A2 at 1.6 Å resolution. Proteins: Structure, Function and Genetics 59:856-863 (2005)

L. Redecke, W. Meyer-Klaucke, M. Koker, J. Clos, D. Georgieva, N. Genov, H. Echner, H. Kalbacher, M. Perbandt, R. Bredehorst, W. Voelter and Ch. Betzel. Comparative analysis of the human and chicken PrP copper binding region at pH 6.5. J. Biol. Chem. 280:13987-13992 (2005)

M. Perbandt, J. Höppner, Ch. Betzel, R.D. Walter and E. Liebau. Structure of the major cytosolic glutathione S-transferase from the parasitic nematode Onchocerca volvulus. J. Biol. Chem. 280:12630-12636 (2005)

N. Singh, T. Jabeen, S. Sharma, I. Roy, M.N. Gupta, S. Bilgrami, R. K. Somvanshi, S. Dey, M. Perbandt, Ch. Betzel, A. Srinivasan and T.P. Singh. Detection of native peptides as potent inhibitors of enzymes. FEBS Letters 272:562-572 (2005)

2004

D. Georgieva, W. Rypniewski, H. Echner, M. Perbandt, M. Koker, C. Clos, L. Redecke, R. Bredehorst, W. Voelter, N. Genov and Ch. Betzel. Synthetic human prion protein octapeptide repeat binds to the proteinase K active site. Biochem. Biophys. Res. Commun. 325:1406-1411 (2004)

D. Georgieva, M. Koker, L. Redecke, M. Perbandt, J. Clos, R. Bredehorst, N. Genov and Ch. Betzel. Oligomerization of the proteolytic products is an intrinsic property of prion proteins. Optimization of the prion proteolysis. Biochem. Biophys. Res. Commun. 323:1278-1286 (2004)

J Höppner, M. Perbandt, Ch. Betzel, R.D. Walter and E. Liebau. Crystallization of the major cytosolic glutathione S-transferase from Onchocerca volvulus. Acta Crystallogr. D Biol. Crystallogr. 60:1496-1497 (2004)

D.Georgieva, N. Genov, M. Perbandt, W. Voelter and Ch. Betzel. Contribution of Disulfide Bonds and Calcium to the Molluscan Hemycyanin Stability. Zeitschrift f. Naturforschung Sec. C. 59:281-287 (2004)

D. Georgieva, M. Perbandt, W.R. Rypniewski, K. Hristov, N. Genov and Ch. Betzel. The X-ray structure of a snake venom Gln48 phospholipase A2 at 1.9 Å resolution reveals anion-binding sites. Biochem. Biophys. Res. Commun. 316:33-38 (2004)

M. Perbandt, C. Burmeister, R.D. Walter, C. Betzel and E. Liebau. Native and inhibited structure of a MU-class related glutathione S-transferase from Plasmodium falciparum. J. Biol. Chem. 279:1336-1342 (2004)

M. Vallazza, M. Perbandt, S. Klussmann, W. Rypniewski, H.M. Einspahr, V.A. Erdmann, C. Betzel. First look at RNA in L-configuration. Acta Crystallogr. D Biol. Crystallogr. 60:1-7 (2004)

2003

M. Perbandt, I.H. Tsai, A. Fuchs, S. Banumathi, K.R. Rajashankar, I. Tsai, D, Georgieva, N. Kalkura, T.P. Singh, N. Genov, C. Betzel. Crystal Structure of the Hetereodimeric Neurotoxic Complex Daboiatoxin F (RV-4/RV-7) from the Venom of Daboia ruselli formosensis (Taiwan Viper) at 1.9 Å. Acta Crystallogr. D Biol. Crystallogr. 59:1679-1687 (2003)

D. Georgieva, W.R. Rypniewski, M. Perbandt, M. Jain, N.Genov and Ch Betzel. Crystallization and preliminary X-ray diffraction studies of a toxic phospholipase A2 from the venom of Vipera ammodytes meridionalis complexed to a synthetic inhibitor. Biochim. Biophys. Acta  1650:1-3 (2003)

C. Burmeister, M. Perbandt, C. Betzel, R.D. Walter and E. Liebau. Crystallization of the glutathione S-transferase from Plasmodium falciparum. Acta Crystallogr. D Biol. Crystallogr. 59:1650-1652 (2003)

M. Perbandt, E. Guthöhrlein, W.R. Rypniewski, K. Idakieva, S. Stoeva, W. Voelter, N. Genov and Ch. Betzel. The Structure of a Functional Unit from the Wall of a Gastropod Hemocyanin Offers a Possible Mechanism for Cooperativity. Biochemistry, 42(21), 6341-6346 (2003)

M. Perbandt, M. Barciszewska, C. Betzel, V.A. Erdmann & J. Barciszewski. A critical role in the specific cleavage of the anticodon loop of some eukaryotic methionine initiator tRNAs. Mol. Biol. Reports 30:27-31 (2003)

2002

V. Chandra, J. Jasti, P. Kaur, S. Dey, M. Perbandt, A. Srinivasan, C. Betzel & T.P. Singh. Design of specific peptides as inhibitors of phospholipase A2: crystal structure of a complex formed between phospholipase A2 and a designed peptide Phe-Leu-Ser-Tyr-Lys at 1.8 Å resolution. J. Biol. Chem. 277:41079-41085 (2002)

S. Shlyapnikov, V. Lunin, E.V. Blagova, L.V. Abaturov, M. Perbandt, Ch. Betzel and A.M. Mikhailov A Comprarative Structure-Function Analysis and Molecular Mechanism of Action from Serratia Marcescens and Physarium polycephalum. Russian J. of Bioorg. Chem. 38:20-27 (2002)

C. Nötzel, V. Chandra, M. Perbandt, K.R. Rajashankar, T.P. Singh, B. Aleksiev, N. Kalkura, N. Genov & Ch. Betzel. Enzymatic Activity and Inhibition of the neurotoxic complex Vipoxin from the Venom of Vipera ammodytes meridionalis. Z. Naturforsch. 57c:1078-1083 (2002)

M. Vallazza, S. Banumathi, M. Perbandt, K. Moore, L. deLucas, C. Betzel & V.A. Erdmann. Crystallization and structure of Thermus flavus 5S rRNA helix B. Acta Crystallogr. D Biol. Crystallogr. 58:1700-1703 (2002)

2001

S.V. Shliapnikov, V.V. Lunin, E.V. Blagova, M. Perbandt, Ch. Betzel and A. Mikhailov X-ray structural analysis of magnesium-containing Serratia marcescens endonuclease. Bioorg Khim. 27:417-425 (2001)

C. Betzel, S. Gourinath. P. Kumar, P. Kaur, M. Perbandt, S. Eschenburg and T.P. Singh. Structure of a serine protease Proteinase K from Tritirachium album limber at 0.98 Å resolution. Biochemistry 40:3080-3088 (2001)

M. Perbandt, V. Chandra, K.R. Rajashankar, K. Idakieva, K. Parvanova, W. Rypniewski, S. Stoeva. W. Voelter, N. Genov and Ch. Betzel. Crystallization and preliminary studies of the external functional unit RtH2-e from Rapana thomasiana. Acta Crystallogr. D Biol. Crystallogr. 57:1663-1665 (2001)

M. Perbandt, V. Chandra, K. Idakieva, K. Parvanova, W. Rypniewski, N. Genov, S. Stoeva. W. Voelter and Ch. Betzel. Crystallization, Preliminary X-ray Analysis and Amino Acid Sequence Studies of External Functional Unit from the Rapana thomasiana Grosse (Mollusc, Gastropod) Hemocyanin. J. Cryst. Growth 232:353-360 (2001)

M. Perbandt, M. Vallazza, C. Lippmann, Ch. Betzel and V. A. Erdmann. Crystal structure of an RNA duplex with an unusual GC pair in wobble-like conformation at 1.6 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 57:219-224 (2001)

M. Vallazza, A. Senge, C. Lippmann, M. Perbandt, Ch. Betzel, R. Bald and V.A. Erdmann. Crystallization and X-ray diffraction data of Thermus flavus 5S rRNA helices. J. Cryst. Growth 232:340-352 (2001)

2000

S.S. Funari, G. Rapp, M. Perbandt, M. Vallazza, V.A. Erdmann, Ch. Betzel, D. Svergun. Structure of free Thermus flavus 5S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering. J. Biol. Chem. 40:31283-31288 (2000)

S.V. Shlyapnikov, V.V. Lunin, M. Perbandt, K.M. Polyakov, V.Yu. Lunin, V.M. Levdikov, Ch. Betzel and A.M. Mikhailov. Atomic structure of the Serratia marcescens-endonuclease at 1.1 Å resolution and the enzyme reaction mechanism. Acta Crystallogr. D Biol. Crystallogr. 56:567-572 (2000)

S. Lorenz, M. Perbandt, Lippmann, C., Moore, K., DeLucas, L.J., Ch. Betzel and V. A. Erdmann. Crystallization of engineered Thermus flavus 5S rRNA under earth and microgravity conditions. Acta Crystallogr. D Biol. Crystallogr. 56:498-500 (2000)

1999

S.V. Shlyapnikov, E.V. Blagova, V.M. Levdikov, V.Yu. Lunin, V.V. Lunin, A.M. Mikhailov, Ch. Betzel, K.R. Rajashankar and M. Perbandt. The Extracellular Endonuclease of Serratia marcescens. II. Actice Site Amino Acid Residues and Hypothetical Mechanism of Enzyme Function. Mol. Biol. 33:398-404 (1999)

V.Y. Lunin, E.V. Blagova, V.M. Levdikov, V.V. Lunin, S.V. Shlyapnikov, M. Perbandt, K.R. Rajashankar, Ch. Betzel and A.M. Mikhailov. Extracellular Endonuclease of Serratia marcescens. First Three-Dimensional Structure of crystalline Protein at 1.7 Å. Mol. Biol. 33:180-187 (1999)

R. Krauspenhaar, S. Eschenburg, M. Perbandt, V. Kornilov, N. Konareva, I. Mikailova, S. Stoeva, R. Wacker, T. Maier, T. Singh, A. Mikhailov, W. Voelter and Ch. Betzel. Crystal Structure of Mistletoe Lectin I from Viscum album. Biochem. Biophys. Res. Commun. 257:418-424 (1999)

1998

Ch. Zoerb, K. Brunner, M. Perbandt, Ch. Betzel and G. Wagner. Cloning, Recombinant Expression and Characterization of Wild-Type-105-Trp-Calmodulin of the Green Alga Mougeotia scalaris. Bot. Acta 111:346-353 (1998)

M. Perbandt, A. Nolte, S. Lorenz, R. Bald, Ch. Betzel and V. A. Erdmann. Crystal structure of domain E of Thermus flavus 5S rRNA: a helical RNA structure including a hairpin loop. FEBS Lett. 429:211-215 (1998)

1997

M. Perbandt, J. Wilson, S. Eschenburg, I. Mancheva, B. Aleksiev, N. Genov, P. Willingmann, W. Weber, T. Singh and Ch. Betzel. Crystal structure of vipoxin at 2.0 Å: an example of regulation of a toxic function generated by molecular evolution. FEBS Lett. 412:573-577 (1997)

1996

A. Bufe, Ch. Betzel, G. Schramm, A. Petersen, W. Becker, M. Schlaak, M. Perbandt, Z. Dauter and W. Weber. Crystallization and Preliminary Diffraction Data of a Major Pollen Allergen. J. Biol. Chem. 271:27193-27196 (1996)