Martin Luther University Halle-Wittenberg

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List of Publications

List of Publications


129. Prasad A, Breithaupt C, Nguyen DA, Lilie H, Ziegler J, Stubbs MT (2022) Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis. J Biol Chem. in press. doi: 10.1016/j.jbc.2022.102601.


128. Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT (2021) Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J Biol Chem. 296, 100263. doi: 10.1074/jbc.RA120.016836.


127. Hamdi F, Tüting C, Semchonok DA, Visscher KM, Kyrilis FL, Meister A, Skalidis I, Schmidt L, Parthier C, Stubbs MT*, Kastritis PL (2020) 2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope. PLoS One 15:e0232540. doi: 10.1371/journal.pone.0232540.


126. Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Miyaji T, Omote H, Iwata S, Nomura N, Stubbs MT, Tanabe M (2018) Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism.    Nat Commun. 9, 4005. doi: 10.1038/s41467-018-06306-x   .


125. Cotrim CA, Weidner A, Strehmel N, Bisol TB, Meyer D, Brandt W, Wessjohann LA and Stubbs MT (2017) A distinct aromatic prenyltransferase associated with the futalosine pathway   . ChemistrySelect 2, 9319-9325.

124. Nagarathinam K, Jaenecke F, Nakada-Nakura Y, Hotta Y, Liu K, Iwata S, Stubbs MT, Nomura N, Tanabe M (2017) The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis.    Acta Crystallogr F Struct Biol Commun. 73, 423-430.

123. Piechotta A, Parthier C, Kleinschmidt M, Gnoth K, Pillot T, Lues I, Demuth HU, Schilling S, Rahfeld JU, Stubbs MT (2017) Structural and functional analyses of pyroglutamate-amyloid-β-specific antibodies as a basis for Alzheimer immunotherapy.    J Biol Chem. 292, 12713-12724.


122. Jaenecke F, Epler-Friedrich B, Parthier C and Stubbs MT (2015) Membrane composition influences the activity of in vitro refolded human vitamin K epoxide reductase   . Biochemistry 54, 6454-6461.

121. Osadnik H, Schöpfel M, Heidrich E, Mehner D, Lilie H, Parthier C, Risselada HJ, Grubmüller H, Stubbs MT and Brüser T (2015) The PspF-binding domain PspA1-144 and the PspA·F complex - New insights into the coiled-coil dependent regulation of AAA+ proteins   . Mol. Microbiol. 98, 743-759.

120. Zimmermann S, Pfennig S, Neumann P, Yonus H, Weininger U, Kovermann M, Balbach J and Stubbs MT (2015) High-resolution  structures of the d-alanyl carrier protein (Dcp) DltC from Bacillus  subtilis reveal equivalent conformations of apo- and holo-forms   . FEBS Lett. 589, 2283-2289.


119. Stubbs MT and Wahle E (2014) Deadenylation: a piece of PANcake. EMBO J. 33, 1503-1505.

118. Menzel A, Neumann P, Schwieger C and Stubbs MT (2014) Thermodynamic signatures in macromolecular interactions involving conformational flexibility. Biol. Chem. 395, 905-911.

117. Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Bräuer U, Ursel C, Steinmetzer P, Stürzebecher J, Schweinitz A, Steinmetzer T and Stubbs MT (2014) Correlating structure and ligand affinity in drug discovery: A cautionary tale involving second shell residues. Biol. Chem. 395, 891-903.

116. Stubbs MT (2014) Conformational transitions in macromolecular interactions. Biol. Chem. 395, 685-687.

115. Parthier C, Stelter M, Ursel C, Fandrich U, Lilie H, Breithaupt C and Stubbs MT (2014) Structure of the Toll-Spätzle complex, a molecular hub in Drosophila development and innate immunity. PNAS 111, 6281-6286.

114. Simon C, Klose T, Herbst S, Han BG, Sinz A, Glaeser RM, Stubbs MT and Lilie H (2014) Disulfide linkage and structure of highly stable yeast-derived virus-like particles of murine polyomavirus. J. Biol. Chem. 289, 10411-10418.

113. Liebscher S, Schöpfel M, Aumüller T, Sharkhuukhen A, Pech A, Höss E, Parthier C, Jahreis G, Stubbs MT* and Bordusa F* (2014) N-Terminal Protein Modification by Substrate-Activated Reverse Proteolysis. Angew Chem Int Ed Engl. 53, 3024-3028.


112. Stelter M, Fandrich U, Franzke K, Schierhorn A, Breithaupt C, Parthier C and Stubbs MT (2013) High level expression of the Drosophila Toll receptor ectodomain and crystallization of its complex with the morphogen Spätzle. Biol Chem. 394, 1091-1096.

111. Ursel C, Fandrich U, Hoffmann A, Sieg T, Ihling C and Stubbs MT (2013) In-vitro maturation of Drosophila melanogaster Spätzle protein with refolded Easter reveals a novel cleavage site within the prodomain. Biol Chem. 394, 1069-1075.

110. Kolenko P, Koch B, Rahfeld JU, Schilling S, Demuth HU and Stubbs MT (2013) Crystal structure of the glutaminyl cyclase from Drosophila melanogaster in space group I4. Acta Cryst. F69, 358-361.

109. Funkner A, Parthier C, Schutkowski M, Zerweck J, Lilie H, Gyrych N, Fischer G, Stubbs MT and Ferrari DM (2013) Peptide Binding by Catalytic Domains of the Protein Disulfide Isomerase-Related Protein ERp46. J Mol Biol. 425, 1340-1362.


108. Stubbs MT and Baumann U (2012) No end in sight: the development of protein crystallography in Martinsried. Biol Chem. 393, 1025-1026.

107. Koch B, Kolenko P, Buchholz M, Carrillo DR, Parthier C, Wermann M, Rahfeld JU, Reuter G, Schilling S, Stubbs MT and Demuth HU (2012) Crystal structures of glutaminyl cyclases (QCs) from Drosophila melanogaster reveal active site conservation between insect and mammalian QCs. Biochemistry 51, 7383-7392.

106. Morgado I, Wieligmann K, Bereza M, Rönicke R, Meinhardt K, Annamalai K, Baumann M, Wacker J, Hortschansky P, Malešević M, Parthier C, Mawrin C, Schiene-Fischer C, Reymann KG, Stubbs MT, Balbach J, Görlach M, Horn U and Fändrich M (2012) Molecular basis of β-amyloid oligomer recognition with a conformational antibody fragment. PNAS 109, 12503-12508.

105. Löw C, Haupt C, Stubbs MT and Balbach J (2012) Metallochaperone SlyD. In Encyclopedia of Inorganic and Bioinorganic Chemistry (R. Huber, T. Poulos, K. Wieghardt and A. Messerschmidt, eds.), John Wiley and Sons, in press.

104. Han BG, Walton RW, Song A, Hwu P, Stubbs MT, Yannone SM, Arbelaez P, Dong M, Glaeser RM. (2012) Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals. J Struct Biol 180, 249-253.

103. Parthier C, Görlich S, Jaenecke F, Breithaupt C, Bräuer U, Fandrich U, Clausnitzer D, Wehmeier UF, Böttcher C, Scheel D, Stubbs MT (2012) The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction. Angew Chem Int Ed Engl. 51, 4046-4052.

102. Pfennig S and Stubbs MT (2012) Flexing and stretching in nonribosomal Peptide synthetases. Chem. Biol. 19, 167-169.


101.    Ruiz-Carrillo D, Koch B, Parthier C, Wermann M, Dambe T, Buchholz M, Ludwig HH, Heiser U, Rahfeld JU, Stubbs MT*, Schilling S and Demuth HU (2011) Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center. Biochemistry 50, 6280-6288.

100.    Parthier C and Stubbs MT (2011) Peptide Hormone Recognition in Class B GPCRs: Role of the Extracellular Domain in Receptor Activation. In G Protein-Coupled Receptors: From Structure to Function (J. Giraldo and J.-P. Pin, eds.), Royal Society of Chemistry (Cambridge), pp. 75-89.

99.    Schöpfel M, Tziridis A, Arnold U and Stubbs MT (2011) Towards a restriction proteinase: construction of a self-activating enzyme. Chembiochem 12, 1523-1527.

98.    Maestre-Martínez M, Haupt K, Edlich F, Neumann P, Parthier C, Stubbs MT, Fischer G and Lücke C (2011) A charge-sensitive loop in the FKBP38 catalytic domain modulates Bcl-2 binding. J Mol Recognit. 24, 23-34.

97.    Haupt C, Morgado I, Kumar ST, Parthier C, Bereza M, Hortschansky P, Stubbs MT, Horn U and Fändrich M (2011) Amyloid fibril recognition with the conformational B10 antibody fragment depends on electrostatic interactions. J Mol Biol. 405, 341-348.


96.   Carrillo DR, Parthier C, Jänckel N, Grandke J, Stelter M, Schilling S, Boehme M, Neumann P, Wolf R, Demuth HU, Stubbs MT* and Rahfeld JU (2010) Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus. Biol Chem. 391, 1419-1428.

  95.  Schulenburg, C., Weininger, U., Neumann, P., Meiselbach, H., Stubbs, M.T.,  Sticht, H., Balbach, J., Ulbrich-Hofmann, R. and Arnold, U. (2010)  Impact of the C‑terminal disulfide bond on the folding and stability  of onconase. ChemBioChem, 11, 976-986

  94.  Löw, C., Neumann, P., Tidow, H., Weininger, U., Haupt, C., Friedrich-Epler,  B., Scholz, C., Stubbs, M.T.* and Balbach, J. (2010) Crystal  structure determination and functional characterization of the  metallochaperone SlyD from Thermus thermophilus. J.  Mol. Biol. 398, 375-390.


 93.  Weininger,  U., Zeeb, M., Neumann, P., Löw, C., Stubbs, M.T., Lipps, G.  and Balbach, J. (2009) Structure-based stability analysis of an  extremely stable dimeric DNA binding protein from Sulfolobus  islandicus. Biochemistry 48, 10030-10037

92.  Stehle,  F., Brandt, W., Stubbs, M.T., Milkowski, C. and Strack, D.  (2009) Sinapoyltransferases in the light of molecular evolution.  Phytochemistry 70, 1652-1662

91. Parthier, C.,  Runge, S., Rudolph, R. and Stubbs, M.T. (2009)  Passing  the baton in class B GPCRs: peptide hormone activation via helix  induction? TiBS 34, 303-310

90. Neumann, P., Lieber, D., Meyer, S., Dautel, P., Kerth, A., Kraus, I., Garten, W. and Stubbs, M.T. (2009) Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals single-stranded RNA binding properties. PNAS 106, 3710-3715

89. Barak, N.N., Neumann, P., Sevanna, M., Schutkowski, M.,  Naumann, K., Malesevic, M., Reichardt, H., Fischer, G., Stubbs, M.T.,  and Ferrari, D.M. (2009) Crystal structure and functional  analysis of the protein disulfide isomerase related chaperone ERp29.  J. Mol. Biol.385, 1630-1642


88. Neumann, P., Weidner, A., Pech, A., Stubbs, M.T.* and  Tittmann, K. (2008) Structural basis for membrane binding and  catalytic activation of the peripheral membrane enzyme pyruvate oxidase  from Escherichia coli. PNAS 105, 17390-17395.  

87.  Hoffmann, A., Funkner, A., Neumann, P., Juhnke, S., Walther, M.,  Weininger, U., Schierhorn, A., Balbach, J., Reuter, G. and Stubbs, M.T.  (2008) Biophysical characterisation of refolded Drosophila Spätzle, a cystine knot protein, reveals distinct properties of three  isoforms. J. Biol. Chem. 283, 32598-32609.

86.  Yonus, H., Neumann, P., Zimmermann, S., May, J.J., Marahiel, M.A.  and Stubbs, M.T. (2008) Crystal structure of DltA: Implications for the reaction mechanism of non-ribosomal  peptide synthetase (NRPS) adenylation domains. J.  Biol. Chem. 283, 32484-32491.    

85.  Hoffmann, A., Neumann, P., Schierhorn, A. and Stubbs, M.T. (2008) Crystallisation  of Spätzle, a cystine-knot protein involved in embryonic  development and innate immunity in Drosophila  melanogaster. Acta Cryst. F64, 707-710.

84. Kopycki, J.G., Stubbs, M.T., Hagemann, M.,  Porzel, A., Schmidt, J., Schliemann, W., Zenk, M.H. and Vogt, T.  (2008) Functional characterization and structural  properties of a cation dependent O-methyltransferase from the  cyanabacterium Synechocystis sp. Strain PCC 6803. J. Biol. Chem. 283, 20888-20896.  

83. Kopycki, J.G., Rauh, D., Chumanevich, A.A.,  Neumann, P., Vogt, T. and Stubbs, M.T. (2008) Biochemical  and structural analysis of substrate specific and promiscuous Mg2+-dependent  O-methyltransferases. J. Mol. Biol. 378, 154-164.    

82. Weidner, A., Neumann, P.,  Wille, G., Stubbs, M.T. and Tittmann, K. (2008) Crystallization  and preliminary X-ray diffraction analysis of full-length and  proteolytically activated pyruvate oxidase from Escherichia  coli. Acta Cryst. F64, 179-181.  

81. Löw, C., Weininger, U., Neumann, P.,  Lilie, H., Stubbs, M.T. and Balbach, J. (2008) Structural  insights into an equilibrium folding intermediate of an archael ankyrin  repeat protein. PNAS 105, 3779-3784.  

80.  Stehle, F., Stubbs, M.T., Strack, D. and Milkowski, C. (2008) Heterologous  expression of a serine carboxypeptidase-like acyltransferase and  characterization of the kinetic mechanism. FEBS J. 275, 775-787.


79. Parthier, C., Kleinschmidt, M.,  Neumann, P., Rudolph, R., Manhart, S., Schlenzig, D., Fanghänel, J.,  Rahfeld, J.-U., Demuth, H.-U. and Stubbs, M.T. (2007) Crystal structure of the incretin-bound extracellular domain of a G-protein  coupled receptor. PNAS 104, 13942-13947.

78.  Ebersbach, H., Fiedler, E., Scheuermann, T., Fiedler, M., Stubbs, M.T.,  Reimann, C., Proetzel, G., Rudolph, R. and Fiedler, U. (2007) AffilinTM – novel binding molecules based on γ-crystallin, an  all β-sheet protein}. J. Mol. Biol. 372,  172-185.    

77. Linne, U.,  Schäfer, A., Stubbs, M.T. and Marahiel, M.A. (2007) Aminoacyl-coenzyme  A synthesis catalyzed by adenylation domains. FEBS Lett. 581,  905-910.


76. Stubbs, M.T. (2006) Protein ligand interactions  studied by X-ray. In Encyclopedic reference of genomics  and proteomics in molecular medicine (D. Ganten & K. Ruckpaul,  eds.), Springer Verlag (Heidelberg).  

75.  Stubbs, M.T. (2006) Protein crystallography. Chapter 3.21,  Comprehensive Medicinal Chemistry II (D.J. Triggle and J.B.  Taylor, eds.) Elsevier (Oxford), 449-472.  

74. Bodtke, A., Stubbs, M.T. and Otto,  H.-H. (2006) Azasteroids. Reaction of chiral N,N-maleoyl amino  acids with 1-(1-trimethylsiloxyvinyl)-3,4-dihydronaphthlene.  Monatshefte für Chemie 137, 83-103.


73. Werner, C., Stubbs, M.T. , Krauth-Siegel, R.L. and  Klebe, G. (2005) The Crystal Structure of Plasmodium falciparum  Glutamate Dehydrogenase, a Putative Target for Novel Antimalarial Drugs.  J. Mol. Biol. 349, 597-607


72. Brenk, R., Meyer, E.A., Reuter, K., Stubbs, M.T. ,  Garcia, G.A., Diederich, F. and Klebe, G. (2004) Crystallographic  study of inhibitors of tRNA-guanine transglycosylase suggests a new  structure-based pharmacophore for virtual screening. J. Mol. Biol.  338, 55-75

71. Rauh, D., Klebe, G. and Stubbs, M.T. (2004)  Understanding protein-ligand interactions: The price of protein  flexibility. J. Mol. Biol. 335, 1325-1341


70. Brenk, R., Stubbs, M.T., Heine, A., Reuter, K. and Klebe, G.  (2003) Flexible adaptations in the structure of the tRNA-modifying  enzyme tRNA-guanine transglycosylase and their implications for  substrate selectivity, reaction mechanism and structure-based drug  design. Chem.Bio.Chem. 4, 1066-1077

69. Bocola, M.,  Stubbs, M.T., Sotriffer, C., Hauer, B., Friedrich, T., Dittrich, K.  and Klebe, G. (2003) Structural and energetic determinants for  enantiopreferences in kinetic resolution of lipases. Protein Eng. 16,  319-322

68. Rauh, D., Klebe, G., Stürzebecher, J. and Stubbs, M.T.  (2003) ZZ made EZ: Influence of inhibitor configuration on enzyme  selectivity. J. Mol. Biol. 330, 761-770

67. Schmitt, L.,  Benabdelhak, H., Blight, M.A., Holland, I.B. and Stubbs, M.T.  (2003) Crystal structure of the NBD of the ABC-transporter HlyB:  Identification of a variable region within ABC helical domains. J. Mol.  Biol. 330, 333-342

66. Stubbs, M.T. and Klebe, G. (2003)  Das  Nadelöhr - Von der Forschung zur Entwicklung. Kapitel 2.1, Die  pharmazeutische Industrie (D. Fischer und J. Breitenbach, Hrsg.)  Spektrum Akademischer Verlag, Heidelberg, 35-61

65. Brenk, R.,  Naerum, L., Gradler, U., Gerber, H.-D., Garcia, G.A., Reuter, K.,  Stubbs, M.T. and Klebe, G. (2003) Virtual screening for  submicromolar leads of tRNA-guanine transglycosylase based on a new  unexpected binding mode detected by crystal structure analysis. J. Med.  Chem. 46, 1133-1143

64. Bergemann, S., Brecht, R., Buttner, F.,  Guenard, D., Gust, R., Seitz, G., Stubbs, M.T. and Thoret, S.  (2003)  Novel B-ring Modified Allocolchicinoids of the NCME-Series:  Design, Synthesis, Antimicrotubule Activity and Cytotoxicity. Bioorg.  Med. Chem. 11, 1269-1281

63. Reyda, S., Sohn, C., Klebe, G., Rall,  K., Ullmann, D., Jakubke, H.-D. and Stubbs, M.T. (2003)  Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced  structural plasticity. J. Mol. Biol. 325, 963-977


62. Stubbs, M.T. (2002) Anthrax X-rayed: New opportunities  for biodefence. Trends Pharm. Sci. 23, 539-541

61. May, J.J.,  Keßler, N., Marahiel, M.A. and Stubbs, M.T. (2002) Crystal  structure of DhbE, an archetype for carboxy acid activating domains of  modular nonribosomal peptide synthetases. Proc. Natl. Acad. Sci. USA 99,  12120-12125

60. Rauh, D., Reyda, S., Klebe, G. and Stubbs, M.T.  (2002) Trypsin mutants for structure based drug design: expression,  refolding and crystallisation. Biol. Chem. 383, 1309-1314

59.  Grüneberg, S., Stubbs, M.T. and Klebe, G. (2002) Successful virtual  screening for novel inhibitors of human carbonic anhydrase: Strategy  and experimental confirmation. J. Med. Chem. 45, 3588-3602.

58.  Abbate, F., Supuran, C.T., Scozzafava, A., Orioli, P., Stubbs, M.T.,  and Klebe, G. (2002) Nonaromatic sulfonamide group as an ideal anchor  for potent human carbonic anhydrase inhibitors: Role of hydrogen-bonding  networks in ligand binding and drug design. J. Med. Chem. 45,  3583-3587.

57. Kraus, I., Scheffczik, H., Eickmann, M., Kiermayer,  S., Stubbs, M.T., and Garten, W. (2002) Crystallization and  preliminary X-ray analysis of the matrix protein of Borna disease  virus. Acta Cryst. D58, 1371-1373.

56. Reuter, K., Sanderbrand,  S., Jomaa, H., Wiesner, J., Steinbrecher, I., Beck, E., Hintz, M.,  Klebe, G. and Stubbs, M.T. (2002) Crystal structure of 1-deoxy-D-xylulose-5-phosphate  reductoisomerase, a crucial enzyme in the non-mevalonate pathway  of isoprenoid biosynthesis. J. Biol. Chem.277, 5378-5384.

55.  Bruner, S., Weber, T., Kohli, R.M., Schwarzer, D., Marahiel, M.A.,  Walsh, C.T. and Stubbs, M.T. (2002) Structural basis for  peptide cyclisation by surfactin synthetase thioesterase SrfTE.  Structure 10, 301-310.

54. Stubbs, M.T., Reyda, S.,  Dullweber, F., Möller, M., Klebe, G., Dorsch, D., Mederski, W.W.K.R.  and Wurziger, H. (2002) pH-dependent binding modes observed in  trypsin crystals - Lessons for structure-based drug design. Chem.Bio.Chem.3,  246-249.


53. Dullweber, F., Stubbs, M.T.*, Musil, D., Stürzebecher, J.  and Klebe, G.* (2001) Factorising ligand affinity: A combined  thermodynamic and crystallographic study of trypsin and thrombin  inhibition. J. Mol. Biol. 313, 593-614.

52. Kamm, W.,  Hauptmann, J., Behrens, I., Stürzebecher, J., Dullweber, F., Gohlke, H.,  Stubbs, M., Klebe, G. and Kissel, T. (2001) Transport of peptidomimetic  thrombin inhibitors with a 3-amino-phenylalanine structure:  permeability and efflux mechanism in monolayers of a human intestinal  cell line (Caco-2). Pharm. Res. 18, 1110-1118.

51.  Gündisch, D., Harms, K., Schwarz, S., Seitz, G., Stubbs, M.T. and  Wegge, T. (2001) Synthesis and Evaluation of Diazine Containing  Bioisosteres of (-)-Ferruginine as Ligands for Nicotinic Acetylcholine  Receptors. Bioorg. Med. Chem. 9, 2683-2691.

50. Imming,  P., Klaperski, P., Stubbs, M.T., Seitz, G. and Gündisch, D. (2001)  Syntheses and Evaluation of Halogenated Cytisine Derivatives and of the  Biosteric Thiocystine as Potent and Selective nAChR-Ligands. Eur.  J. Med. Chem. 36, 375-388.

49. Stubbs, M.T. and  Huber, R. (2001) Locating heavy atom sites. Chapter 12.2, International  Tables for Crystallography, Volume F: Crystallography of Biological  Macromolecules (M.G. Rossmann and E. Arnold, eds.) Kluwer Academic  Publishers, Dordrecht, The Netherlands, 256-262.

48.  Grädler, U., Gerber, H.-D., Goodenough-Lashua, D.M., Garcia,  G.A., Ficner, R., Reuter, K., Stubbs, M.T. and Klebe, G.  (2001) A new Target for Shigellosis: Rational Design and  Crystallographic Studies of Inhibitors of tRNA-Guanine  Transglycosylase. J. Mol. Biol. 306, 455-467.

47.  García Díaz, B., Groß, S., Assfalg-Machleidt, I., Pfeiler, D.,  Gollmitzer, N., Gabrijelcic-Geiger, D., Stubbs, M.T., Fritz,  H., Auerswald, E.A. and Machleidt, W. (2001) Cystatins as calpain  inhibitors: Engineered chicken cystatin- and stefin B-kininogen  domain 2 hybrids support a cystatin-like mode of interaction with  the catalytic subunit of µ-calpain. Biol. Chem. 382, 97-107.

46.  Che, D., Wegge, T., Stubbs, M.T., Seitz, G., Meier, H. and  Methfessel, C. (2001) 2-(Pyridazin-4-yl)-7-azabicyclo[2.2.1]heptanes:  Design, syntheses and biological characterization of potent pyridazine  analogues of (±)-Epibatidine. J. Med. Chem. 44, 47-57.


45. Bode, W., Brandstetter, H., Hopfner, K.P. and Stubbs, M.T.  (2000) Three-dimensional structures of coagulation factors: pieces  of a complicated puzzle. In New Frontier in Vascular Biology;  Thrombosis and Hemostasis (K. Suzuki, Y. Ikeda, and I. Maruyama, eds.)  Eibun Press, Ltd., Osaka, 75-92.


44. Macedo-Ribeiro, S., Bode, W., Huber, R., Quinn-Allen,  M.A., Kim, S.W., Ortel, T.L., Bourenkov, G.P.,  Bartunik, H.D., Stubbs, M.T., Kane, W.H. and Fuentes-Prior,  P. (1999) Crystal Structures of the C2 Domain of Human Coagulation  Factor V: Implications for Ca2+-Independent Membrane Binding. Nature  402, 434-439.

43. Stürzebecher, J., Vieweg, H.,  Steinmetzer, T., Schweinitz, A., Stubbs, M.T., Renatus, M. and  Wikström, P. (1999) 3-Amidinophenylalanine- based inhibitors of  urokinase. Bioorg. Med. Chem. Lett. 9, 3147-3152.

42.  Sommerhoff, C.P., Bode, W., Pereira, P.J.B., Stubbs, M.T.,  Piechottka, G., Matschiner, G. and Bergner, A. (1999) The structure of  human bII-tryptase: Fo(u)r better or worse. Proc. Natl. Acad. Sci.  USA 96, 10984-10991.

41. Grädler, U., Ficner, R.,  Garcia, G.A., Stubbs, M.T., Klebe, G. and Reuter, K. (1999).  Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine  transgycosylase to elucidate the role of serine 103 for enzymatic  activity. FEBS Lett. 454, 142-146.

40. Stubbs, M.T.  and Bauer, M.M.T. (1999) Crystallization conditions for  proteinases. In Proteolytic Enzymes (E. Sterchi and W. Stoecker, eds.),  Heidelberg, Springer Lab Manual, 337-368.

39. Bauer, M.M.T.  and Stubbs, M.T. (1999) Crystallization of proteinases. In  Proteolytic Enzymes (E. Sterchi and W. Stoecker, eds.), Heidelberg,  Springer Lab Manual, 128-151.

38. Bode, W. and Stubbs,  M.T. (1999). Struktur und Funktion des Thrombins in  Hämostaseologie. (G. Müller-Berghaus and B. Pötzsch, eds.),  Heidelberg, Springer Verlag, 269-284.


37. Renatus, M., Bode, W., Huber, R., Stürzebecher, J. and Stubbs, M.T.  (1998) Structural and functional analyses of benzamidine-based  inhibitors in complex with trypsin: Implications for the inhibition of  factor Xa, tPA and urokinase. J. Med. Chem.41, 5445-5456.

36.  Gabriel, B., Stubbs, M.T., Bergner, A., Hauptmann, J., Bode, W.,  Stürzebecher, J. and Moroder, L. (1998) Structure-based design of  benzamidine-type inhibitors of Factor Xa. J. Med. Chem. 41,  4240-4250.

35. Becker. M., Stubbs, M.T., and  Huber, R. (1998) Crystallization of phycoerythrin 545 of Rhodomonas lens  using detergents and unusual additives. Protein Sci. 7, 580-586.

34.  Stubbs, M.T., Renatus, M., and Bode, W. (1998) An active zymogen:  Unravelling the mystery of tissue-type plasminogen activator.Biological  Chemistry 379, 95-103


33. Renatus, M., Engh, R.A., Stubbs, M.T., Huber, R.,  Fischer, S., Kohnert, U. and Bode, W. (1997) Lys156 promotes the  anomalous proenzyme activity of t-PA: X-ray crystal structure  of single chain human tPA, EMBO J. 16, 4797-4805.

32.  Renatus, M., Stubbs, M.T., Huber, R., Bringmann, P., Donner, P.,  Schleuning, W.-D., and Bode, W. (1997) Catalytic domain structure of  vampire bat plasminogen activator: A molecular paradigm for proteolysis  without activation cleavage, Biochemistry 36, 13483-13493.

31.  Renatus, M., Bode, W., Huber, R., Stürzebecher, J., Prasa, D., Fischer,  S., Kohnert, U. and Stubbs, M.T.(1997) Structural mapping of the  active site specificity determinants of human t-PA: Implications  for the design of low molecular weight substrates and inhibitors, J.  Biol. Chem. 272, 21713-21719.

30. Morenweiser, R.,  Auerswald, E.A., van deLocht, A., Fritz, H., Stürzebecher, J. and  Stubbs, M.T. (1997) Structure-based design of a potent  chimeric thrombin inhibitor, J. Biol. Chem. 272, 19938-19942.

29.  Stubbs, M.T., Morenweiser, R., Stürzebecher, J., Bauer, M., Bode,  W., Huber, R., Piechottka, G.P., Matschiner, G., Sommerhoff, C.P.,  Fritz, H. and Auerswald, E.A. (1997) The three dimensional  structure of recombinant leech-derived tryptase inhibitor in  complex with trypsin: Implications for the structure and function of  human mast cell tryptase and its inhibition, J. Biol. Chem. 272,  19931-19937.

28. Bode, W., Brandstetter, H., Mather,  T., and Stubbs, M.T. (1997) Comparative analysis of haemostatic  proteinases: Structural aspects of thrombin, factor Xa, factor IXa and  protein C, Thromb. Haemost. 78, 501-511.

27. Stubbs, M.T.,  and Bode, W. (1997) Beziehung zwischen Raumstruktur und Funktion des  Thrombins. In Blutgerinnung und Blutungskomplikation (F.R.  Matthias, ed.), Schattauer Verlag, 197-227.

26.  Burgering, M.J.M., Orbons, L.P.M., van der Doelen, A.,  Mulders, J., Theunissen, H.J.M., Grootenhuis, P.D.J., Bode,  W., Huber, R. and Stubbs, M.T. (1997) The second Kunitz domain of  human tissue factor pathway inhibitor. Cloning, structure determination  and interaction with factor Xa, J. Mol. Biol. 269, 395-407.

25.  van de Locht, A., Bode, W., Huber, R., Le Bonniec, B.F., Stone, S.R.,  Esmon, C.T. and Stubbs, M.T. (1997) The thrombin E192Q:BPTI-complex  reveals gross structural rearrangements: implications for the  interaction with antithrombin and thrombomodulin, EMBO J. 16, 2977-2984.


24. van deLocht, A., Stubbs, M.T., Bode, W., Friedrich, T.,  Bollschweiler, C., Hoeffken, W. and Huber, R. (1996) The  Ornithodorin:Thrombin Crystal Structure, a Key to the TAP Enigma?, EMBO  J. 15, 6011-6017.

23. Stubbs, M.T.(1996)  Structural Aspects of Factor Xa Inhibition, Current Pharmaceutical  Design 2, 543-552.

22. van deLocht, A., Stubbs, M.T.,  Bauer, M., and Bode, W. (1996) Conformation of the thrombin A-chain:  Crystallographic evidence that the F2 kringle catalytic domain linker  of prothrombin does not cover the fibrinogen recognition exosite, J.  Biol. Chem.271, 3413-3416.

21. Auerswald, E.A.,  Nägler, D.K., Assfalg-Machleidt, I., Stubbs, M.T.,  Machleidt, W., and Fritz, H. (1996) Hybrids of chicken cystatin with  human kininogen 2 sequences exhibit novel inhibition of calpain,  improved inhibition of actinidin and impaired inhibition of papain,  cathepsin L and cathepsin B, Eur. J. Biochem. 235, 534-542.

20.  Stubbs, M.T., Nar, H., Löwe, J., Huber, R., Ladenstein, R.,  Spangfort, M.D., and Svensson, L.A. (1996) Locating a local  symmetry axis from Patterson map cross vectors: application to crystal  data from GroEL, GTP cyclohydrolase I and the proteosome, Acta Cryst.  D52, 447-452.


19. Stubbs, M.T., Huber, R., and Bode, W.  (1995) Crystal structures of factor Xa specific inhibitors in complex  with trypsin: Structural grounds for inhibition of factor Xa and  selectivity against thrombin, FEBS Letts. 375, 103-107.

18. Stubbs, M.T., and Bode, W. (1995) Structure and specificity  in coagulation and its inhibition, Trends in Cardiovascular Medicine 5,  157-166.

17. Bode, W., and Stubbs, M.T. (1995) Die Raumstruktur des  Thrombin: ein Wegweiser zu seinen vielfältigen Funktionen,  Hämostaseologie 15, 1-13.

16. Machleidt, W., Nägler, D.K., Assfalg-Machleidt, I.,  Stubbs, M.T., Fritz, H., and Auerswald, E.A. (1995) Temporary  inhibition of papain by hairpin mutants of chicken cystatin: distorted  binding of the loops results in cleavage of the Gly9-Ala10 bond, FEBS  Letts. 361,185-190.

15. Auerswald, E.A., Nägler, D.K., Stubbs, M.T.,  Assfalg-Machleidt, I., Machleidt, W., and Fritz, H. (1995) Hairpin  loop mutations of chicken cystatin have different effects on the  inhibition of cathepsin B, cathepsin L and papain, FEBS Letts.  361,179-184.

14. Stubbs, M.T., and Bode, W. (1995) The clot thickens... clues  provided by thrombin structure, Trends in Biochemical Sciences 20,  23-28.


13. Stubbs, M.T., and Bode, W. (1994)  Coagulation factors and their inhibitors, Current Opinion in Structural  Biology 4, 823-832.

12. Stubbs, M.T., and Bode, W. (1994) The structural basis for  thrombin inhibition by hirudin and serpins, in Thrombin: its key role in  thrombogenesis: implications for its inhibition clinically (M.R.  Buchanan, S.J. Brister and F. Ofosu, eds.), CRC Press, 19-51.


11. Stubbs, M.T., and Bode, W. (1993)  Crystal structures of thrombin and thrombin complexes as a framework for  antithrombotic drug design, Perspectives in Drug Discovery and Design  1, 431-452.

10. Bode, W., and Stubbs, M.T. (1993) Crystal structures of  thrombin as signposts to its multiple functions, Actual. Chim. Ther. 21,  3-22.

9. Stubbs, M.T., and Bode, W. (1993) A model for the specificity  of fibrinogen cleavage by thrombin, Sem. Throm. Hemost. 19, 344-351.

8. Bode, W., and Stubbs, M.T. (1993) The spatial structure of  thrombin as a guide to its multiple sites of interaction, Sem. Throm.  Hemost. 19, 321-333.

7. Stubbs, M.T., and Bode, W. (1993) A player of many parts: the  spotlight falls on thrombin's structure, Thromb. Res. 69, 1-58.


6. Stubbs, M.T., Oschkinat, H., Mayr, I.,  Huber, R., Angliker, H., Stone, S.R., and Bode, W. (1992) The  interaction of thrombin with fibrinogen - a structural basis for its  specificity, Eur. J. Biochem. 206, 187-195.


5. Stubbs, M.T., Miller, A., Sizer, P.J.H.,  Stephenson, J.R., and Crooks, A.J. (1991) X-ray solution  scattering of Sindbis virus: changes in conformation induced at low pH,  J. Mol. Biol. 221, 39-42.

4. Stubbs, M.T., and Huber, R. (1991) An analytical packing  function employing Fourier transforms, Acta Cryst. A47, 521-526.


3. Bode, W., Engh, R., Musil, D., Laber, B.,  Stubbs, M., Huber, R., and Turk, V. (1990) Mechanism of interaction of  cysteine proteinases and their protein inhibitors as compared to the  serine proteinase-inhibitor interaction, Biol. Chem. Hoppe-Seyler  (Suppl.) 371, 111-118.

2. Stubbs, M.T., Laber, B., Bode, W., Huber, R., Jerala, R.,  Lenarcic, B., and Turk, V. (1990) The refined 2.4 Å X-ray crystal  structure of recombinant human stefin B in complex with the cysteine  proteinase papain: a novel type of proteinase inhibitor interaction,  EMBO J. 9, 1939-1947.

1. Stubbs, M.T., Summers, L., Mayr, I., Schneider, M., Bode, W.,  Huber, R., Ries, A., and Kühn, K. (1990) Crystals of the NC1 domain of  type IV collagen, J. Mol. Biol. 211, 683-684.