• Keine Ergebnisse gefunden

Bei allen berechneten Oberflächen in dieser Arbeit handelt es sich um lösungsmittel-zugängliche Oberflächen („Connolly surfaces“, „solvent accessible surfaces“). Für die Berechnung der Connolly-Oberflächen durch das Programm MS (Connolly, 1983) wurde ein Probenradius von 1.5 Å benutzt.

Der Anteil der polaren Oberfläche beeinhaltet alle Sauerstoff- und Stickstoffatome mit den an ihnen gebundenen Wasserstoffatomen, während sich der nicht-polare Oberflächenanteil aus der Differenz von Gesamtoberfläche und polarem Oberflächenanteil ergibt. Die bei der Ligandenbindung vergrabene Oberfläche ist die Differenz aus der Summe der Oberflächen des freien Liganden und Enzyms einerseits und der Oberfläche der Komplexes andererseits.

Die verwendeten Atomradien wurden Bondi (1968) entnommen.

7 L

ITERATUR

Andrews, P. R., Craik, D.J. & Martin, J.L. (1984). Functional group contributions to drug-receptor interactions.J. Med. Chem.27, 1648-1657.

Avdeef, A. & Bucher, J.J. (1978). Accurate measurements of the concentration of hydrogen ions with a glass electrode: calibrations using the Prideaux and other universal buffer solutions and a computer-controlled automatic titrator.Anal. Chem.50, 2137-2142.

Avdeef, A., Kearney, D.L., Brown, J.A. & Chemotti, A.R. (1982). Bjerrum plots for the determimation of systematic concentration errors in titration data. Anal. Chem. 54, 2322-2326.

Ayala, Y. & DiCera, E. (1994). Molecular recognition by thrombin. Role of slow-fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components.J. Mol. Biol.235, 733-746.

Ayala, Y. M., Vindigni, A., Nayal, M., Spolar, R., Record, M.T. & DiCera, E. (1995).

Thermodynamic investigations of hirudin binding to the slow and fast forms of thrombin: Evidence for folding transitions in the Inhibitor and protease coupled to binding.J. Mol. Biol.253, 787-798.

Baker, B. M. & Murphy, K.P. (1996). Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry.Biophys. J.71, 2049-2055.

Bergner, A., Bauer, M., Brandstetter, H., Stürzebecher, J. & Bode, W. (1995). The X-ray crystal structure of thrombin in complex with N-α -2naphthylsulfonyl-L-3amidino-phenylalanyl-4-methylpiperidide: the benefical effect of filling out an empty cavity.

J. Enzyme Inhib.9, 101-110.

Berliner, L. J. (1992).Thrombin: Structure and function, Plenum Press, New York, USA.

Blokzijl, W. & Engberts, J.B.F.N. (1993). Hydrophobe Effekte - Ansichten und Tatsachen.

Angew. Chem.105, 1610-1648.

Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R. & Hofsteenge, J. (1989). The refined 1.9 Å crystal structure of human alpha-thrombin: Interaction with D-Phe-Pro-Arg chloromethylketone and the significance of the Tyr-Pro-Pro-Trp insertion.

EMBO J.8, 3467-3475.

Bode, W., Turk, D. & Stürzebecher, J. (1990). Geometry of binding of the benzamidine- and arginine-based inhibitors NAPAP and MQPA to human α-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin. European Journal of Biochemistry193, 175-182.

Bode, W., Turk, D. & Karshikov, A. (1992). The refined 1.9 Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone inhibited human a-thrombin. Structure analysis, overall structure, electrostatic properties, detailed active site geometry, structure-function relationships.Protein Sci.1, 426-471.

Bode, W. & Stubbs, M.T. (1995). Die Raumstruktur des Thrombins: ein Wegweiser zu seinen vielfältigen Functionen.Hämostaseologie15, 1-13.

Böhm, H. J. & Klebe, G. (1996). Was läßt sich aus der molekularen Erkennung in Protein-Ligand-Komplexen für das Design neuer Wirkstoffe lernen?Angew. Chem.108, 2750-2778.

Bondi, A. (1968). Physical properties of molecular crystals, liquids and glasses, John Wiley

& Sons Inc., New York, USA.

Brandstetter, H., Turk, D., Hoeffken, H.W., Grosse,D., Stürzebecher, J., Martin, P.D., Edwards, B.F.P. & Bode, W. (1992). Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA.J. Mol. Biol.226, 1085-1099.

Brünger, A. (1992). X-PLOR (Version 3.1). A system for X-ray crystallography and NMR, Yale University Press, New Haven, USA.

CCP4. (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. Section D 50, 760-763.

Christensen, J. J., Hansen, L.D. & Izatt, R.M. (1976). Handbook of proton ionization heats ande related thermodynamic quantities, John Wiley and Sons, New York, USA.

Connelly, P. R., Varadarajan, R., Sturtevant, J.M. & Richards, F.M. (1990). Thermodynamics of protein-peptide interactions in the ribonuclease S system studied by titration calorimetry.Biochem.29, 6108-6114.

Connelly, P. R. & Thompson, J.A. (1992). Heat capacity changes and hydrophobic interactions in the binding of FK506 and rapamycin to the FK506 binding protein.

Proc. Natl. Acad. Sci. USA89, 4781-4785.

Connelly, P. R. (1994). Acquisition and use of calorimetric data for prediction of the thermodynamics of ligand-binding and folding reaction of proteins. Curr. Opin.

Biotech.5, 381-388.

Connolly, M. L. (1983). Solvent accessible surfaces of proteins and nucleic acids. Science 221, 709-713.

Dang, Q.D. & DiCera, E. (1996). Residue 225 determines the Na+-induced allosteric regulation of catalytic activity in serine proteases. Proc. Natl. Acad. Sci. USA 93, 10653-10656.

Davies, T. G., Hubbard, R.E. & Tame, J.R.H. (1999). Relating structure to thermodynamics:

The crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci.8, 1432-1444.

DiCera, E., Guinto, E.R., Vindigni, A., Dang, Q.D., Ayala, Y.M., Wuyi, M. & Tulinsky, A.

(1995). The Na+binding site of thrombin.J. Biol. Chem.270, 22089-22092.

Dixon, M. (1953). Determination of enzyme inhibitor constants.Biochem. J.1953, 170-171.

Dodt, J. (1995). Gerinnungshemmende Wirkstoffe blutsaugender Tiere: von Hirudin zu Hirudinmimetica.Angew. Chem.107, 948-962.

Doyle, M. L. (1997). Characterization of binding interactions by isothermal titration calorimetry.Curr. Opin. Biotech.8, 31-35.

Dunitz, J. D. (1994). The entropic cost of bound water in crystals and biomolecules. Science 264, 670.

Edsall, J. T. (1935). Apparent molal heat capacities of amino acids and other organic compounds.J. Am.Chem. Soc.57, 1506-1507.

Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein-structure-refinement.Acta Cryst. Section A47, 392-400.

Fischer, E. (1894). Einfluß der Konfiguration auf die Wirkung der Enzyme. Ber. Dt. Chem.

Ges.27, 2985-2992.

Fukada, H. T., K. (1998). Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Prot. Struct. Funct. Gen. 33, 159-166.

Furton, J. (1972). Human thrombins: production, evaluation and peptide of a-thrombin. J.

Biol. Chem.252, 2587-3598.

Glusker, J. P., Lewis, M. & Rossi, M. (1994). Crystal structure analysis for chemists and biologists, VCH, Weinheim, Deutschland.

Gómez, J. & Freire, E. (1995). Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.J. Mol. Biol.252, 337-350.

Guinto, E. R. & DiCera, E. (1996). Large heat capacity change in a protein-monovalent cation interaction.Biochem.35, 8800-8804.

Guinto, E. R. & DiCera, E. (1997). Critical role of W60d in thrombin allostery. Biophys.

Chem.64, 103-109.

Gustafsson, D., Antonsson, T., Bylund, R., Eriksson, U., Gyzander, E., Nilsson, I., Elg, M., Mattsson, C., Deinum, J., Karlsson, O., Nilsson, A. & Sörenser, H. (1998). Effects of melagatran, a new low-molecular-weight thrombin inhibitor, on thrombin and fibrinolytic enzymes.Thromb. Haemost.79, 110-118.

Ha, J.-H., Spolar, R.S. & Record, M.T. (1989). Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.J. Mol. Biol.209, 801-816.

Hauptmann, J. & Stürzebecher, J. (1999). Synthetic inhibitor of thrombin and factor Xa: From bench to bedside.Thromb. Res.93, 203-241.

Hilpert, K., Ackermann, J., Banner, D.W., Gast, A., Gubernator, K., Hadvary, P., Labler, L., Müller, K., Schmid, G., Tschopp, T.B. & van de Waterbeemd, H. (1994). Design and synthesis of potent and highly selective thrombin inhibitors. J. Med. Chem. 37, 3889-3901.

Hyre, D. E. & Spicer, L.D. (1995). Thermodynamic evaluation of binding interactions in the methionine represssor system of E. coli using isothermal titration calorimetry.

Biochem.34, 3212-3221.

Inoue, M., Yamada, H., Yasukochi, T., Kuroki, R., Miki, T., Horiuchi, T. & Imoto, T. (1992).

Multiple role of hydrophobicity of tryptophan-108 in chicken lysozyme: Structural stability, sacciride binding ability, and abnormal pKa of glutamic acid-35. Biochem.

31, 5545-5553.

Jones, T. A., Zou, J.Y., Cowan, S.W. & Kjeelgaard, M. (1991). Improved methods for building rotein models in electron density maps and location of errors in these models.

Acta Cryst.5, 802-810.

Kézdy, F. J. & Kaiser, E.T. (1970). Principles of active site titration of proteolytic enzymes.

Meth. Enzym.19, 3-27.

Kimball, S. D. (1995). Challenges in the development of orally bioavailable thrombin active site inhibitors.Blood Coagulation and Fibrinolysis6, 511-519.

Krem, M. M. & DiCera, E. (1998). Conserved water molecules in the specifity pocket of serine proteases and the molecular mechanism of Na+ binding. Prot. Struct. Funct.

Gen.30, 34-42.

Ladbury, J. E., Wright, J.G., Sturtevant, J.M. & Sigler, P.B. (1994). A thermodynamic study of thetrprepressor-operator interaction.J. Mol. Biol.238, 669-681.

Ladbury, J. E. & Chowdhry, B.Z. (1996). Sensing the heat: The application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem.

Biol.3, 791-801.

Ladbury, J. E. & Chowdhry, B.Z. (1998). Biocalorimetry: applications of calorimetry in the biological sciences, John Wiley & Sons, Chicester, England.

Lai, M.-T., DiCera, E. & Shafer, J.A. (1997). Kinetic pathway for the slow to fast transition of thrombin.J. Biol. Chem.48, 30275-30282.

Langsetmo, K., Fuchs, J.A. & Woodward, C. (1991a). The conserved, buried aspartic acid in oxidized E. coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability.Biochem.30, 7603-7609.

Langsetmo, K., Fuchs, J.A., Woodward, C. & Sharp, K.A. (1991b). Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa.Biochem.30, 7609-7614.

Liu, Y. & Sturtevant, J. M. (1995). Significant discrepancies between van't Hoff and calorimetric enthalpies. II.Prot. Sci.4, 2559-2561.

Livingstone, J. R., Spolar, R.S. & Record, M.T. (1991). Contribution of the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area.

Biochem.30, 4237-4244.

Massa, W. (1996).Kristallstrukturbestimmung, Teubner-Verlag, Stuttgart, Deutschland.

Morgan, B. P., Scholtz, J.M., Ballinger, M.D., Zipkin, I.D. & Bartlett, P.A. (1991). Detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhbition of thermolysin by phosphorus-containing inhibitors.J. Am. Chem. Soc. 113, 297-307.

Morrison, J.E. & Stone, S.R. (1985) Approaches to the study and analysis of the inhibition of enzymes by slow- and tight-binding inhibitors. Comments Mol. Cell. Biophys. 2, 347-368

Murphy, K. P. & Freire, E. (1992). Thermodynamics of structural stability and cooperative folding behaviour in proteins.Adv. Protein Sci.43, 313-361.

Naghibi, H., Tamura, A. & Sturtevant, J.M. (1995). Significant discrepancies between van't Hoff and calorimetric enthalpies.Proc. Natl. Acad. Sci. USA92, 5597-5599.

Nayal, M. & DiCera, E. (1996). Valence screening of water in protein crystals reveals potential Na+binding sites.J. Mol. Biol.256, 228-234.

Nilsson, T., Sjöling-Erickson, A. & Deinum, J. (1998). The mechanism of binding of low-molecular-weight active site inhibitors to human a-thrombin. J. Enzyme Inhib. 13, 11-29.

Obst, U. (1997). De-novo-Design und Synthese neuartiger, nichtpeptidischer Thrombin-Inhibitoren.Dissertation Nr. 12037, ETH Zürich, Schweiz.

Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode.Meth. Enzym.276, 307-326.

Privalov, P. L. & Gill, S.J. (1988). Stability of protein structure and hydrophobic interaction.

Adv. Prot. Chem.39, 191-234.

Privalov, P. L. & Makhatadze, G.I. (1990). Heat capacity of proteins: II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects.

J. Mol. Biol.213, 385-391.

Reers, M., Koschinsky, R., Dickneite, G., Hoffmann, D., Czech, J. & Stüber, W. (1995).

Synthesis and characterization of novel thrombin inhibitors based on 4-amidinophenylalanine.J. Enzyme Inhib.9, 61-72.

Renatus, M., Bode, W., Huber, R., Stürzebecher, J. & 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.

Ripka, W. C. (1997). New thrombin inhibitors in cardiovascular disease. Curr. Opin. Chem.

Biol.1, 242-253.

Rydel, T. J., Tulinsky, A., Bode, W. & Huber, R. (1991). Refined structure of the hirudin-thrombin complex.J. Mol. Biol.221, 583-601.

Schaefer, M., Sommer, M. & Karplus, M. (1997). pH-Dependence of protein stability:

absolute electrostatic free energy differences between conformations.J. Phys. Chem. B 101, 1663-1683.

Schaefer, M., Van Vlijmen, H.W.T. & Karplus, M. (1998). Electrostatic contributions to molecular free energies in solution.Adv. Prot. Chem.51, 1-57.

Schechter, I. & Berger, O. (1967). On the size of the active site in proteases. I. Papain.

Biochem. Biophys. Res. Commun.27, 157.

Sleigh, S. H., Seavers, P.R., Wilkinson, A.J., Ladbury,J.E. & Tame, J.R.H. (1999).

Crystallographic and calorimetric analysis of peptide binding to OppA protein. J. Mol.

Biol.291, 393-415.

Spolar, R. S. & Record, M.T. (1994). Coupling of local folding to site-specific binding of proteins to DNA.Science263, 777-784.

Stubbs, M. T., Huber, R. & 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 Lett.375, 103-107.

Sturtevant, J. M. (1977). Heat capacity and entropy changes in processes involving proteins.

Proc. Natl. Acad. Sci. USA74, 2236-2240.

Stürzebecher, J., Walsmann, P., Voigt, B. & Wagner, G. (1984). Inhibition of bovine and human thrombins by derivatives of benzamidine.Thromb. Res.36, 457-467.

Stürzebecher, J., Prasa, D., Wikström, P. & Vieweg, H. (1995). Structure-activity relationships of inhibitors derived from 3-amidinophenylalanine. J. Enzyme Inhib. 9, 87-99.

Suelter, C. H. (1970). Enzymes activated by Monovalent Cations.Science168, 789-795.

Tame, J. R. H. (1999). Scoring functions: A view from the bench. J. Comput.-Aided Mol.

Design13, 99-108.

Turk, D., Stürzebecher, J. & Bode, W. (1991). Geometry of the binding of the Na-tosylated piperidides of m-amidino, p-amidino and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes.FEBS Lett.287, 133-138.

Urry, D. W., Gowda, D.C., Peng, S.Q., Parker, T.M. & Harris, R.D. (1992). Design at nanometric dimensions to enhance hydrophobic-induced pKashifts.J. Am. Chem. Soc.

114, 8716-8717.

Urry, D. W., Peng, S.Q., Parker, T.M., Gowda, D.C. & Harris, R.D. (1993). Die relative Bedeutung elektrostatisch und hydrophob induzierter pKa-Verschiebungen in modellproteinen: der Asparaginsäuretest.Angew. Chem.105, 1523-1525.

Varadarajan, R. V., Connelly, P.R., Sturtevant, J.M. & Richards, F.M. (1992). Heat capacity changes for protein-peptide interactions in the ribonuclease S system. Biochem. 31, 1421-1426.

Wells, C. M. & DiCera, E. (1992). Thrombin is a Na+activated enzyme.Biochem.31, 11721-11730.

Wiseman, T., Williston, S., Brandts, J.F. & Lin L.-N. (1989). Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179, 131-137.

Zalucky, T. B., Malspeis, L., Patel, H. & Hite, G. (1995). Chemistry of some 3-Benzoyl-piperidines.J. Pharm. Sci.54, 687-691.

Zhang, E. & Tulinsky, A. (1997). The molecular environment of the Na+ binding site of thrombin.Biophys. Chem.63, 185-200.

Geburtstag: 31. Dezember 1971

Geburtsort: Osterholz-Scharmbeck (Niedersachsen)

1978 – 1984 Grundschule und Orientierungsstufe in Hambergen 1984 – 1991 Gymnasium in Osterholz-Scharmbeck

Mai 1991 Allgemeine Hochschulreife

1992 / 1993 Grundwehrdienst

1991 – 1996 Studium der Chemie an der Universität Bremen

1992 – 1996 Stipendiat der Begabtenförderung der Konrad-Adenauer-Stiftung

Juli-Dezember 1996 Anfertigung der Diplomarbeit „Synthese von donor-substituierten Chlorinen nach dem Thiadiazolinverfahren“

am Institut für Organische Chemie der Universität Bremen (Betreuer: Prof. Dr. F.-P. Montforts)

Dezember 1996 Verleihung des akademischen Grades „Diplom-Chemiker“

1997 – 2000 Anfertigung der vorliegenden Dissertation

am Institut für Pharmazeutische Chemie der Philipps-Universität Marburg (Betreuer: Prof. Dr. G. Klebe)

Wissenschaftlicher Mitarbeiter am selbigen Institut