Publications

2012

Tomas Jacso; Erwin Schneider; Bernd Rupp; Bernd Reif.
Substrate-transport activation is mediated through the second periplasmic loop P2 of MalF in the maltose transporter MalFGK 2 -E of Escherichia coli.
The Journal of Biological Chemistry; (2012); in press; (doi)

2011

Rupp, Bernd; Günther, Sebastian; Makhmoor, Talat; Schlundt, Andreas; Dickhaut, Katharina; Gupta, Shashank; Choudhary, Iqbal; Wiesmüller, Karl-Heinz; Jung, Günther; Freund, Christian; Falk, Kirsten; Rötzschke, Olaf; Kühne, Ronald
Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules.
PLoS ONE; (2011); 6(4): e18662. (doi)

Jörg D. Wichard; Antonius ter Laak; Gerd Krause; Nikolaus Heinrich; Ronald Kühne; Gunnar Kleinau
Chemogenomic Analysis of G-Protein Coupled Receptors and Their Ligands Deciphers Locks and Keys Governing Diverse Aspects of Signalling.
PLoS ONE; (2011); 6(2): e16811. (doi)

Bleif, S.; Hannemann, F.; Lisurek, M.; von Kries, J.P.; Zapp, J.; Dietzen, M.; Antes, I.; Bernhardt, R.
Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase.
Chembiochem.; (2011); 6(4): 576–582; (doi)

2010

Cirauqui, Nuria; Schrey, Anna K.; Galiano, Silvia; Ceras, Javier; Pérez-Silanes, Silvia; Aldana, Ignacio; Monge, Antonio; Kühne, Ronald.
Building a MCHR1 homology model provides insight into the receptor-antagonist contacts that are important for the development of new anti-obesity agents
Bioorganic & Medicinal Chemistry; (2010);18(21): 7365-7379;(doi)

Zaminer, Jan; Brockmann, Christoph; Huy, Peter; Opitz, Robert; Reuter, Cédric; Beyermann, Michael; Freund, Christian; Müller, Matthias; Oschkinat, Hartmut; Kühne, Ronald; Schmalz, Hans-Günther.
Addressing Protein-Protein Interactions by Small Molecules: A Designed Pro-Pro Dipeptide Mimic with a PPII Helix Conformation as a Module for the Synthesis of PRD-binding Ligands
Angewandte Chemie International Edition; (2010); 49(39): 7111–7115; (doi)

Jehle, S; Rajagopal, P; Bardiaux, B; Markovic, S; Kühne, R; Stout, JR; Higman, VA; Klevit, RE; van Rossum, BJ; Oschkinat, H.
Solid-state NMR and SAXS studies provide a structural basis for the activation of alphaB-crystallin oligomers.
Nat Struct Mol Biol.; (2010); 17(9):1037-42; (doi)

Rupp, B; Appel, KE; Gundert-Remy, U.
Chronic oral LOAEL prediction by using a commercially available computational QSAR tool.
Arch Toxicol; (2010);84(9): 681-688; (doi)

Stübs, G.; Rupp, B.; Schumann, R. R.; Schröder, N. W. J.; Rademann, J.
Chemoenzymatic synthesis of a glycolipid library and elucidation of the antigenic epitope for construction of a vaccine against Lyme disease.
Chemistry; (2010); 16 (11): 3536-44; (doi)

Lisurek, M; Rupp, B.; Wichard, J.; Neuenschwander, M.; von Kries, J.P.; Frank, R; Rademann, J.; Kühne, R.
Design of chemical libraries with potentially bioactive molecules applying a maximum common substructure concept
Mol Divers.; (2010); 14 (2): 401-408; (doi)

Fischer, JJ; Graebner Baessler, OY; Dalhoff, C; Michaelis, S; Schrey, AK; Ungewiss, J; Andrich, K; Jeske, D; Kroll, F; Glinski, M; Sefkow, M; Dreger, M; Koester, H.
Comprehensive identification of staurosporine-binding kinases in the hepatocyte cell line HepG2 using Capture Compound Mass Spectrometry (CCMS).
J Proteome Res.; (2010); 9(2): 806-17; (doi)

Luo, Y; Fischer, JJ; Baessler, OY; Schrey, AK; Ungewiss, J; Glinski, M; Sefkow, M; Dreger, M; Koester; H.
GDP-capture compound--a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS).
J Proteomics; (2010);73(4):815-9;  (doi)

Fischer, JJ; Michaelis, S; Schrey, AK; Graebner, OG; Glinski, M; Dreger, M; Kroll, F; Koester, H.
Capture compound mass spectrometry sheds light on the molecular mechanisms of liver toxicity of two Parkinson drugs.
Toxicol Sci.; (2010); 113(1): 243-53; (doi)

2009

Ahsanullah; Schmieder, P; Kühne, R; Rademann, J.
Metal-free, regioselective triazole ligations that deliver locked cis peptide mimetics.
Angew Chem Int Ed Engl. (2009); 48(27):5042-5; (doi)

Merkwirth, C.; Wichard, J. and Ogorzalek, M.
Ensemble Modeling for Bio-medical Applications
In: Modelling Dynamics in Processes and Systems
Mitkowski, W. & Kacprzyk, J. (ed.)  
Modelling Dynamics in Processes and Systems, Springer Berlin / Heidelberg, (2009); 119-13;  (doi)

Wichard, J.; Bandholtz, S.; Grötzinger, C. and Kühne, R.
Topology Preserving Neural Networks for Peptide Design in Drug Discovery
In: Computational Intelligence Methods for Bioinformatics and Biostatistic
Masulli, F.; Tagliaferri, R. & Verkhivker, G. M. (ed.)
Computational Intelligence Methods for Bioinformatics and Biostatistics, Springer Berlin / Heidelberg. (2009); 232-241;  (doi)

Goñi, G.; Zöllner, A.; Lisurek, M.; Velázquez-Campoy, A.; Pinto, S.; Gómez-Moreno, C.; Hannemann, F.; Bernhardt, R.; Medina, M.;
Cyanobacterial electron carrier proteins as electron donors to CYP106A2 from Bacillus megaterium ATCC 13368
Biochim Biophys Acta. (2009); 1794 (11): 1635-1642; (doi)

2008

Gupta, S.; Höpner, S.; Rupp, B.; Günther, S.; Dickhaut, K.; Agarwal, N.; Cardoso, M. C.; Kühne, R.; Wiesmüller, K.; Jung, G.; Falk, K. & Rötzschke, O.
Anchor side chains of short peptide fragments trigger ligand-exchange of class II MHC molecules.
PLoS ONE, (2008); 3, e1814

Ueffing, N.; Keil, E.; Freund, C.; Kuhne, R.; Schulze-Osthoff, K. & Schmitz, I.
Mutational analyses of c-FLIPR, the only murine short FLIP isoform, reveal requirements for DISC recruitment Cell Death Differ,
Nature Publishing Group, (2008)

Schmidt MF.; Isidro-Llobet A.; Lisurek M.; El-Dahshan A.; Tan J.; Hilgenfeld R.; Rademann J.
Sensitized detection of inhibitory fragments and iterative development of non-peptidic protease inhibitors by dynamic ligation screening.
Angew Chem Int Ed. (2008); 47(17): 3275 – 3278

Freund C.; Schmalz HG.; Sticht J.; Kühne R.
Proline-rich sequence recognition domains (PRD): ligands, function and inhibition.
Handb Exp Pharmacol. (2008); 186 :407-29 (Review)

Lisurek M.; Simgen B.;  Antes I.; Bernhardt R.
Theoretical and experimental evaluation of a CYP106A2 low homology model and production of mutants with changed activity and selectivity of hydroxylation.
Chembiochem.  (2008); 9(9):1439-49.

Wichard JD; Cammann H; Stephan C; Tolxdorff T.
Classification models for early detection of prostate cancer.
J Biomed Biotechnol. (2008); 2008:218097.

2007

Appelt, C., Schrey, A. K., Söderhäll, J. A., Schmieder, P.
Design of antimicrobial compounds based on peptide structures.
Bioorg Med Chem Lett, (2007) 17, 2334-2337

Chevelkov, V., Faelber, K., Schrey, A., Rehbein, K., Diehl, A., Reif, B.
Differential line broadening in MAS solid-state NMR due to dynamic interference.
J Am Chem Soc, (2007) 129, 10195-10200

Hahn, J., Kühne, R., Schmieder, P.
Solution-State (15)N NMR Spectroscopic Study of alpha-C-Phycocyanin: Implications for the Structure of the Chromophore-Binding Pocket of the Cyanobacterial Phytochrome Cph1.
Chembiochem. (2007)

Podust, L. M., von Kries, J. P., Eddine, A. N., Kim, Y., Yermalitskaya, L. V., Kuehne, R., Ouellet, H., Warrier, T., Alteköster, M., Lee, J., Rademann, J., Oschkinat, H., Kaufmann, S. H. E., Waterman, M. R.
Small-Molecule Scaffolds for CYP51 Inhibitors Identified by High-Throughput Screening and Defined by X-Ray Crystallography.
Antimicrob Agents Chemother (2007) 51, 3915-3923

Scholz I., Jehle S., Schmieder P., Hiller M., Eisenmenger F., Oschkinat H., van Rossum B.-J.
J-deconvolution using maximum entropy reconstruction applied to ¹³C-¹³C solid-state cross-polarization magic-angle-spinning NMR of proteins.
J. Am. Chem. Soc. (2007) 129, 6682-6683.

J.D. Wichard, M. Ogorzalek
Time Series Prediction with Ensemble Models applied to the CATS Benchmark
Neurocomputing, Vol. 70, Nos. 13-15, pp. 2371-2378, Aug. 2007.

J.D. Wichard, H. Cammann, C. Stephan and T. Tolxdorff
Classification Models for Early Detection of Prostate Cancer
To appear in: Biomedicine and Biotechnology, Special Issue of the FBIT 2007.

Zimmermann, J., Kühne, R., Sylvester, M., Freund, C.
Redox-regulated conformational changes in an SH3 domain.
Biochemistry (2007) 46, 6971-6977

2006

Eisenmenger F., Hansmann U.H.E., Hayryan Sh., Hu C.-K.
An enhanced version of SMMP – open-source software package for simulation of proteins.
Comput. Phys. Comm. (2006) 174, 422-429.

Höpner, S., Dickhaut, K., Hofstätter, M., Krämer, H., Rückerl, D., Söderhäll, J. A., Gupta, S., Marin-Esteban, V., Kühne, R., Freund, C., Jung, G., Falk, K., Rötzschke, O.
Small organic compounds enhance antigen loading of class II major histocompatibility complex proteins by targeting the polymorphic P1 pocket.
J Biol Chem, (2006) 281, 38535-38542

Mueller-Dieckmann, C., Kernstock, S., Lisurek, M., von Kries, J. P., Haag, F., Weiss, M. S., Koch-Nolte, F.
The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.
Proc Natl Acad Sci U S A, (2006) 103, 15026-15031

Rothfuss A., Steger-HartmannT., Heinrich N., and Wichard J.
Computational Prediction of the Chromosome-Damaging Potential of Chemicals
Chemical Research in Toxicology,   2006 Sep., 19(10): 1313 -1319,

Virus, C., Lisurek, M., Simgen, B., Hannemann, F., Bernhardt, R.
Function and engineering of the 15beta-hydroxylase CYP106A2.
Biochem. Soc. Trans. (2006) 34, 1215-1218

Wichard J.D.
Model Selection in an Ensemble Framework
Proceedings of the IEEE World Congress on Computational Intelligence WCCI
2006, pp. 2187- 2192, Vancouver, Canada.

2005

Appelt C., Eisenmenger F., Kühne R., Schmieder P., Söderhäll J.A.
Interaction of the Antimicrobial Peptide Cyclo(RRWWRF) with Membranes by Molecular Dynamics Simulations.
Biophys. J. (2005) 89, 2296-2306.

Appelt C., Eisenmenger F., Kühne R., Schmieder P., Söderhäll J.A.
Antimicrobial peptide induces lethal membrane order and strain: a combined molecular dynamics and NMR investigation. QSAR and molecular modelling in rational design of bioactive molecules, E. Aki and I. Yalcin (Eds.) Computer aided drug design & development society in Turkey, 2005, 302-303.

Appelt, C., Wessolowski, A., Söderhäll, J. A., Dathe, M., Schmieder, P.
Structure of the antimicrobial, cationic hexapeptide cyclo(RRWWRF) and its analogues in solution and bound to detergent micelles. Chembiochem, (2005) 6, 1654-1662

Ball, L. J., Kühne, R., Schneider-Mergener, J., Oschkinat, H.
Recognition of Proline-Rich Motifs by Protein-Protein-Interaction Domains. Angew Chem Int Ed Engl, (2005) 44, 2852-2869

Söderhäll, J. A., Polymeropoulos, E. E., Paulini, K., Günther, E., Kühne, R.
Antagonist and agonist binding models of the human gonadotropin-releasing hormone receptor.
Biochem Biophys Res Commun, (2005) 333, 568-582

2004

Gaiser OJ, Ball LJ, Schmieder P, Leitner D, Strauss H, Wahl M, Kuhne R, Oschkinat H, Heinemann U
Solution structure, backbone dynamics, and association behavior of the C- terminal BRCT domain from the breast cancer-associated BRCA1
Biochemistry (2004) 43 (51), 15983-95

Baumgart S, Lindner Y, Kuhne R, Oberemm A, Wenschuh H, Krause E
The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry
Rapid Commun Mass Spectrom (2004) 18 (8), 863-868

Ball LJ, Kuhne R,Schneider-Mergener J, Oschkinat H
Recognition of proline-rich motifs (PRMs) by protein-protein interaction domains
Angew Chem Int Ed Engl, (2005) 44, 2852-2869

Brockmann C, Diehl A, Rehbein K, Strauss H, Schmieder P, Korn B, Kuhne R, Oschkinat H
The oxidized subunit b8 from human complex I adopts a thioredoxin fold
Structure (Camb). 2004 Sep;12(9):1645-54

Brockmann C, Leitner D, Labudde D, Diehl A, Sievert V, Bussow K, Kuhne R, Oschkinat H.
The solution structure of the SODD BAG domain reveals additional electrostatic interactions in the HSP70 complexes of SODD subfamily BAG domains
FEBS Lett. 2004 Jan 30;558(1-3):101-6

Pope BJ, Zierler-Gould KM, Kuhne R, Weeds AG, Ball LJ.
Solution structure of human cofilin: actin binding, pH sensitivity, and relationship to actin-depolymerizing factor.
J Biol Chem. 2004 Feb 6;279(6):4840-8

Waldmann H, Karaguni IM, Carpintero M, Gourzoulidou E, Herrmann C, Brockmann C, Oschkinat H, Muller O.
Sulindac-derived Ras pathway inhibitors target the Ras-Raf interaction and downstream effectors in the Ras pathway
Angew Chem Int Ed Engl. 2004 Jan 16;43(4):454-8

2003

Freund C, Kühne R, Park S, Thiemke K, Reinherz EL, Wagner G.,
Structural investigations of a GYF domain covalently linked to a proline-rich peptide.
J Biomol NMR. 2003 Oct;27(2):143-9.

Pires JR, Hong X, Brockmann C, Volkmer-Engert R, Schneider-Mergener J, Oschkinat H, Erdmann R.
The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p
J Mol Biol. 2003 Mar 7;326(5):1427-35

Zimmermann J, Kühne R, Volkmer-Engert R, Jarchau T, Walter U, Oschkinat H, Ball LJ.,
Design of N-substituted peptomer ligands for EVH1 domains.
J Biol Chem. 2003 Jul 10

Karges B, Karges W, Mine M, Ludwig L, Kühne R, Milgrom E, de Roux N.,
Mutation Ala(171)Thr stabilizes the gonadotropin-releasing hormone receptor in its inactive conformation, causing familial hypogonadotropic hypogonadism.
J Clin Endocrinol Metab. 2003 Apr;88(4):1873-9

2002

C. Freund; R. Kühne; H. Yang; S. Park; E.L. Reinherz; G. Wagner;
Dynamic interaction of CD2 with the GYF and the SH3 domain of compartimentalized effector mole-cules
EMBO J. 21, 5985-5995 (2002)

H. Patzelt; B. Simon; A. terLaak; B. Kessler; R. Kühne; P. Schmieder; D. Oesterhelt*; H. Oschkinat*;
The structure of the active center in dark-adapted Bacteriorhodopsin by solution-state NMR spectroscopy
Proc. Natl. Acad. Sci. USA 99, 9765-9770 (2002).

M. Blomenrohr; T. ter Laak; R. Kühne; M. Beyermann; E. Hund; J. Bogerd; R. Leurs
Chimeric gonadotropin-releasing hormone (GnRH) peptides with improved affinity for the catfish (Clarias gariepinus) GnRH receptor
Biochem. J. 361,515-523 (2002).

S. Hövelmann; S.H. Hoffmann;R. Kühne;T. ter Laak; H. Reiländer; T. Beckers; Impact of aromatic residues within transmembrane helix 6 of the human gonadotropin-releasing hormone receptor upon agonist and antagonist binding
Biochemistry 41, 1129-1136 (2002).

2001

M.J.S. Kelly*; L.J. Ball; C. Krieger; Y. Yu; M. Fischer; S. Schiffmann, P. Schmieder; R. Kühne; W. Bermel; A. Aacher, G. Richter; H. Oschkinat*; The NMR Structure of the 47 kDa Dimeric Enzyme 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase and the Ligand Binding Studies Reveal the location of the active site
Proc. Natl. Acad. Sci. USA 98, 13025-13030 (2001)

J.R. Pires; F. Taha-Nejad; F. Toepert; T. Ast; U. Hoffmuller; J. Schneider-Mergener; R. Kühne; M.J. Macias; H. Oschkinat
Solution structures of the YAP65 WW domain and the variant L30K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope
J.Mol.Biol. 314, 1147-1156 (2001)

T. Beckers; B.M. Kutscher; R. Kühne; S. Hoffmann; T. Reissmann
Structure- function studies of linear and cyclized peptide antagonists of the GnRH receptor
Biochem. Biopys. Res. Comm. 289, 653-663 (2001)

M. Blomenrohr; R. Kühne; E. Hund; R. Leurs; J. Bogerd; T. ter Laak
Proper receptor signaling in a mutant catfish gonadotropin-releasing hormone receptor lacking the highly conserved Asp(90) residue
FEBS Lett. 501, 131-134 (2001)

2000

Ball LJ, Kuhne R, Hoffmann B, Hafner A, Schmieder P, Volkmer-Engert R, Hof M, Wahl M, Schneider-Mergener J, Walter U, Oschkinat H, Jarchau T.
Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity
EMBO J. 2000 Sep 15;19(18):4903-14

Hoffmann SH, ter Laak T, Kuhne R, Reilander H, Beckers T.
Residues within transmembrane helices 2 and 5 of the human gonadotropin-releasing hormone receptor contribute to agonist and antagonist binding
Mol Endocrinol. 2000 Jul;14(7):1099-115

Elz S, Kramer K, Pertz HH, Detert H, ter Laak AM, Kuhne R, Schunack W.
Histaprodifens: synthesis, pharmacological in vitro evaluation, and molecular modeling of a new class of highly active and selective histamine H(1)-receptor agonists
J Med Chem. 2000 Mar 23;43(6):1071-84

1999

Schade M, Turner CJ, Kuhne R, Schmieder P, Lowenhaupt K, Herbert A, Rich A, Oschkinat H
The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA
Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12465-70

Wieland K, Laak AM, Smit MJ, Kuhne R, Timmerman H, Leurs R
Mutational analysis of the antagonist-binding site of the histamine H(1) receptor
J Biol Chem. 1999 Oct 15;274(42):29994-30000

ter Laak AM, Kuhne R
Bacteriorhodopsin in a periodic boundary water-vacuum-water box as an example towards stable molecular dynamics simulations of G-protein coupled receptors
Receptors Channels. 1999;6(4):295-308

Anders J, Bluggel M, Meyer HE, Kuhne R, ter Laak AM, Kojro E, Fahrenholz F
Direct identification of the agonist binding site in the human brain cholecystokininB receptor
Biochemistry. 1999 May 11;38(19):6043-55 (doi)

Book Chapter

R. Kühne, G. Krause und W. Rosenthal
Entwicklungsstrategien in der Wirkstoffforschung
in:  Handbuch der Psychpharmakotherapie, p 43-60 (Holsboer, Grüner, Benkert eds.) Springer 2007

R. Kühne
Virtual Screening
in: Enzclopedic reference of genomics and proteomics in molecular medicine, Vol.2 p. 1986-1990 (D. Ganten and K. Ruckpaul eds. ) Springer 2006

Proceedings

J.D. Wichard
Agnostic Learning with Ensembles of Classifiers
Proceedings of the IJCNN 2007, Orlando, Florida, USA.

J.D. Wichard, H. Cammann, T. Tolxdorff and C. Stephan
Early Detection of Prostate Cancer with Classifier Ensembles
Proceedings of the FBIT 2007, Jeju Island, Korea.

Wichard J.D.
Model Selection in an Ensemble Framework
Proceedings of the IEEE World Congress on Computational Intelligence WCCI
2006, pp. 2187- 2192, Vancouver, Canada.

Appelt C., Eisenmenger F., Kühne R., Schmieder P., Söderhäll J.A.
Antimicrobial peptide induces lethal membrane order and strain: a combined molecular dynamics and NMR investigation. QSAR and molecular modelling in rational design of bioactive molecules, E. Aki and I. Yalcin (Eds.) Computer aided drug design & development society in Turkey, 2005, 302-303.