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Department of Biochemistry

Publications 2004

by date of publication in PubMed, most recent at the top:

Baici, A., Lang, A., Zwicky, R. & Müntener, K. Cathepsin B in osteoarthritis: uncontrolled proteolysis in the wrong place. Seminars in Arthritis and Rheumatism 34 Suppl. 1, 24-28 (2004).

Binz, H. K. A., P. Kohl, A. Stumpp, M. T. Briand, C. Forrer, P. Grütter, M. G. & Plückthun, A. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22, 575-582 (2004).

Bosshard, H. R., Marti, D. N. & Jelesarov, I. Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings. J. Mol. Recognit. 17, 1-16 (2004).

Caflisch, A. Protein folding: Simple models for a complex process. Structure 12, 1750-1752 (2004).

Capitani, G., De Biase, D., Gut, H., Ahmed, S. & Grütter, M. G. Structural model of human GAD65: prediction and interpretation of biochemical and immunogenic features. Proteins (2004).

Capitani, G. & Schurmann, P. On the quaternary assembly of spinach chloroplast thioredoxin m. Photosynthesis Res. 79, 281-285 (2004).

Cecchini, M., Kolb, P., Majeux, N. & Caflisch, A. Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. J. Comput. Chem. 25, 412-422 (2004).

Cecchini, M., Rao, F., Seeber, M. & Caflisch, A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J. Chem. Physics 121, 10748-10756 (2004).

Chang, C., Plückthun, A. & Wlodawer, A. Crystal structure of a truncated version of the phage ? protein gpD. Proteins 57, 866-868 (2004).

Cranz, S., Berger, C., Baici, A., Jelesarov, I. & Bosshard, H. R. Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site. Biochemistry 43, 718-727 (2004).

Deriu, D. G., M. Firbank, S. Ristig, D. Lampert, C. Mosbacher, J. Froestl, W. Kaupmann, K. Bettler, B. & Grütter, M. G. Determination of the minimal functional ligand binding domain of the GABA B (1b) receptor. Biochem. J. 14, (2004).

Devi, V. S., Binz, H. K., Stumpp, M. T., Plückthun, A., Bosshard, H. R. & Jelesarov, I. Folding of a designed simple ankyrin repeat protein. Protein Sci. 13, 2864-2870 (2004).

Dutzler, R. The structural basis of ClC chloride channel function. Trends Neurosci. 27, 315-20 (2004).

Dutzler, R. Structural basis for ion conduction and gating in ClC chloride channels. FEBS Lett. 564, 229-33 (2004).

Ewert, S., Honegger, A. & Plückthun, A. Stability improvement of antibodies for extracellular and intracellular applications: CDR grafting to stable frameworks and structure-based framework engineering. Methods 34, 184-199 (2004).

Fernandez, F. J., Vega, M. C., Lehmann, F., Sandmeier, E., Gehring, H., Christen, P. & Wilmanns, M. Structural studies of the catalytic reaction pathway of a hyperthermophilic histidinol-phosphate aminotransferase. J. Biol. Chem. 279, 21478-21488 (2004).

Forrer, P., Binz, H. K., Stumpp, M. T. & Plückthun, A. Consensus design of repeat proteins. Chembiochem 5, 183-189 (2004).

Forrer, P., Chang, C., Ott, D., Wlodawer, A. & Plückthun, A. Kinetic stability and crystal structure of the viral capsid protein SHP. J. Mol. Biol. 344, 179-193 (2004).

Gorfe, A. A., Caflisch, A. & Jelesarov, I. The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis. J. Mol. Recognit. 17, 120-131 (2004).

Gorfe, A. A., Pellarin, R. & Caflisch, A. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J. Am. Chem. Soc. 126, 15277-15286 (2004).

Han, W. & Christen, P. cis-Effect of DnaJ on DnaK in ternary complexes with chimeric DnaK/DnaJ-binding peptides. FEBS Lett. 563, 146-50 (2004).

Hu, K., Plückthun, A. & Pervushin, K. Backbone HN, N, C?, C' and C? chemical shift assignments and secondary structure of FkpA, a 245-residue peptidyl-prolyl cis/trans isomerase with chaperone activity. J. Biomol. NMR 28, 405-406 (2004).

Huang, D. & Caflisch, A. Efficient evaluation of binding free energy using continuum electrostatics solvation. J. Med. Chem. 47, 5791-5797 (2004).

Iwai, H., Forrer, P., Plückthun, A. & Güntert, P. Assignments of 1H and 15N resonances of the bacteriophage ? capsid stabilizing protein gpD. J Biomol. NMR 28, 89-90 (2004).

Kohl, A. & Grütter, M. G. Fire and death: the pyrin domain joins the death-domain superfamily. C. R. Biol. 327, 1077-86 (2004).

Koller, M.F., Mohajeri, M. H., Huber, M., Wollmer, M.,A., Roth Z'graggen, B. V., Sandmeier, E., Moritz, E., Tracy, J., Nitsch, R. M. & Christen, P. Active immunization of mice with an abeta-hsp70 vaccine. Neurodegener. Dis. 1, 20-8 (2004).

Levy, Y., Caflisch, A., Onuchic, J. N. & Wolynes, P. G. The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations. J. Mol. Biol. 340, 67-79 (2004).

Lipovsek, D. & Plückthun, A. In-vitro protein evolution by ribosome display and mRNA display. J .Immunol. Methods 290, 51-67 (2004).

Lüthy, L., Grütter, M. G. & Mittl, P. R. The crystal structure of Helicobacter cysteine-rich protein C at 2.0 A resolution: similar peptide-binding sites in TPR and SEL1-like repeat proteins. J.  Mol. Biol. 340, 829-41 (2004).

Marti, D. N., Bjelic, S., Lu, M., Bosshard, H. R. & Jelesarov, I. Fast folding of the HIV-1 and SIV gp41 six-helix bundles. J. Mol. Biol. 336, 1-8 (2004).

Matsuura, T., Ernst, A., Zechel, D. L. & Plückthun, A. Combinatorial approaches to novel proteins. Chembiochem 5, 177-182 (2004).

Matsuura, T. & Plückthun, A. Strategies for selection from protein libraries composed of de novo designed secondary structure modules. Origins of Life and Evolution of the Biosphere 34, 151-157 (2004).

Milev, S., Bosshard, H. R. & Jelesarov, I. in Biocalorimetry 2: Applications of Calorimetry in Biological Sciences (eds. Ladbury, J. E. & Doyle, M.) 189-202 (John Wiley & Sons, 2004).

Müntener, K., Zwicky, R., Csucs, G., Rohrer, J. & Baici, A. Exon skipping of cathepsin B: mitochondrial targeting of a lysosomal peptidase provokes cell death. J. Biol. Chem. 279, 41012-41017 (2004).

Nasser, I., Mohsen, A. W., Jelesarov, I., Vockley, J., Macheroux, P. & Ghisla, S. Thermal unfolding of medium-chain acyl-CoA dehydrogenase and iso(3)valeryl-CoA dehydrogenase: study of the effect of genetic defects on enzyme stability. BBA-Molecular Basis of Disease 1690, 22-32 (2004).

Navarro-Yubero, C., Cuadrado, A., Sonderegger, P. & Munoz, A. Neuroserpin is post-transcriptionally regulated by thyroid hormone. Mol. Brain Res. 123, 56-65 (2004).

Ott, D., Frischknecht, R. & Plückthun, A. Construction and characterization of a kappa opioid receptor devoid of all free cysteines. Protein Eng. Des. Sel. 17, 37-48 (2004).

Rao, F. & Caflisch, A. The protein folding network. J. Mol. Biol. 342, 299-306 (2004).

Rhoades, E., Cohen, M., Schuler, B. & Haran, G. Two-state folding observed in individual protein molecules. J. Am. Chem. Soc. 126, 14686-14687 (2004).

Röthlisberger, D., Pos, K. M. & Plückthun, A. An antibody library for stabilizing and crystallizing membrane proteins - selecting binders to the citrate carrier CitS. FEBS Lett. 564, 340-348 (2004).

Rozhkova, A., Stirnimann, C. U., Frei, P., Grauschopf, U., Brunisholz, R., Grütter, M. G., Capitani, G. & Glockshuber, R. Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD. EMBO J. 23, 1709-19 (2004).

Settanni, G., Gsponer, J. & Caflisch, A. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophys. J. 86, 1691-1701 (2004).

Siegenthaler, R. K., Grimshaw, J. P. & Christen, P. Immediate response of the DnaK molecular chaperone system to heat shock. FEBS Lett. 562, 105-10 (2004).

Tartaglia, G. G., Cavalli, A., Pellarin, R. & Caflisch, A. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Sci. 13, 1939-1941 (2004).

Thomas, A. M., Ginj, C., Jelesarov, I., Amrhein, N. & Macheroux, P. Role of K22 and R120 in the covalent binding of the antibiotic fosfomycin and the substrate-induced conformational change in UDP-N-acetylglucosamine enolpyruvyl transferase. Eur. J.  Biochemistry 271, 2682-2690 (2004).

Türk, K., Puhar, A., Neese, F., Bill, E., Fritz, G. & Steuber, J. NADH oxidation by the Na+ -translocating NADH:quinone oxidoreductase from Vibrio cholerae: Functional role of the NqrF subunit. J. Biol. Chem. 279, 21349 - 21355 (2004).

Zahnd, C., Spinelli, S., Luginbühl, B., Amstutz, P., Cambillau, C. & Plückthun, A. Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. J. Biol. Chem. 279, 18870-18877 (2004).