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Department of Biochemistry

Publications 2010

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

Backus, EH., Bloem, R., Donaldson, PM., Ihalainen, JA., Pfister, R., Paoli, B., Caflisch, A. & Hamm, P. 2D-IR study of a photoswitchable isoptope-labeled alpha-helix. J. Phys. Chem. B. 114, 3735-40 (2010).

Bányai L, Sonderegger P & Patthy L. Agrin binds BMP2, BMP4 and TGFbeta1. PLoS One. 5(5):e10758 (2010).

Bichsel, M., Barbour, AD. & Wagner, A. The early phase of a bacterial insertion sequence infection. Theor Popul Biol. 78, 278-288 (2010).

Bolliger, MF., Zurlinden, A., Lüscher, D., Bütikofer, L., Shakhova, O., Francolini, M., Kozlov, SV., Cinelli, P., Stephan, A., Kistler, AD., Rülicke, T., Pelczar, P., Ledermann, B., Fumagalli, G., Gloor, SM., Kunz, B. & Sonderegger, P. Specific proteolytic cleavage of agrin regulates maturation of the neuromuscular junction. J Cell Sci. 123, 3944-3955 (2010).

Bourquin, F., Riezman, H., Capitani, G. & Grütter, M. Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism. Structure 18, 1054-1065 (2010).

Bragg, JG. & Wagner, A. The evolution of protein material costs. In: Caetano-Anolles, G. Evolutionary genomics and systems biology. New York , 203-211 (2010).

Brient-Litzler, E., Plückthun, A. & Bedouelle, H. Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein. Protein Eng. Des. Sel. 23, 229-241 (2010).

Burkhart, V.,Siegenthaler, RK., Blasius, E., Vandenbroeck, K., Alloza, I., Fingberg, W., Schloot, NC., Christen, P. & Kolb, H. High affinity binding of hydrophobic and autoantigenic regions of proinsulin to the 70kDa chaperone DnaK. BMC Biochem. 11(1):44 (2010).

Casutt MS, Huber T, Brunisholz R, Tao M, Fritz G & Steuber J. Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. J Biol Chem. 285, 27088-27099 (2010).

Casutt MS., Wendelspiess, S., Steuber, J. & Fritz, G. Crystallization of the Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae. Acta Crystallogr Sect F Struct Biol Cryst Commun. 66, 1677-1679 (2010).

De Groot, CO., Jelesarov, I., Damberger, FF., Bjelic, S., Schaerer, MA., Bhavesh, NS., Grigoriev, I., Buey, RM., Wüthrich, K., Capitani, G., Akhmanova, A. & Steinmetz, MO. Molecular insights into mammalian end binding protein heterodimerization. J Biol. Chem. 285, 5802-5814 (2010).

Dityatev, A., Schachner, M. & Sonderegger, P. The dual role of the extracellular matrix in synaptic plasticity and homeostasis. Nat Rev Neurosci. 11, 735-746 (2010).

Dutzler, R., Ernst, B., Hediger, MA., Keppler, D., Mohr, P., Neidhart, W. & Märki, HP. Channels and transporters. Mini-symposium of the Division of Medicinal Chemistry (DMC) of the Swiss Chemical Society (SCS) at the Department of Chemistry, University of Basel, May 27, 2010. Chimia (Aarau) 64, 662-666 (2010).

Durand, J., Meloni, G., Talmard, C., Vasak, M. & Faller, P. Zinc release of Zn(7)-metallothionein-3 induces fibrillar type amyloid-beta aggregates. Metallomics 2, 741-744 (2010).

Espinosa-Soto, C. & Wagner, A. Specialization can drive the evolution of modularity. PLoS Comput. Biol. 6, e1000719 (2010).

Exner,V., Alexandre, C., Rosenfeldt, G., Alfarano, P., Nater, M., Caflisch, A., Gruissem, W., Batschauer, A. & Hennig, L. A gain-of-function mutation of arabidopsis CRYPTOCHROME1 promotes flowering. Plant Physiol. 154, 1633-1645 (2010).

Falconer, RJ., Penkova, A., Jelesarov, I. & Collins, BM: Survey of the year 2008: applications of isothermal titration calorimetry. J. Mol. Recognit. 23, 395-413 (2010).

Ferrada, E. & Wagner, A. Evolutionary innovations and the organization of protein functions in genotype space. PLoS One. 5(11):e14172 (2010).

Friedmannn, R. & Caflisch, A. On the orientation of the catalytic dyad in aspartic proteases. Proteins 78, 1575-1582 (2010). 

Friedmannn, R. , Pellarin , R. & Caflisch, A. Soluble protofibrils as metastable intermediates in simulations of amyloid fibril degradation induced by lipid vesicles. J. Physical Chem. Letters 1, 471-474 (2010).

Hilf, R., Bertozzi, C., Zimmermann, I., Reiter, A., Trauner, D., & Dutzler R. Structural basis of open channel block in a prokaryotic pentameric ligand-gated ion channel. Nat. Struct. Mol. Biol. 17, 1330-1336 (2010).

Hofmann H, Hillger F, Pfeil SH, Hoffmann A, Streich D, Haenni D, Nettels D, Lipman EA & Schuler B. Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc Natl Acad Sci U S A. 107, 11793-11798 (2010).

Huang, D. & Caflisch, A. Library screening by fragment-based docking. J. Mol. Recognit. 23, 183-193 (2010).

Huang, D., Zhou, T., Lafleur, K., Nevado, C. & Caflisch, A. Kinase selectivity portential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics 26, 198-204 (2010).

Kaiser-Bunbury, CN., Muff, S., Memmott, J., Müller, CB. & Caflisch, A. The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecol Lett. 13, 442-452  (2010).

Keller, N., Grütter, MG. & Zerbe, O. Studies of the molecular mechanism of caspase-8 activation by solution NMR. Cell Death Differ. 17, 710-718 (2010).

Kindermann, M., Roschitzki-Voser, H., Caglic, D., Repnik, U., Miniejew, C., Mittl, PR., Kosec, G., Grütter, MG., Turk, B.& Wendt, KU. Selective and sensitive monitoring of caspase-1 activity by a novel bioluminescent activity-based probe. Chem Biol. 17, 999-1007 (2010).

Kramer, MA., Wetzel, SK., Plückthun, A., Mittl, PR. & Grütter, MG. Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned c-capping module. J Mol Biol. 404, 381-391 (2010).

Manso Y, Serra M, Comes G, Giralt M, Carrasco J, Cols N, Vašák M, González-Duarte P, Hidalgo J. The comparison of mouse full metallothionein-1 versus alpha and beta domains and metallothionein-1- to-3 mutation following traumatic brain injury reveals different biological motifs. J Neurosci Res. 88, 1708-1718 (2010).

Melkko S, Mannocci L, Dumelin CE, Villa A, Sommavilla R, Zhang Y, Grütter MG, Keller N, Jermutus L, Jackson RH, Scheuermann J & Neri D. Isolation of a small-molecule inhibitor of the antiapoptotic protein Bcl-xL from a DNA-encoded chemical library. Chem Med Chem. 5, 584-590 (2010).

Messner S, Altmeyer M, Zhao H, Pozivil A, Roschitzki B, Gehrig P, Rutishauser D, Huang D, Caflisch A &  Hottiger MO. PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Res. 38, 6350-6362 (2010). 

Müller-Späth, S., Soranno, A., Hirschfeld, V., Hofmann, H., Rüegger, S., Reymond, L., Nettels, D. & Schuler, B. Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci U S A. 107, 14609-14614 (2010).

Nikolaev Y, Deillon C, Hoffmann SR, Bigler L, Friess S, Zenobi R, Pervushin K, Hunziker P & Gutte B. The leucine zipper domains of the transcription factors GCN4 and c-Jun have ribonuclease activity. PLoS One. 5(5):e10765 (2010).

Novinec, M., Kova?i?, L., Lenar?i?, B. & Baici, A. Conformational flexibility and allosteric regulation of cathepsin K. Biochem J. 429, 379-389 (2010).

Paoli, B., Pellarin, R. & Caflisch, A. Slow folding of cross-linked alpha-helical peptides due to steric hindrance. J Phys Chem B. 114, 2023-2027 (2010).

Pellarin, R., Schütz, P., Guarnera, E. & Caflisch, A. Amyloid fibril polymorphism is under kinetic control. J Am Chem Soc. 132, 14960-14970 (2010).

Pham, QT., Bouchard, A., Grütter, MG. & Berthoux, L. Generation of human TRIM5alpha mutants with high HIV-1 restriction acitivity. Gene Ther. 17, 859-871 (2010).

Plückthun, A. HIV: antibodies with a split personality. Nature 467, 537-538 (2010).

Qi, B., Muff, S., Caflisch, A. & Dinner, AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B. 114, 6979-6989 (2010).

Rankin, DJ., Bichsel, M. & Wagner, A. Mobile DNA can drive lineage extinction in prokaryotic populations. J Evol Biol. 23, 2422-2431 (2010).

Romero-Isart, N., Oliva, B. & Vasak,  M. Influence of bonding interactions on the structure and dynamics of metallothioneins. J Mol Model. 16, 387-394 (2010).

Samal, A., Matias Rodrigues JF., Jost J., Martin OC. & Wagner A. Genotype networks in metabolic reaction spaces. BMC Syst Biol. 4, 30 (2010)

Schärer, MA., Grütter, MG. & Capitani, G. CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts. Proteins 78, 2707-2713 (2010).

Schenker, P. & Baici. T. Paradoxical interactions between modifiers and elastase-2. FEBS J. 277, 2486-2495 (2010).

Scherzer-Attali, R., Pellarin, R., Convertino, M., Frydman-Marom, A., Egoz-Matia N., Peled, S., Levy-Sakin, M., Shalev, DE., Caflisch, A., Gazit, E. & Segal, D. Complete phenotypic recovery of an Alzheimer's disease model by quinone-tryptophan hybrid aggregation inhibitor. PLoS One. 5(6):e11101 (2010).

Schoep,TD., Fulurija, A., Good, F., Lu, W., Hirnbeck, RP., Schwan, C., Choi, SS., Berg, DE., Mittl, PR., Benghezal, M. & Marshall, BJ. Surface properties of Helicobacter pylori urease complex are essential for persistence. PLoS One. 5 (11): e15042 (2010).

Schütz, P.,Wuttke, R., Schuler, B. & Caflisch, A. Free energy surfaces from single-distance information. J. Phys. Chem. B. 114, 15227-15235 (2010). 

Serra-Batiste, M.,Cols, N., Alcaraz, LA., Donaire, A., Gonzalez-Duarte, P. & Vasak, M. The metal-binding properties of the blue crab copper specific CuMT-2: a crustacean metallothionein with two cysteine triplets. J. Biol. Inorg. Chem. 15, 759-776 (2010).

Shalaby, T., von Bueren, AO., Hürlimann, ML., Fiaschetti, G., Casteletti, D., Masayuki, T., Nagasawa, K., Arcaro, A., Jelesarov, I., Shin-ya, K. & Grotzer, M. Disabling c-Myc in childhood medulloblastoma and atypical teratoid/rhabdoid tumor cells by the potent G-quadruplex interactive agent S2T1-6OTD. Mol Cancer Ther. 9, 167-179 (2010).

Sharma, SK., de los Rios, P., Christen, P., Lustig, A. & Goloubinoff, P. The kinetic parameters and energy costs of the Hsp 70 chaperone as a polypeptide unfoldase. Nat Chem Biol. 6, 914-920 (2010).

Sonda S., Morf, L., Bottova, I., Baetschmann, H., Rehrauer, H., Caflisch, A., Hakimi, MA. & Hehl, AB. Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Mol Microbiol. 76, 48-67 (2010).

Steffen W, Gemperli AC, Cvetesic N & Steuber J. Organelle-specific expression of subunit ND5 of human complex I (NADH dehydrogenase) alters cation homeostasis in Saccharomyces cerevisiae. FEMS Yeast Res10, 648-659 (2010).

Steuble M, Gerrits B, Ludwig A, Mateos JM, Diep TM, Tagaya M, Stephan A, Schätzle P, Kunz B, Streit P & Sonderegger P. Molecular characterization of a trafficking organelle: dissecting the axonal paths of calsyntenin-1 transport vesicles. Proteomics. 10, 3775-3788 (2010).

Sulc, P., Wagner, A. & Martin, OC. Quantifying slow evolutionary dynamics in RNA fitness landscapes. J Bioinform Comput Biol. 8, 1027-1040 (2010).

Theurillat JP, Dreier B, Nagy-Davidescu G, Seifert B, Behnke S, Zürrer-Härdi U, Ingold F, Plückthun A & Moch H. Designed ankyrin repeat proteins: a novel tool for testing epidermal growth factor receptor 2 expression in breast cancer. Mod Pathol. 23, 1289-1297 (2010).

Vitalis, A. & Caflisch, A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-beta peptide in aqueous solution and its implications for abeta aggregation. J Mol Biol. 403, 148-165  (2010).

Wetzel, SK., Ewald, C., Settanni, G., Jurt, S., Plückthun, A. & Zerbe, O. Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. J Mol Biol. 402, 241-258 (2010).

Zahnd C, Kawe M, Stumpp MT, de Pasquale C, Tamaskovic R, Nagy-Davidescu G, Dreier B, Schibli R, Binz HK, Waibel R, Plückthun A. Efficient tumor targeting with high-affinity designed ankyrin repeat proteins: effects of affinity and molecular size. Cancer Res. 70, 1595-1605 (2010).

Zahnd, C., Sarkar, CA. & Plückthun, A. Computational analysis of off-rate selection experiments to optimize affinity maturation by directed evolution. Protein Eng Des Sel. 23, 175-184 (2010).

Zhou, T., Lafleur, K. & Caflisch,A. Complementing ultrafast shape recognition with an optical isomerism descriptor. J Mol Graph Model. 29, 443-449 (2010).

Zhou, T. , Huang, D. & Caflisch, A. Quantum mechanical methods for drug design. Curr. Top. Med. Chem 10, 33-45 (2010).

Zhou, T.  & Caflisch, A. High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. Chem Med Chem. 5, 1007-1014 (2010).