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Department of Biochemistry

Publications 2009

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

Baici, A., Schenker, P., Wächter, M. & Rüedi, P. 3-Fluoro-2,4-dioxa-3-phospadecalins as inhibitors of acetylcholinesterase. A reappraisal of kinetic mechanisms and diagnostic methods. Chem Biodivers. 6, 261-82 (2009).

Baumgartner, R., Meder, G. , Briand, C., Decock, A., D'arcy, A., Hassiepen, U., Morse, R. & Renatus, M. The crystal structure of caspase-6, a selective effector of axonal degeneration. Biochem. J. 423, 429-439 (2009).

Benedix, A., Becker, CM., de Groot, BL., Caflisch, A. & Böckmann, R. Predicting free energy changes using structural ensembles. Nat. Methods 6, 3-4 (2009).

Binter, A., Staunig, N., Jelesarov, I., Lohner, K., Palfey, BA., Deller, S., Gruber, K., &  Macheroux, P. A single intersubunit salt bridge affects oligomerization and catalytic activity in a bacterial quinone. FEBS J. 276, 5263-5274 (2009).

Bodenreider C, Beer D, Keller TH, Sonntag S, Wen D, Yap L, Yau YH, Shochat SG, Huang D, Zhou T, Caflisch A, Su XC, Ozawa K, Otting G, Vasudevan SG, Lescar J, Lim SP. A fluorescence quenching assay to discriminate between specific and non-specific inhibitors of Dengue virus. Anal Biochem. 395, 195-204 (2009).

Bragg, JG. & Wagner, A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 25, 5-8 (2009).

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545-1614 (2009).

Convertino, M., Pellarin, R., Catto, M., Carotti, A. & Caflisch, A. 9,10-Anthraquinone hinders beta-aggregation: How does a small molecule interfere with Abeta-peptide amyloid fibrilles? Protein Sci. 18, 792-800 (2009).

de la Chaux, N. & Wagner, A. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. BMC Evol Biol. 9, 205 (2009).

Derfuss T, Parikh K, Velhin S, Braun M, Mathey E, Krumbholz M, Kümpfel T, Moldenhauer A, Rader C, Sonderegger P, Pöllmann W, Tiefenthaller C, Bauer J, Lassmann H, Wekerle H, Karagogeos D, Hohlfeld R, Linington C & Meinl E. Contactin-2/TAG-1-directed autoimmunity is identified in multiple sclerosis patients and mediates gray matter pathology in animals. Proc Natl Acad Sci U S A. 106, 8302-8327 (2009).

Dumrese, C., Slomianka, L., Ziegler, U., Choi, SS., Kalia, A., Fulurija, A., Lu, W., Berg, DE., Benghezal, M. , Marshall, B. & Mittl, PR. The secreted Heliobacter cysteine-rich protein A causes adherence of human monocytes and differentiation into a macrophage-like phenotype. FEBS Lett. 583, 1637-1643 (2009).

Ekonomiuk, D. & Caflisch, A. Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Sci. 18, 1003-11 (2009).

Ekonomiuk, D., Su, XC., Ozawa, K., Bodenreider, C., Lim, SP., Yin Z., Keller TH., Beer D., Patel V., Otting G., Caflisch A. & Huang D. Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Negl. Trp. Dis. 3(1): e356 (2009).

Ekonomiuk, D., Su, XC., Ozawa, K., Bodenreider, C., Lim, SP., Huang, D. & Caflisch A. Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics.  J Med Chem. 52, 4860-4868 (2009).

Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, Caflisch A, Gruissem W, Köhler C & Hennig L. The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS ONE. 4(4):e5335 (2009).

Friedmann, R., Pellarin, R. & Caflisch, A. Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J. Mol. Biol. 387, 407-415 (2009).

Friedmann, R. & Caflisch, A. Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. Chem. Med. Chem. 4, 1317-1326 (2009). 

Gopich, IV., Nettels, D., Schuler, B. & Szabo, A. Protein dynamics from single-molecule fluorescence intensity correlation functions. J Chem Phys. 131, 095102 (2009).

Guarnera, E., Pellarin, R. & Caflisch, A. How does a simplified-sequence protein fold? Biophys. J. 97, 1737-1746 (2009).

Gut H, Dominici P, Pilati S, Astegno A, Petoukhov MV, Svergun DI, Grütter MG & Capitani G. A common structural basis for pH- and calmodulin-mediated regulation in plant glutamate decarboxylase. J Mol Biol. 392, 334-351 (2009). 

Hafner, M., Koeppl, H., Hasler, M. & Wagner, A. "Glocal" robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biol. 5: e1000534 (2009).

Hafner, M., Koeppl, H. & Wagner, A. Evolution of feedback loops in oscillatory systems. In: Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009). Denver, CO / USA, 157-160.

Hidalgo, J., Chung, R., Penkowa, M., & Vašák, M., in Metallothioneins and Related Chelators, Structure and Functions of Vertebrate Metallothioneins, Vol. 5 of 'Metal Ions in Life Sciences'; (A. Sigel, H. Sigel, R. K. O. Sigel, Eds.) 279-317 (The Royal Society of Chemistry, Cambridge, UK, 2009)

Hilf, R. & Dutzler, R. Structure of a potentially open state of a proton-activated pentameric ligand-gated channel. Nature 457, 115-118 (2009). 

Hilf, R. & Dutzler, R. A prokaryotic perspective on pentameric ligand-gated ion channel structure. Curr Opin Struct Biol. 19, 418-424 (2009). 

Honnappa S, Gouveia SM, Weisbrich A, Damberger FF, Bhavesh NS, Jawhari H, Grigoriev I, van Rijssel FJ, Buey RM, Lawera A, Jelesarov I, Winkler FK, Wüthrich K, Akhmanova A & Steinmetz MO. An EB1-binding motic acts as a microtubule tip localization signal. Cell 138, 366-376 (2009).

Honegger, A., Malebranche, AD., Röthlisberger, D. & Plückthun, A. The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains. Protein Eng. Des. Sel. 22, 121-134 (2009).

Interlandi, G. Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics stimulation. Proteins 75, 659-670 (2009).

Jelesarov, I. & Karshikoff, A. Defining the role of salt bridges in protein stability. In: Shriver, JW. Protein structures, stability and interactions. Totowa, NJ, Chapter 10, pp. 227-260. Book Series: Methods in Mol. Biol. 490, (2009).

Karotki, A. & Vasak, M. Reaction of human metallothionein-3 with cisplatin and transplatin. J Biol Inorg Chem  14, 1129-1138 (2009).

Kawe, M., Horn, U. & Plückthun, A. Facile promotor deletion in Escherichia coli in response to leaky expression of very robust and benign proteins from common expression vectors. Microb. Cell. Fact. 8, 8 (2009). 

Keller, N., Mares, J., Zerbe, O. & Grütter, MG. Structural and biochemical studies on procaspase-8: new insights on initiator caspase inactivation. Structure 17, 438-448 (2009).

Kochhar, S., Mouratou, B. & Christen, P. Amino acid analysis by precolumn derivatization with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide (Marfey reagent). In: The Protein Protocols Handbook, 3rd ed., Walker, JM: (Ed.), Humana Press, Totowa, NJ, pp. 567-572 (2009).

Kovacic, L., Novinek, M., Petan, T., Baici, A. & Krizaj, I. Calmodulin is a non-essential activator of secretory phospholipase A2. Biochemistry 48, 11319-11328 (2009).

Kügler, M., Stein C., Schwenkert M., Saul D., Vockentanz L., Huber T., Wetzel SK., Scholz O., Plückthun A., Honegger A. &  Fey GH. Stabilization and humanization of a single-chain Fv antibody fragment specific for human lymphocyte antigen CD19 by designed point mutations and CDR-grafting onto a human framework. Protein Eng. Des. Sel. 22, 135-147 (2009).

Lafleur, K., Huang, D., Zhou, T., Caflisch, A. & Nevado, C. Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). J Med Chem. 52, 6433-6446 (2009).

Leemann-Zakaryan, R., Pahlich, S., Sedda, M., Quero, L., Grossenbacher, D. & Gehring, H. Dynamic subcellular localization of Ewing Sarcoma proto-oncoprotein and its association with and stabilization of microtubules. J. Mol. Biol. 386, 1-13 (2009).

Ludwig, A., Blume, J., Diep, TM., Yuan, J., Mateos, JM., Leuthäuser, K., Steuble, M., Streit, P. & Sonderegger, P. Calsyntenins mediate TGN exit of APP in a Kinesin-1-dependent manner. Traffic  10, 572-589 (2009).

Martin, OC. & Wagner, A. Effects of recombination on complex regulatory circuits. Genetics 183, 673-684 (2009). 

Matias Rodrigues, JF., & Wagner, A. Evolutionary plasticity and innovations in compex metabolic reaction networks. PLoS Comput. Biol. 5, e1000613 (2009).

Matsumoto-Miyai K, Sokolowska E, Zurlinden A, Gee CE, Lüscher D, Hettwer S, Wölfel J, Ladner AP, Ster J, Gerber U, Rülicke T, Kunz B & Sonderegger P. Coincident pre- and postsynaptic activation induces dendritic filopodia via neurotrypsin-dependent agrin cleavage. Cell  136, 1161-1171 (2009).

Meloni G, Polanski T, Braun O & Vas?a?k M. Effects of Zn(2+), Ca(2+), and Mg (2+) on the structure of Zn(7)methallothionein-3: evidence for an additional zinc binding site. Biochemistry 48, 5700-5777 (2009).

Milovnik P, Ferrari D, Sarkar CA & Plückthun A. Selection and characterization of DARPins specific for the neurotensin receptor 1. Protein Eng Des Sel. 22, 357-66 (2009).

Muff, S. & Caflisch, A. ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations. J Phys Chem B. 113, 3218-3226 (2009).

Muff, S. & Caflisch, A. Identification of the protein folding transition state from molecular dynamics trajectories. J. Chem Phys. 130, 125104 (2009).

Müller, IB., Wu, F., Bergmann, B., Knöckel, J., Walter, RD., Gehring, H. & Wrenger, C. Poisoning pyridoxal 5-phosphate-dependent enzymes: a new strategy to target the malaria parasite plasmodium falciparumPLoS ONE. 4(2):e4406 (2009).

Neagu, MR., Ziegler, P., Pertel, T., Strambio-De-Castillia, C., Grütter, C., Martinetti, G., Mazzucchelli, L., Grütter, M., Manz, MG. &  Luban, J. Potent inhibition of HIV-1 by TRIM5-cylophilin fusion proteons engineered from human components. J Clin Invest. 119, 3035-3047 (2009).

Nettels, D., Müller-Späth, S., Küster, F., Hofmann, H., Haenni, D., Rüegger, S., Reymond, L., Hoffmann, A., Kubelka, J., Heinz, B., Gast, K., Best, RB. & Schuler, B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A. 106, 20740-20745 (2009).

Pahlich, S., Quero, L., Roschitzki, B., Leemann-Zakaryan, RP. & Gehring, H. Analysis of Ewing Sarcoma (EWS)-binding proteins: interaction with hnRNP M, U and RNA-helicases p68/72 with protein-RNA complexes. J. Proteome Res. 8, 4455-4465 (2009).  

Paoli, B., Seeber, M., Backus, EH., Ihalainen, JA., Hamm, P. & Caflisch, A. Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: a combined molecular dynamics and time-resolved infrared spectroscopy study. J Phys Chem B113, 4435-4442 (2009).

Plückthun, A. Alternative scaffolds: expanding the options of antibodies. In: Little, M (ed.), Recombinant antibodies for immunotherapy. New York, USA, Cambridge University Press, 243-271  (2009).

Schenker, P. & Baici, A. Simultaneous interaction of enzymes with two modifiers: reappraisal of kinetic models and new paradigms. J Theor Biol261, 318-329 (2009).

Schulz BL, Stirnimann CU, Grimshaw JP, Brozzo MS, Fritsch F, Mohorko E, Capitani G, Glockshuber R, Grütter MG & Aebi M. Oxidoreductase activity of oligosaccharyltransferase subunits Ost3p and Ost6p defines site-specific glycosylation efficiency. Proc Natl Acad Sci U S A. 106, 11061-11066 (2009).

Scocchi, M., Lüthy, C., Decarli, P., Mignogna, G., Christen, P. & Gennaro, R. The proline-rich antibacterial peptide Bac7 binds to and inhibits in vitro the molecular chaperone DnaK. Int J Pept Res Ther 15, 147-155 (2009).

Sebastian, S., Grütter, C., Strambio de Castillia, C., Pertel, T., Olivari, S., Grütter, M. & Luban, J. An invariant surface patch on the TRIM5(alpha) PRYSPRY domain is required for retroviral restriction but dispensable for capsid-binding. J. Virol. 83, 3365-3373 (2009). 

Sennhauser, G., Bukowska, MA., Briand, C. & Grütter, MG. Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa. J Mol Biol 389, 134-145 (2009).

Sharma, SK., Christen, P. & Goloubinoff, P. Disaggregating chaperones: an unfolding story. Curr Protein Pept Sci. 10, 432-446 (2009).

Su, XC, Ozawa, K, Yagi, H, Lim, SP, Wen, D, Ekonomiuk, D, Huang, D, Keller, TH, Sonntag, S, Caflisch, A, Vasudevan, SG & Otting G. NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS J.  276, 4244-4255 (2009).

Vašák, M. & Meloni, G., in Metallothioneins and Related Chelators, Metallothionein-3, Zinc, and Copper in the Central Nervous System, Vol. 5 of 'Metal Ions in Life Sciences'; (A. Sigel, H. Sigel, R. K. O. Sigel, Eds.) 319-351 (The Royal Society of Chemistry, Cambridge, UK, 2009)

Veesler, D., Dreier, B., Blangy, S., Lichiere, J., Tremblay, D., Moineau, S., Spinelli, S., Tegoni, M., Plückthun, A., Campanacci, V. & Cambillau, C. Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode. J Biol Chem. 284, 30718-30726 (2009).

Vorburger T, Stein A, Ziegler U, Kaim G & Steuber J. Functional role of a conserved aspartic acid residue in the motor of the Na(+)-driven flagellum from Vibrio cholerae. Biochim Biophys Acta. 1787, 1198-1204 (2009).

Wagner A. Transposable elements as genomic diseases. Mol. Biosyst. 5, 32-35 (2009).

Wagner A. Evolutionary constraints permeate large metabolic networks. BMC Evol Biol 9, 231 (2009). 

Wagner, A. Networks in molecular evolution. In: Meyers, RA. (ed.), Encyclopedia of complexity and systems science, Part 13. New York, NY, USA, Springer, 5655-5667 (2009).

Wagner, A. Andreas Wagner. In: Oftedal, G. et al (ed.), Evolutionary Theory: 5 questions. Automatic Press/ VIP , ? (2009).

Warmuth, S., Zimmermann, I. & Dutzler, R. X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. Structure 17, 538-546 (2009).

Weinert, C., Grütter, C., Roschitzki-Voser, H., Mittl, PR. & Grütter, M. The crystal structure of human pyrin B30.2 domain: implications for mutations associated with familial mediterranean fever. J Mol Biol. 394, 226-236 (2009).

Winkler, J., Martin-Kilias,P., Plückthun,A. & Zangemeister-Wittke, U. EpCAM-targeted delivery of nanocomplexed siRNA to tumor cells with designed ankyrin repeat proteins. Mol Cancer Ther. 8, 2674-2683 (2009).

Wu, F. & Gehring, H. Structural requirements for novel coenzyme-substrate derivatives to inhibit intracellular ornithine decarboxylase and cell proliferation.  FASEB J. 23, 565-574 (2009).

Zhou, T. & Caflisch, A. Data management system for distributed virtual screening. J. Chem. Inf. Model. 49, 145-152 (2009).