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Department of Biochemistry

Publications 2008

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

Bjelic,  S. & Jelesarov, I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J. Mol. Recognit. 21, 289-312 (2008).

Bjelic, S., Wieninger, S., Jelesarov, I. & Karshikoff, A. Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study. Proteins 70, 810-822 (2008).

Bragg, JG. & Wagner, A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 2008, Nov. 14 (Epub ahead of print)

Coutelier, M., Andries, S., Ghariani, S., Dan, B., Duyckaerts, C., van Rijckevorsel, K., Raftopoulos, C., Deconinck, N., Sonderegger, P., Scaravilli, F., Vikkula, M. & Godfraind, C. Neuroserpin mutation causes electrical status epilepticus of slow-wave sleep. Neurology 71, 64-66 (2008).

Cui, T., Gao, Y., Ang, CX., Puah, CM., Gutte, B. & Lam, Y. Hydrogen peroxide enhances enterokinase-catalysed proteolytic cleavage of fusion protein. Recent Pat. Biotechnol. 2, 189-190 (2008).

Curioni-Fontecedro, A., Knights, AJ., Tinguely, M., Nuber, N., Schneider, C., Thomson, CW., von Boehmer, L., Bossart, W., Pahlich, S.,  Gehring, H., Moch, H., Renner, C., Knuth, A.  & Zippelius, A. MAGE -C1/CT7 is the dominant cancer-testis antigen targeted by humoral immune responses in patients with multiple myeloma. Leukemia 22, 1646-1648 (2008).

Dey, F. & Caflisch, A. Fragment-based de novo ligand design by multiobjective evolutionary optimization. J. Chem. Inf. Model. 48, 679-690 (2008).

Eidam, O., Dworkowski, FS., Glockshuber, R., Grütter, MG & Capitani, G. Crystal structure of the ternary FimC-FimF(T)-FimD(N) complex indicates conserved pilus chaperone-subunit complex recognition by the usher FimD. FEBS Lett582, 651-655 (2008).

Felix, M. & Wagner, A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity 100, 132-140 (2008).

Ferrada, E. & Wagner, A. Protein robustness promotes evolutionary innovations in large evolutionary time-scales. Proceedings. Biological Sciences/ Royal Society 275, 1595-1602 (2008).

Frey, D., Huber, T., Plückthun, A. & Grütter, MG. Structure of the recombinant antibody Fab fragment f3p4. Acta Crystallogr D Biol Crystallogr64, 636-643 (2008).

Friedmann, R. & Caflisch, A. Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins 73, 814-827 (2008).

Frischknecht, R., Fejtova, A., Viesti, M., Stephan, A. & Sonderegger, P. Activity-induced synaptic capture and exocytosis of the neuronal serine protease neurotrypsin. J. Neurosci. 28, 1568-1579 (2008).

Fuller, A., Wagner, A. & Enquist, J. Using network analysis to chracterize forest structure. Natural Resources Modeling 21, 225-247 (2008).

Grimshaw, JP., Stirnimann, C., Brozzo, MS., Malojcic, G., Grütter, MG., Capitani, G. & Glockshuber, R. DsbL and DsbI form a specific dithiol oxidase system for periplasmic arylsulfate sulfotransferase in uropathogenic Escherichia coli. J. Mol. Biol. 18, 667-680 (2008).

Grütter, C., Wilkinson, T., Turner, R., Podichetty, S., Finch, D., Mc Court, M., Loning, S., Jermutus, L. & Grütter, MG. A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions. PNAS USA 105, 20251-20256 (2008).

Gutte, B. Solid-phase synthesis for a lifetime. Biopolymers. 90, 215 (2008).

Haberthür, U. & Caflisch , A. FACTS: Fast analytical continuum treatment of solvation. J. Computat. Chem29, 701-715 (2008). 

Hartmann, C., Chami, M., Zachariae, U., de Groot, BL., Engel, A. & Grütter, MG. Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J. Mol. Biol. 377, 352-363 (2008).

Hilf, R. & Dutzler, R. X-ray structure of a prokaryotic pentameric ligand-gated channel. Nature 452, 375-379 (2008).

Hillger, F., Hänni, D., Nettels, D., Geister, S., Grandin, M., Textor, M. & Schuler, B. Probing Protein-Chaperone Interactions with Single-Molecule Fluorescence Spectroscopy. Angew Chem Int Ed Engl47, 6184-6188 (2008).

Honegger, A. Engineering antibodies for stability and efficient folding. in: Handb. Exp. Pharmacol. 181, 47-68 (2008).  

Ihalainen, JA., Paoli, B., Muff, S., Backus, EH., Bredenbeck, J., Woolley, GA., Caflisch, A. & Hamm, P. Alpha-Helix folding in the presence of structural constraints. PNAS USA 195, 9588-9593 (2008).

Interlandi, G., Wetzel, S.K., Settani, G. , Plückthun, A. & Caflisch, A. Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. J. Mol. Biol375, 837-854 (2008).

Interlandi, G. Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations. Proteins: Structure, Function, Bioinformatics,  Epub ahead of print (2008).

Ishihara, H., Kubota, H., Lindberg, RL., Leppert, D., Gloor, SM., Errede, M., Virgintino, D., Fontana, A., Yonekawa, Y. & Frei, K. Endothelial cell barrier impairment induced by glioblastomas and transforming growth factor beta2 involves matrix metalloproteinases and tight junction proteins. J. Neuropathol. Exp. Neurol. 67, 435-448 (2008).

Jelesarov, I. & Karshikoff, A. Meet to fold: the peculiar folding of oligomeric proteins. Biotechnology and Biotechnological Equipment 22, 598-605 (2008).

Jorg, T., Martin, OC. & Wagner, A. Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinformatics 9, 464 (2008).

Kane, AS., Hoffmann, A., Baumgärtel, P., Seckler, R., Reichardt, G., Horsley, DA., Schuler, B. & Bakajin, O. Microfluid mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy. Anal. Chem. 80, 9534-9541 (2008).

Karotki, A. & Vasak. M. Interaction of metallothionein-2 with platinum-modified 5'-guanosine monophosphate and DNA. Biochemistry 47, 10961-10969 (2008).

Karshikoff, A. & Jelesarov, I. Salt bridges and conformational flexibility: effect on protein stability. Biotechnology and Biotechnological Equipment 22, 606-611 (2008).

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 (2008).

Kolb, P., Huang, D.,  Dey, F. & Caflisch, A. Discovery of kinase inhibitors by high-throughput docking and  scoring based on a transferable linear interaction energy model. J. Med. Chem51, 1179-1188 (2008). 

Kolb, P., Kipouros, CB., Huang, D. & Caflisch, A. Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors. Proteins 73, 11-18 (2008). 

Krivov, SV., Muff, S., Caflisch, A. & Karplus, M. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B. 112, 8701-8714 (2008).

Lebeurrier, N., Launay, S., Macrez, R., Maubert, E., Legros H., Leclerc, A., Jamin, SP., Picard, JY., Marret, S. Laudenbach, V., Berger, P., Sonderegger, P., Ali, C., di Clemente, N. & Vivien, D. Anti-Mullerian-hormone-dependent regulation of the brain serine-protease inhibitor neuroserpin. J Cell Sci. 121, 3357-3365 (2008).

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. (2008) Epub ahead of print

Lin, PC., Puhar, A. & Steuber, J. NADH oxidation drives respiratory Na(+) transport in mitochondria from Yarrowia lipolytica. Arch Microbiol. 190, 471-480 (2008).

Martin, OC. & Wagner, A. Multifunctionality and robustness trade-offs in model genetic circuits. Biophys J. 94, 2927-2937 (2008).

Meloni, G., Sonois, V., Delaine, T., Guilloreau, L., Gillet, A., Teissié, J., Faller, P. & Vasak. M. Metal swap between Zn7-metallothionein-3 and amyloid-beta-Cu protects against amyloid-beta toxicity. Nat Chem Biol. 4, 366-372 (2008).

Merz, T., Wetzel, SK., Firbank, S., Plückthun, A., Grütter, MG. & Mittl, PR. Stabilizing Ionic Interactions in a Full-Consensus Ankyrin Repeat Protein. J.Mol. Biol. 376, 231-240 (2008).

Muff, S. & Caflisch, A. Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins. 70, 1185-1195 (2008).

Mukhopadhyay D., Howell, KS., Riezmann, H. & Capitani, G. Sphinganine-1-phosphate lyase: Identifying key residues for function in vivo and in vitro. J Biol Chem. 283, 20159-20169 (2008).

Narzi, D., Siu, SW., Stirnimann, CU., Grimshaw, JP., Glockshuber, R., Capitani, G. & Böckmann, RA. Evidence for proton shuffling in a thioredoxin-like protein during catalysis. J Mol Biol. 382, 978-986 (2008).

Nettels, D., Hoffmann, A. & Schuler, B. Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. J Phys Chem B. 112, 6137-6146 (2008).

Okhrimenko, O. & Jelesarov, I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J. Mol. Recognit. 21, 1-19 (2008).

Orihuela, R., Domènech, J., Bofill, R., You, C., Kägi, JH., Capdevila, M. & Atrian, S. The metal-binding features of the recombinant mussel Mytilus edulis MT-10-IV metallothionein. J Biol Inorg Chem. 13, 801-812 (2008).  

Pahlich, S. Zakaryan, RP. & Gehring, H. Identification of proteins interacting with protein arginine methyltransferase 8: The Ewing sarcoma (EWS) protein binds independent of its methylation state. Proteins 72, 1125-1137 (2008).

Parmeggiani, F., Pellarin, R., Larsen, AP:, Varadamsetty, G., Stumpp, MT., Zerbe, O., Caflisch, A. & Plückthun, A. Designed Armadillo Repeat Proteins as general peptide-binding scaffolds: consensus design and computational optimization of hydrophobic core. J. Mol. Biol. 378, 1282-1304 (2008).  

Puorger, C., Eidam, O., Capitani, G., Erilov, D., Grütter, M. & Glockshuber, R. Infinite kinetic stability against dissociation of supramolecular protein complexes through donor strand complementation. Structure 16, 631-642 (2008).

Reif, R., Sales, S., Dreier, B., Lüscher, D., Wölfel, J., Gisler, C., Baici, A., Kunz, B. & Sonderegger, P. Purification and enzymological characterization of murine neurotrypsin. Protein Expr. Purif. 61, 13-21 (2008).

Rindler, MJ., Xu, CF., Gumper, I., Cen, C., Sondergger, P. & Neubert, TA. Calsynthenins are secretory granule proteins in anterior pituitary gland and pancreatic islet alpha cells. J. Histochem. Cytochem56, 381-388 (2008).

Rothe, C., Urlinger, S., Löhning, C., Prassler, J., Stark, Y., Jäger, U., Hubner, B., Bardroff, M., Pradel, I., Boss, M., Bittlingmaier, R., Bataa, T., Frisch, C., Brocks, B., Honegger, A. & Urban, M. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J Mol Biol 376, 1182-1200 (2008).

Sarkar, CA., Dodevski, I.,Kenig, M., Dudli, S., Mohr, A., Hermans, E. & Plückthun, A. Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity. PNAS USA 105, 14808-14813 (2008).

Schenker, P., Alfarano, P., Kolb, P., Caflisch, A. & Baici, A. A double-headed cathepsin B inhibitor devoid of warhead. Protein Sci. 17, 2145-2155 (2008). 

Schuetz, P. & Caflisch, A. Efficient modularity optimization by multi-step greedy algorithm and vertex mover refinement. Phys. Rev. E 77, 046112 (2008).

Schuetz, P. & Caflisch, A. Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. Phys. Rev. E 78, 026112 (2008). 

Schuler, B. Single molecule spectroscopy in protein folding: from ensembles to single molecules. In: Protein Folding, Misfolding and Aggregation (ed. Munoz, V.) Cambridge, UK, p. 139-160 (2008).

Schuler, B. & Eaton, WA. Protein folding studied by single-molecule FRET. Curr. Opin. Struct. Biol. 18, 16-26 (2008).

Sennhauser, G. & Grütter, M. Chaperone-assisted crystallography with DARPins. Structure 16, 1443-1453 (2008).

Sharma, SK., Goloubinoff,  P. & Christen P. Heavy metal ions are potent inhibitors of protein folding. Biochem Biophys Res Commun. 372, 341-345 (2008).

Stallmach, R. & Gloor, SM. Neurobin/TMPRSS 11c, a novel type II transmembrane serine protease that cleaves fibroblast growth factor-2 in vitro. Biochem. J. 412, 81-91 (2008).

Steiner, D., Forrer, P. & Plückthun, A. Efficient selection of DARPins with sub-nanomolar affinities using SRP phage display. J Mol Biol 382, 1211-1227(2008).

Stephan, A., Mateos, JM., Kozlov, SV., Cinelli, P., Kistler, AD., Hettwer, S., Rülicke, T. , Streit, P., Kunz, B. & Sonderegger, P. Neurotrypsin cleaves agrin locally at the synpase. FASEB J. 22, 1861-1873 (2008). 

Tao, M., Casutt, M. & Steuber, J. Oxidant-induced formation of a neutral flavosemiquinone in the Na(+)-translocating NADH:Quinone oxidoreductase (Na(+)-NQR) from Vibrio cholerae. Biochim Biophys Acta. 1777, 696-702 (2008).

Tao, M., Fritz, G. & Steuber, J. The Na+ -translocating NADH:quinone oxidoreductase (Na+ -NQR) from Vibrio cholerae enhances insertion of FeS in overproduced NqrF subunit. J. Inorg. Biochem. 102, 1366-1372 (2008).

Vacca, RA., Giannattasio, S., Capitani, G., Marra, E.  & Christen, P. Molecular evolution of B6 enzymes: Binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B6 protoenzyme. BMC Biochem. 9, 17 (2008).

Vamvaca, K., Jelesarov, I & Hilvert, D. Kinetics and thermodynamics of ligand binding to a molten globular enzyme and its native counterpart. J Mol Biol. 382, 971-977 (2008).

Vašák, M. & Meloni, G., in Metallothioneins in Biochemistry and Pathology, Metallothionein Structure and Reactivity (P. Zatta Ed.) 1-24 (World Scientific Publishing, Singapore, 2008).

Wagner, A. Neutralism and selectionism: a network-based reconciliation. Nat. Rev. Genet. 9, 965 -974 (2008).

Wagner, A. Gene duplications, robustness and evolutionary innovations. Bioessays 30, 367-373 (2008).

Wagner, A. Robustness and evolvability: a paradox resolved. Proc Biol Sci. 275, 91-100 (2008).

Wagner, A. & de la Chaux. N. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol Genet Genomics 280, 397-408 (2008).  

Wahl, M., Rahn, HJ., Röhlicke, T., Kell, G., Nettels, D., Hillger, F., Schuler, B. & Erdmann, R. Scalable time-correlated photon counting system with multiple independent input channels. Rev. Sci. Instrum. 79, 123113-1 - 123113-8 (2008).

Wetzel SK., Settani, G., Kenig. M., Binz, HK. & Plückthun, A. Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J. Mol. Biol376, 241-257 (2008). 

Wright, J. & Wagner, A. The Systems Biology Research Tool: evolvable open-source software. BMC Syst Biol. 2, 55 (2008).

Wright, J. & Wagner, A. Exhaustive identification of steady state cycles in large stochiometric networks. BMC Syst Biol. 2, 61 (2008).

Wu, F. & Gehring, H. Structural requirements for novel coenzyme-substrate derivatives to inhibit intracellular ornithine decarboxylase and cell proliferation.  FASEB J. , Oct15 Epub ahead of print (2008).

Wu, F., Yu, J. & Gehring, H. Inhibitory and structural studies of novel coenzyme-substrate analogs of human histidine decarboxylase. FASEB J.  22, 890-897 (2008).

Zhou, T. & Caflisch, A. Data management system for distributed virtual screening. J. Chem. Inf. Model. 2008 Dec 12. [Epub ahead of print] (2008).

Zhou, T., Huang, D. & Caflisch, A. Is quantum mechanics necessary for the predicting binding free energy? J. Med. Chem. 51, 4280-4288 (2008).