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Department of Biochemistry

Publications 2007

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

Alioth, S., Meyer, S., Dutzler, R., & Pervushin, K. The Cytoplasmic Domain of the Chloride Channel ClC-0: Structural and Dynamic Characterization of Flexible Regions. J. Mol. Biol. 369,1163-1169 (2007).

Best, RB., Merchant, KA., Gopich, IV., Schuler, B., Bax, A. & Eaton, WA. Effect of flexibility and cis residues in single-molecule FRET studies of polyproline. PNAS U.S.A. 104, 18964-18969 (2007).

Bragg, J.G. &  Wagner A. Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proc. Biol. Sci. 274, 1063-70 (2007).

Braun, O., Knipp, M., Chesnov, S., and Vasak, M. Specific reactions of S-nitrosothiols with cysteine hydrolases: A comparative study between dmethylargininase-1 and CTP synthetase, Protein Sci. 16, 1522-1534 (2007).

Ciliberti, S, Martin, OC & Wagner, A. Innovation and robustness in complex regulatory gene networks. PNAS U.S.A. 104, 13591-13596 (2007).

Ciliberti, S, Martin, OC & Wagner, A. Robustness can evolve gradually in complex regulatory networks with varying topology. PLoS Computational Biology 3(2), e15 (2007).

Cui, T., Gao, Y., Puah, CM & Gutte, B. Efficient preparation of an acyclic permutant of kalata B1 from a recombinant fusion protein with thioredoxin. J. Biotechnol. 130, 378-384 (2007).

Dutzler R. A structural perspective on ClC channel and transporter function. FEBS Lett. 581, 2839-2844 (2007).

Friedmann, R. & Caflisch, A. The protonation state of the catalytic aspartates in plasmepsin II. FEBS Lett. 581, 4120-4124 (2007).

Galliciotti, G., Glatzel, M., Kinter, J., Kozlov, SV., Cinelli, P., Rulicke, T. & Sonderegger, P. Accumulation of mutant neuroserpin precedes development of clinical symptoms in familial encephalopathy with neuroserpin inclusion bodies. Am. J. Pathol. 170, 1305-13 (2007).

Gemperli, A.C., Schaffitzel, C., Jacob, C. & Steuber, J. Transport of Na+ and K+ by an antiporter-related subunit from the Escherichia coli NADH dehydrogenase I produced in Saccharomyces cerevisiae. Arch. Microbiol. 188, 509-521 (2007).  

Georgiev, O. & Jelesarov, I. Energetics of peptide recognition by the second PDZ domain of human protein tyrosine phosphatase 1E. Biochemistry 46, 1064-1078 (2007). 

Gfeller, D.,  De Los Rios, P . Caflisch, A.  &  Rao, F. Complex network analysis of free-energy landscapes. PNAS U.S.A. 104,1817-1822 (2007).

Gorfe, A. & Caflisch, A. Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: Implication for conversion and species barrier. FASEB J. 21, 3279-32787 (2007).

Göschke, R., Stutz, Rasetti V., Cohen, NC., Rahuel , J., Rigollier, P., Baum, HP., Forgiarini, P., Schnell, CR., Wagner, T., Grütter, MG., Fuhrer, W., Schilling, W., Cumin, F., Wood, JM. & Maibaum, J. Novel 2.7-dialkyl-substituted 5 (S) amino-4(S)-hydroxy-8-phenyl-octanecarboxamide transition state peptidomimetics are potent and orally active inhibitors of human renin. J. Med.Chem. 50, 4818-4831 (2007).

Gourfinkel-An, I., Duyckaerts, C., Camuzat, A., Meyrignac, C., Sondergger, P., Baulac, M. & Brice, A. Clinical and neuropathologic study of a French family with a mutation in the neuroserpin gene. Neurology 69, 79-83 (2007).

Hillger, F., Nettels, D., Dorsch, S. & Schuler B. Detection and Analysis of Protein Aggregation with Confocal Single Molecule Fluorescence Spectroscopy. J. Fluoresc. 17, 759-765 (2007).

Hoffmann, A., Kane, A.,Nettels, D., Hertzog, D., Baumgärtel, P., Lengefeld, J., Reichardt, G., Horsley, D.A., Seckler, R., Bakajin, O & Schuler, B. Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. PNAS U.S.A. 104, 105-110 (2007).

Huber, T., Steiner, D., Rothlisberger, D., Plückthun, A. In vitro selection and characterization of DARPins and Fab fragments for the co-crystallization of membrane proteins: The Na(+)-citrate symporter CitS as an example. J. Struct. Biol. 159, 206-211 (2007).

Hussain, S., Plückthun, A., Allen, TM. & Zangenmeister-Wittke, U. Antitumor activity of an epithelial cell adhesion molecule targeted nanovesicular drug delivery system. Mol. Cancer Ther. 6, 3019-3027 (2007).

Jelesarov, I. & Bosshard, HR. Isothermal titration calorimetry in studies of protein binding and protein conformational transitions. In "Protein Structures: Methods in Protein Structure Analysis." (Uversky, V. N. and E. A. Permyakov, Eds.), Nova Science Publishers, Inc., Hauppauge, N. Y. Chapter 1.2, pp. 29-55 (2007).

Knipp, M., Karotki, A. V., Chesnov, S., Natile, G., Sadler, P.J., Brabec, V., and Vasak, M. The reaction of Zn7metallothionein with cis- and trans-[Pt(N-donor)2Cl2] anticancer complexes: Trans-PtII complexes retain their N-donor ligands. J. Med. Chem. 50, 4075-4086 (2007).

Koch, M., Bhattacharya, S., Kel, T., Gimona, M., Vasak, M., Chazin, W., Heizmann, C.W., Kroneck, P.M. & Fritz, G. Implications on zinc binding to S100A2. Biochim. Biophys. Acta. 1773, 457-70 (2007).

Kolly,R., Thiel, M.A., Herrmann, T. & Plückthun, A. Monovalent antibody scFv fragments selected to modulate T-cell activation by inhibition of CD86-CD28 interaction. Protein Eng. Des. Sel. 20, 91-98 (2007).
Lin, P.-C.,Türk, K.,Häse, C.C.,Fritz, G.& Steuber, J. Quinone reduction by the Na+ -translocating NADH dehydrogenase (Na+-NQR) promotes extracellular superoxide production in Vibrio cholerae. J. Bacteriol. 189, 3902-3908 (2007).

Maibaum J., Stutz, S., Göschke, R., Rigollier, P., Yamaguchi, Y., Cumin, F., Rahuel, J., Baum, HP., Cohen, NC., Schnell, C., Fuhrer, W., Grütter, M., Schillinh, W. & Wood, J. Structural modification of the P2' position of 2,7-dialkyl-substituted 5 (S) amino-4(S)-hydroxy-8-phenyl-octanecarboxamides: the discovery of aliskiren, a potent nonpeptide human renin inhibitor active after once daily dosing in marmosets. J. Med.Chem. 50, 4832-4844 (2007).

Markovic, S. & Dutzler, R. The Structure of the Cytoplasmic Domain of the Chloride Channel ClC-Ka Reveals a Conserved Interaction Interface. Structure 15, 715-725 (2007).

Meyer-Andrejszki, L., Bjelic, S., Naud, JF., Lavigne, P. & Jelesarov, I.Thermodynamics of b-HLH-LZ protein binding to DNA: the energetic importance of protein-DNA contacts in site-specific E-box recognition by the complete gene product of the Max p21 transcription factor. Biochemistry 46, 12427-12440 (2007).

Meloni G., Faller P. & Vasak M.   Redox silencing of copper in metal-linked neurodegenerative disorders: reaction of Zn7metallothionein-3 with Cu2+ ions. J. Biol. Chem. 282, 16068-16078 (2007).

Meyer S., Savaresi S., Forster I.C. & Dutzler R. Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5. Nat. Struct. Mol. Biol. 14, 60-67 (2007).

Milev, S., Bjelic, S., Georgiev, O. & Jelesarov, I. Energetics of peptide recognition by the second PDZ domain of human protein tyrosine phosphatase 1E. Biochemistry 46, 1064-1078 (2007).

Mittl, P.R. & Schneider-Brachert, W. Sel1-like repeat proteins in signal transduction. Cell Signal 19, 20-31 (2007).

Morfill, J., Blank, K.,  Zahnd, C., Luginbühl, B., Kuhner, F., Gottschalk, K.E., Plückthun, A. & Gaub, H.E. Affinity-matured recombinant antibody fragments analyzed by single force spectroscopy. Biophys. J. 93, 3583-3490 (2007).

Mortl, M., Sonderegger, P., Diederichs, K. & Welte, W. The crystal structure of the ligand-binding module of human TAG-1 suggests a new mode of homophilic interaction. Protein Sci. 16, 2174-2183 (2007).

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: Struct. Funct. Bioinf. 70, 1185-1195 (2007).

Nettels, D., Gopich, V.I., Hoffmann, A. & Schuler, B. Ultrafast dynamics of protein collapse from single molecule photon statistics. PNAS U.S.A. 104, 2655-2660 (2007).

Nettels, D. & Schuler, B. Subpopulation-resolved photon statistics of single-molecule energy transfer dynamics. IEEE J. Sel. Top. Quant. Electron. 13, 990-995 (2007)

Novinec, M., Grass R.N., Stark, W. J., Turk, V., Baici, A. & Lenaric, B. Interaction between human cathepsins K,L and S and elastins: Mechanism of elastinolysis and inhibition by macromolecular inhibitors. J. Biol. Chem282, 7893-7902(2007).

Ogura M., Perez, JC., Mittl, PR., Lee, HK., Dailide, G., Tan, S., Ito, Y., Secka, O., Dailidiene, D., Putty, K., Berg, DE. & Kalia, A. Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes. PLoS Comput. Biol. 3, e151 (2007).

Papin, S., Cuenin, S., Agostini, L., Martinon, F., Werner, S., Beer, HD., Grütter, C., Grütter, M. & Tschopp J. The SPRY domain of Pyrin, mutated in familial Mediterranean fever patients, interacts with inflammasome components and inhibits proIL-1beta processing. Cell Death Differ. 14, 1457-1466 (2007).

Rao, F., Settanni, G. & Caflisch A. Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding. Methods Mol. Biol. 350, 225-49 (2007).

Reif, R., Sales, S., Hettwer, S., Dreier, B., Gisler, C., Wölfel, J., Lüscher, D., Zurlinden, A., Stephan, A., Ahmed, S., Baici, A., Ledermann, B., Kunz, B. & Sondergger, P. Specific cleavage of agrin by neurotrypsin, a synaptic protease linked to mental retardation. FASEB J. 21, 3468-3478 (2007).

Schroeder, V.,Vuissoz, J.M, Caflisch, A. & Kohler, H.P Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form. Thrombosis and Haemostasis 97, 890-898 (2007).

Schubert, M., Lapouge, K., Duss, O., Oberstrass, F.C., Jelesarov, I., Haas, D. & Allain, F.H. Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat. Struct. Mol. Biol. 14, 807-813 (2007).

Schuler, B., Application of Single Molecule Förster Resonance Energy Transfer to Protein Folding. in: Protein Folding Protocols (Humana Press; Bai, Nussinov, Eds.), Methods Mol Biol 350, 115–138 (2007).

Schweizer, A., Roschitzki-Voser, H., Amstutz, P., Briand, C., Gulotti-Georgieva, M., Prenosil, E., Binz, HK., Capitani, G., Baici, A., Plückthun, A. & Grütter MG. Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism. Structure 15,625-636 (2007).

Seeber, M., Cecchini, M., Rao, F., Settanni, G. & Caflisch, A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics  23, 2625-2627 (2007).

Sennhauser, G., Amstutz, P., Briand, C., Storchenegger, O., & Grütter, M.G. Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PloS Biol . 5, e7 (ePub), (2007).

Sonderegger, P. & Patty, L. Comment on "Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila". Science 16,1698 (2007)

Steinmetz, MO., Jelesarov, I., Matousek, WM., Honnappa, S., Jahnke, W., Missimer, JH., Frank, S., Alexandrescu, AT. & Kammerer RA. Molecular basis of coiled-coil formation. PNAS U.S.A. 104, 7062-7067 (2007).

Sumedha, M., Martin, OC. & Wagner, A. New structural variaton in evolutionary searches of RNA neutral networks. Biosystems 90, 475-485 (2007).

Tartaglia, G.  & Caflisch, A.. Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins: Struct. Funct. Bioinf. 68, 273-278 (2007).

Taussig, M. J., Stoevesandt, O., Borrebaeck, C. A., Bradbury, A. R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T. J., Gloriam, D., Gold, L., Herberg, F. W., Hermjakob, H., Hoheisel, J. D., Joos, T. O., Kallioniemi, O., Koegll, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P. A., Palcy, S., Plückthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D. J., Skerra, A., Templin, M., Ueffing, M., & Uhlen, M. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods 4, 13-17 (2007).

Wagner A. From bit to it: the transformation of information into living matter by metabolic networks. BMC Systems Biology 1, 33 (2007).

Wagner A. Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176, 2451-2463 (2007).

Wagner A. Energy costs constrain the evolution of gene expression. J. Exp. Zoolog. B. Mol. Dev. Evol. 308B, 322-324 (2007).

Wagner, A. Robustness and evolvability: A paradox resolved. Proc. Roy. Soc. London Series B  275, 91-100 (2007).

Wagner, A. & Wright, J Alternative routes and mutational robustness in complex regulatory networks. Biosystems 88, 163-172 (2007).

Wagner, A. Gene networks and natural selection: Is there a network biology? (In: Pagel, M. Pomiankowski, A. (eds.) Evolutionary Genomics and Proteomics, Sinauer Associates, Sunderland, MA, 2007).

Weisbrich, A., Honnappa, S., Jaussi, R., Okhrimenko, O., Frey, D., Jelesarov, I., Akhmanova, A. & Steinmetz, M.O. Structure-function relationship of the CAP-Gly domains. Nat. Struct. Mol. Biol. 14, 959-967 (2007).

Wu, F., Yu, J. & Gehring, H. Inhibitory and structural studies of novel coenzyme-substrate analogs of human histidine decarboxylase. FASEB J.  Oct 26; [Epub ahead of print], 2007.

Wu F., Grossenbacher D. & Gehring H. New transition state–based inhibitor for human ornithine decarboxylase inhibits growth of tumor cells. Mol. Cancer Ther. 6, 1–9 (2007).

Zahnd, C., Wyler, E., Schwenk, JM., Steiner, D., Lawrence, MC., McKern, NM., Pecorari, F., Ward, CW., Joss, TO. & Plückthun, A. A designed ankyrin repeat protein evolved to picomolar affinity to her2. J. Mol. Biol. 369, 1015-1028 (2007).

Zahnd, C., Amstutz, P. & Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat. Methods 4, 269-279 (2007).