Publikationen 2009

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., 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. & 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., 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, 135-147 (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).