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Department of Biochemistry

Publications 2015

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

Huang, D. & Caflisch, A. The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion 9, 412-9 (2015). PMID: 26689486.

Nettels, D., Haenni, D., Maillot, S., Gueye, M., Barth, A., Hirschfeld, V., Hübner, CG., Léonard, J. & Schuler, B. Excited-state annihilation reduces power dependence of single-molecule FRET experiments. Phys Chem Chem Phys 17, 32304-15 (2015). PMID: 26584062.

Zheng, W., Borgia, A., Borgia, MB., Schuler, B. & Best, RB. Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations. J Chem Theory Comput 11, 5543-53 (2015). PMID: 26574341.

Blöchliger, N., Caflisch, A. & Vitalis, A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. J Chem Theory Comput 11, 5481-92 (2015). PMID: 26574336.

Borgia, A., Kemplen, KR., Borgia, MB., Soranno, A., Shammas, S., Wunderlich, B., Nettels, D., Best, RB., Clarke, J. & Schuler, B. Transient misfolding dominates multidomain protein folding. Nat Commun 6, 8861 (2015). PMID: 26572969.

Schuler, B. & Smith, JL. Editorial overview: Biophysical and molecular biological methods: Structure, dynamics, and single molecules. Curr. Opin. Struct. Biol. 34, iv-vi (2015). PMID: 26547527.

Zou, J., Tran, D., Baalbaki, M., Tang, LF., Poon, A., Pelonero, A., Titus, EW., Yuan, C., Shi, C., Patchava, S., Halper, E., Garg, J., Movsesyan, I., Yin, C., Wu, R., Wilsbacher, LD., Liu, J., Hager, RL., Coughlin, S., Jinek, M., Pullinger, CR., Kane, JP., Hart, DO., Kwok, PY. & Deo, RC. An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin. E Elife 4, (2015).  PMID: 26473617.

Bradbury, AR. & Plückthun, A. Getting to reproducible antibodies: the rationale for sequenced recombinant characterized reagents. Protein Eng. Des. Sel. 28, 303-5 (2015). PMID: 26446960.

Fleishman, SJ. & Plückthun, A. Editorial overview: Protein design and evolution-new protein architectures, evolutionary fine-tuning and analysis. Curr. Opin. Struct. Biol. 33, v-vi (2015). PMID: 26433320.

Geertsma, ER., Chang, YN., Shaik, FR., Neldner, Y., Pardon, E., Steyaert, J. & Dutzler, R. Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Nat. Struct. Mol. Biol. 22, 803-808 (2015). PMID: 26367249

Baici, A. Kinetics of Enzyme-Modifier Interactions. Springer 2015. ISBN 9783709114025 • 9783709114018

Zwerger, M., Roschitzki-Voser, H., Zbinden, R., Denais, C., Herrmann, H., Lammerding, J., Grütter, MG. & Medalia, O. Altering lamina assembly identifies lamina-dependent and -independent functions for A-type lamins. J. Cell. Sci. 128, 3607-20 (2015). PMID: 26275827.

Herrmann, US., Schütz, AK., Shirani, H., Huang, D., Saban, D., Nuvolone, M., Li, B., Ballmer, B., Åslund, AK., Mason, JJ., Rushing, E., Budka, H., Nyström, S., Hammarström, P., Böckmann, A., Caflisch, A., Meier, BH., Nilsson, KP., Hornemann, S. & Aguzzi, A. Structure-based drug design identifies polythiophenes as antiprion compounds. Sci Transl Med 7, 299ra123 (2015). PMID: 26246168.

König, I., Zarrine-Afsar, A., Aznauryan, M., Soranno, A., Wunderlich, B., Dingfelder, F., Stüber, JC., Plückthun, A., Nettels, D. & Schuler, B. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nat. Methods 12, 773-9 (2015). PMID: 26147918.

Eibauer, M., Pellanda, M., Turgay, Y., Dubrovsky, A., Wild, A. & Medalia, O. Structure and gating of the nuclear pore complex. Nat Commun 6, 7532 (2015). PMID: 26112706.

Czar, MF., Zosel, F., König, I., Nettels, D., Wunderlich, B., Schuler, B., Zarrine-Afsar, A. & Jockusch, RA. Gas-phase FRET Efficiency Measurements to Probe the Conformation of Mass-Selected Proteins. Anal. Chem. Anal. Chem. 87, 7559-65 (2015). PMID: 26110465.

Merten, H., Brandl, F., Plückthun, A. & Zangemeister-Wittke, U. Antibody drug conjugates for tumor targeting - novel conjugation chemistries and the promise of non-IgG binding proteins.  Bioconjug. Chem. 26, 2176-85 (2015). PMID: 26086208.

Anders, C., Niewoehner, O. & Jinek, M. In Vitro Reconstitution and Crystallization of Cas9 Endonuclease Bound to a Guide RNA and a DNA Target. Meth. Enzymol. 558, 515-37 (2015). PMID: 26068752.

Weinert, C., Morger, D., Djekic, A., Grütter, MG. & Mittl, PR. Crystal structure of TRIM20 C-terminal coiled-coil/B30.2 fragment: implications for the recognition of higher order oligomers. Sci Rep 5, 10819 (2015). PMID: 26043233.

Best, RB., Hofmann, H., Nettels, D. & Schuler, B. Quantitative Interpretation of FRET Experiments via Molecular Simulation: Force Field and Validation. Biophys. J. 108, 2721-31 (2015). PMID: 26039173.

Marchand, JR. & Caflisch, A. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem 10, 1327-33 (2015). PMID: 26033856.

Sedlák, E., Schaefer, JV., Marek, J., Gimeson, P. & Plückthun, A. Advanced Analyses of Kinetic Stabilities of IgGs modified by Mutations and Glycosylation. Protein Sci. 24, 1100-13 (2015). PMID: 25966898.

Harapin, J., Börmel, M., Sapra, KT., Brunner, D., Kaech, A. & Medalia, O. Structural analysis of multicellular organisms with cryo-electron tomography. Nat. Methods 12, 634-6 (2015). PMID: 25961413.

Blöchliger, N., Xu, M. & Caflisch, A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophys. J. 108, 2362-70 (2015). PMID: 25954893.

Bukowska, MA., Hohl, M., Geertsma, ER., Hürlimann, LM., Grütter, MG. & Seeger, MA. A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter. Biochemistry 54, 3086-99 (2015). PMID: 25947941.

Dubrovsky, A., Sorrentino, S., Harapin, J., Sapra, KT. & Medalia, O. Developments in cryo-electron tomography for in situ structural analysis. Arch. Biochem. Biophys. 581, 78-85 (2015). PMID: 25921875.

Zhao, H. & Caflisch, A. Current kinase inhibitors cover a tiny fraction of fragment space. Bioorg. Med. Chem. Lett. 25, 2372-6 (2015). PMID: 25911301.

Bradbury, AM. & Plückthun, A. Antibodies: validate recombinants once. Nature 520, 295 (2015). PMID: 25877194.

Ewald, C., Christen, MT., Watson, RP., Mihajlovic, M., Zhou, T., Honegger, A., Plückthun, A., Caflisch, A. & Zerbe, O. A Combined NMR and Computational Approach to Investigate Peptide Binding to a Designed Armadillo Repeat Protein.  J. Mol. Biol. 427, 1916-33 (2015). PMID: 25816772.

Baltimore, D., Berg, P., Botchan, M., Carroll, D., Charo, RA., Church, G., Corn, JE., Daley, GQ., Doudna, JA., Fenner, M., Greely, HT., Jinek, M., Martin, GS., Penhoet, E., Puck, J., Sternberg, SH., Weissman, JS. & Yamamoto, KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 348, 36-8 (2015). PMID: 25791083.

Brandmann, T. & Jinek, M. Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3. Proteins 83, 997-1002 (2015). PMID: 25758703.

Hillenbrand, M., Schori, C., Schöppe, J. & Plückthun, A. Comprehensive analysis of heterotrimeric G-protein complex diversity and their interactions with GPCRs in solution. Proc. Natl. Acad. Sci. U.S.A. 112, E1181-90 (2015). PMID: 25733868.

Friedel, T., Hanisch, LJ., Muth, A., Honegger, A., Abken, H., Plückthun, A., Buchholz, CJ. & Schneider, IC. Receptor-targeted lentiviral vectors are exceptionally sensitive toward the biophysical properties of the displayed single-chain Fv. Protein Eng. Des. Sel. 28, 93-106 (2015). PMID: 25715658.

Huang, D. & Caflisch, A. Evolutionary Conserved Tyr169 Stabilizes the β2-α2 Loop of the Prion Protein. J. Am. Chem. Soc. 137, 2948-57 (2015). PMID: 25671636.

Münch, RC., Muth, A., Muik, A., Friedel, T., Schmatz, J., Dreier, B., Trkola, A., Plückthun, A., Büning, H. & Buchholz, CJ. Off-target-free gene delivery by affinity-purified receptor-targeted viral vectors. Nat Commun 6, 6246 (2015). PMID: 25665714.

Holehouse, AS., Garai, K., Lyle, N., Vitalis, A. & Pappu, RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J. Am. Chem. Soc. 137, 2984-95 (2015). PMID: 25664638.

Yuan, H., Gaiduk, A., Siekierzycka, JR., Fujiyoshi, S., Matsushita, M., Nettels, D., Schuler, B., Seidel, CA. & Orrit, M. Temperature-cycle microscopy reveals single-molecule conformational heterogeneity. Phys Chem Chem Phys 17, 6532-44 (2015). PMID: 25659944.

Sorrentino, S., Studt, JD., Medalia, O. & Tanuj Sapra, K. Roll, adhere, spread and contract: Structural mechanics of platelet function. Eur. J. Cell Biol. 94, 129-38 (2015). PMID: 25655000.

Bradbury, A. & Plückthun, A. Reproducibility: Standardize antibodies used in research. Nature 518, 27-9 (2015). PMID: 25652980.

Benke, S., Roderer, D., Wunderlich, B., Nettels, D., Glockshuber, R. & Schuler, B. The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 6, 6198 (2015). PMID: 25652783.

Oude Blenke, E., Klaasse, G., Merten, H., Plückthun, A., Mastrobattista, E. & Martin, NI. Liposome functionalization with copper-free "click chemistry". J Control Release 202, 14-20 (2015). PMID: 25626085.

Dong, J., Zhao, H., Zhou, T., Spiliotopoulos, D., Rajendran, C., Li, XD., Huang, D. & Caflisch, A. Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Med Chem Lett 6, 79-83 (2015). PMID: 25589935.

Plückthun, A. Designed Ankyrin Repeat Proteins (DARPins): Binding Proteins for Research, Diagnostics, and Therapy. Annu. Rev. Pharmacol. Toxicol. 55, 489-511 (2015). PMID: 25562645.

Müller, CS., Knehans, T., Davydov, DR., Bounds, PL., von Mandach, U., Halpert, JR., Caflisch, A. & Koppenol, WH. Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations. Biochemistry  54, 711-21 (2015. PMID: 25545162.

Verdurmen, WP., Luginbühl, M., Honegger, A. & Plückthun, A. Efficient cell-specific uptake of binding proteins into the cytoplasm through engineered modular transport systems. J Control Release 200, 13-22 (2015). PMID: 25526701.

Salvati Manni, L., Zabara, A., Osornio, YM., Schöppe, J., Batyuk, A., Plückthun, A., Siegel, JS., Mezzenga, R. & Landau, EM. Phase behavior of a designed cyclopropyl analogue of monoolein: implications for low-temperature membrane protein crystallization. Angew. Chem. Int. Ed. Engl. 54, 1027-31 (2015). PMID: 25418121.

Goldstein, R., Sosabowski, J., Livanos, M., Leyton, J., Vigor, K., Bhavsar, G., Nagy-Davidescu, G., Rashid, M., Miranda, E., Yeung, J., Tolner, B., Plückthun, A., Mather, S., Meyer, T. & Chester, K. Development of the designed ankyrin repeat protein (DARPin) G3 for HER2 molecular imaging. Eur. J. Nucl. Med. Mol. Imaging 42, 288-301 (2015). PMID: 25391547.

Egloff, P., Deluigi, M., Heine, P., Balada, S. & Plückthun, A. A cleavable ligand column for the rapid isolation of large quantities of homogeneous and functional neurotensin receptor 1 variants from E. coli. Protein Expr. Purif. 108, 106-14 (2015). PMID: 25461958.

Gruenbaum, Y. & Medalia, O. Lamins: the structure and protein complexes. Curr. Opin. Cell Biol. 32, 7-12 (2015). PMID: 25460776.

Marino, J., Hohl, M., Seeger, MA., Zerbe, O. & Geertsma, ER. Bicistronic mRNAs to enhance membrane protein overexpression. J. Mol. Biol. 427, 943-54 (2015). PMID: 25451035.

Bacci, M., Vitalis, A. & Caflisch, A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim. Biophys. Acta 1850, 889-902 (2015). PMID: 25193737.

Zhao, H. & Caflisch, A. Molecular dynamics in drug design. Eur J Med Chem 91C, 4-14 (2015). PMID: 25108504.