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Department of Biochemistry

Publications 2016

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

Schiller CB, Braciak TA, Fenn NC, Seidel UJ, Roskopf CC, Wildenhain S, Honegger A, Schubert IA, Schele A, Lämmermann K, Fey GH, Jacob U, Lang P, Hopfner KP, Oduncu FS. CD19-specific triplebody SPM-1 engages NK and γδ T cells for rapid and efficient lysis of malignant B-lymphoid cells. Oncotarget 7, 83392-83408 (2016) PMID: 27825135.

Spalinger, MR., Kasper, S., Gottier, C., Lang, S., Atrott, K., Vavricka, SR., Scharl, S., Raselli, T., Frey-Wagner, I., Gutte, PM., Grütter, MG., Beer, HD., Contassot, E., Chan, AC., Dai, X., Rawlings, DJ., Mair, F., Becher, B., Falk, W., Fried, M., Rogler, G. & Scharl, M. NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. J. Clin. Invest. 126, 4388 (2016). PMID: 27801679.

Palermo, G., Miao, Y., Walker, RC., Jinek, M. & McCammon, JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Cent Sci 2, 756-763 (2016). PMID: 27800559.

Lim, NK., Lam, AK. & Dutzler, R. Independent activation of ion conduction pores in the double-barreled calcium-activated chloride channel TMEM16A. J. Gen. Physiol. 148, 375-392 (2016). PMID: 27799318.

Reichen, C., Hansen, S., Forzani, C., Honegger, A., Fleishman, SJ., Zhou, T., Parmeggiani, F., Ernst, P., Madhurantakam, C., Ewald, C., Mittl, PR., Zerbe, O., Baker, D., Caflisch, A. & Plückthun, A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. J. Mol. Biol. 428, 4467-4489 (2016). PMID: 27664438.

Arnon, ZA., Vitalis, A., Levin, A., Michaels, TC., Caflisch, A., Knowles, TP., Adler-Abramovich, L. & Gazit, E. Dynamic microfluidic control of supramolecular peptide self-assembly. Nat Commun 7, 13190 (2016). PMID: 27779182.

Spiliotopoulos, D. & Caflisch, A. Fragment-based in silico screening of bromodomain ligands. Drug Discov Today Technol 19, 81-90 (2016). PMID: 27769362.

Roos, M., Pradère, U., Ngondo, RP., Behera, A., Allegrini, S., Civenni, G., Zagalak, JA., Marchand, JR., Menzi, M., Towbin, H., Scheuermann, J., Neri, D., Caflisch, A., Catapano, CV., Ciaudo, C. & Hall, J. A Small-Molecule Inhibitor of Lin28. ACS Chem. Biol. 11, 2773-2781 (2016). PMID: 27548809.

Marchand, JR., Lolli, G. & Caflisch, A. Derivatives of 3-amino-2-methylpyridine as BAZ2B Bromodomain Ligands: in silico Discovery and in crystallo Validation. J. Med. Chem. 59, 9919-9927 (2016). PMID: 27731638.

Reimão-Pinto, M.M., Manzenreither, R.A., Burkard, T.R., Sledz, P., Jinek M, Mechtler K. & Ameres, S.L. Molecular Basis for Cytoplasmic RNA Surveillance by Uridylation-triggered Decay in Drosophila. EMBO J35, 2417-2434 (2016). PMID: 27729457.

Müller, CS., Knehans, T., Davydov, DR., Bounds, PL., von Mandach, U., Halpert, JR., Caflisch, A. & Koppenol, WH. Correction to Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations. Biochemistry 55, 5647 (2016). PMID: 27650703.

Śledź, P. & Jinek, M. Structural insights into the molecular mechanism of the m(6)A writer complex. Elife 5, (2016). PMID: 27627798.

Zheng, W., Borgia, A., Buholzer, K., Grishaev, A., Schuler, B. & Best, RB. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J. Am. Chem. Soc. 138, 11702-13 (2016. PMID: 27583687.

Borgia, A., Zheng, W., Buholzer, K., Borgia, MB., Schüler, A., Hofmann, H., Soranno, A., Nettels, D., Gast, K., Grishaev, A., Best, RB. & Schuler, B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J. Am. Chem. Soc. 138, 11714-26 (2016). PMID: 27583570.

Aznauryan, M., Delgado, L., Soranno, A., Nettels, D., Huang, JR., Labhardt, AM., Grzesiek, S. & Schuler, B. Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR and SAXS. Proc Natl Acad Sci U S A 113, E5389-98 (20169. PMID: 2756640.

Green, AP., Hayashi, T., Mittl, PR. & Hilvert, D. A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme. . Am. Chem. Soc. 138, 11344-52 (2016). PMID: 27500802.

Lindsay, H., Burger, A., Biyong, B., Felker, A., Hess, C., Zaugg, J., Chiavacci, E., Anders, C., Jinek, M., Mosimann, C. & Robinson, MD. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat. Biotechnol. 34, 701-2 (2016). PMID: 27404876.

Ahmad, S., Pecqueur, L., Dreier, B., Hamdane, D., Aumont-Nicaise, M., Plückthun, A., Knossow, M. & Gigant, B. Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Sci Rep 6, 28922 (2016). PMID: 27380724.

Zingerman-Koladko, I., Khayat, M., Harapin, J., Shoseyov, O., Gruenbaum, Y., Salman, A., Medalia, O. & Ben-Harush, K. The assembly of C. elegans lamins into macroscopic fibers. J Mech Behav Biomed Mater 63, 35-43 (2016). PMID: 27341289.

Goricanec, D., Stehle, R., Egloff, P., Grigoriu, S., Plückthun, A., Wagner, G. & Hagn, F. Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding. Proc. Natl. Acad. Sci. U.S.A. 113, E3629-38 (2016). PMID: 27298341.

Brunner, JD., Schenck, S. & Dutzler, R. Structural basis for phospholipid scrambling in the TMEM16 family. Curr. Opin. Struct. Biol. 39, 61-70 (2016). PMID: 27295354.

Bender, RR., Muth, A., Schneider, IC., Friedel, T., Hartmann, J., Plückthun, A., Maisner, A. & Buchholz, CJ. Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment. PLoS Pathog. 12, e1005641 (2016). PMID: 27281338.

Tamaskovic, R., Schwill, M., Nagy-Davidescu, G., Jost, C., Schaefer, DC., Verdurmen, WP., Schaefer, JV., Honegger, A. & Plückthun, A. Intermolecular biparatopic trapping of ErbB2 prevents compensatory activation of PI3K/AKT via RAS-p110 crosstalk. Nat Commun 7, 11672 (2016). PMID: 27255951.

Zhu, J. & Caflisch, A. Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions. J. Med. Chem. 59, 5555-61 (2016). PMID: 27167503.

Schuler, B., Soranno, A., Hofmann, H. & Nettels, D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 45, 207-231 (2016). PMID: 27145874.

Geertsma, ER., Chang, YN., Shaik, FR., Neldner, Y., Pardon, E., Steyaert, J. & Dutzler, R. Corrigendum: Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Nat. Struct. Mol. Biol. 23, 462 (2016). PMID: 27142325.

Burger, A., Lindsay, H., Felker, A., Hess, C., Anders, C., Chiavacci, E., Zaugg, J., Weber, LM., Catena, R., Jinek, M., Robinson, MD. & Mosimann, C. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 143, 2025-37 (2016). PMID: 27130213.

Hanauer, JR., Gottschlich, L., Riehl, D., Rusch, T., Koch, V., Friedrich, K., Hutzler, S., Prüfer, S., Friedel, T., Hanschmann, KM., Münch, RC., Jost, C., Plückthun, A., Cichutek, K., Buchholz, CJ. & Mühlebach, MD. Enhanced lysis by bispecific oncolytic measles viruses simultaneously using HER2/neu or EpCAM as target receptors. Mol Ther Oncolytics 3, 16003 (2016). PMID: 27119117.

Sorrentino, S., Studt, JD., Bokstad Horev, M., Medalia, O. & Sapra, KT. Toward correlating structure and mechanics of platelets. Cell Adh Migr 10, 568-575 (2016). PMID: 27104281.

Spalinger, MR., Kasper, S., Gottier, C., Lang, S., Atrott, K., Vavricka, SR., Scharl, S., Gutte, PM., Grütter, MG., Beer, HD., Contassot, E., Chan, AC., Dai, X., Rawlings, DJ., Mair, F., Becher, B., Falk, W., Fried, M., Rogler, G. & Scharl, M. NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. J. Clin. Invest. 126, 1783-800 (2016). PMID: 27043286.

Zuela, N., Zwerger, M., Levin, T., Medalia, O. & Gruenbaum, Y. Impaired mechanical response of an EDMD mutation leads to motility phenotypes that are repaired by loss of prenylation. J. Cell. Sci. 129, 1781-91 (2016). PMID: 27034135.

Anders, C., Bargsten, K. & Jinek, M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol. Cell 61, 895-902 (2016). PMID: 26990992.

Unzue, A., Zhao, H., Lolli, G., Dong, J., Zhu, J., Zechner, M., Dolbois, A., Caflisch, A. & Nevado, C. The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. J. Med. Chem. 59, 3087-97 (2016). PMID: 26982797.

Batyuk, A., Wu, Y., Honegger, A., Heberling, MM. & Plückthun, A. DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography. J. Mol. Biol. 428, 1574-88 (2016). PMID: 26975886.

Olieric, V., Weinert, T., Finke, AD., Anders, C., Li, D., Olieric, N., Borca, CN., Steinmetz, MO., Caffrey, M., Jinek, M. & Wang, M. Data-collection strategy for challenging native SAD phasing. Acta Crystallogr D Struct Biol 72, 421-9 (2016). PMID: 26960129.

Meyer, PA., Socias, S., Key, J., Ransey, E., Tjon, EC., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, KS., Baxter, RH., Blacklow, SC., Boggon, TJ., Bonvin, AM., Borek, D., Brett, TJ., Caflisch, A., Chang, CI., Chazin, WJ., Corbett, KD., Cosgrove, MS., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, CL., Eck, MJ., Eichman, BF., Fan, QR., Ferré-D'Amaré, AR., Christopher Fromme, J., Garcia, KC., Gaudet, R., Gong, P., Harrison, SC., Heldwein, EE., Jia, Z., Keenan, RJ., Kruse, AC., Kvansakul, M., McLellan, JS., Modis, Y., Nam, Y., Otwinowski, Z., Pai, EF., Pereira, PJ., Petosa, C., Raman, CS., Rapoport, TA., Roll-Mecak, A., Rosen, MK., Rudenko, G., Schlessinger, J., Schwartz, TU., Shamoo, Y., Sondermann, H., Tao, YJ., Tolia, NH., Tsodikov, OV., Westover, KD., Wu, H., Foster, I., Fraser, JS., Maia, FR., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M. & Sliz, P. Data publication with the structural biology data grid supports live analysis. Nat Commun 7, 10882 (2016). PMID: 26947396.

Bertozzi, C., Zimmermann, I., Engeler, S., Hilf, RJ. & Dutzler, R. Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. PLoS Biol. 14, e1002393 (2016). PMID: 26943937.

Lolli, G. & Caflisch, A. High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography. ACS Chem. Biol. 11, 800-7 (2016). PMID: 26942307.

Ben Halima, S., Mishra, S., Raja, KM., Willem, M., Baici, A., Simons, K., Brüstle, O., Koch, P., Haass, C., Caflisch, A. & Rajendran, L. Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein. Cell Rep 14, 2127-41 (2016). PMID: 26923602.

Schütz, M., Schöppe, J., Sedlák, E., Hillenbrand, M., Nagy-Davidescu, G., Ehrenmann, J., Klenk, C., Egloff, P., Kummer, L. & Plückthun, A. Directed evolution of G protein-coupled receptors in yeast for higher functional production in eukaryotic expression hosts. Sci Rep 6, 21508 (2016). PMID: 26911446.

Unzue, A., Lafleur, K., Zhao, H., Zhou, T., Dong, J., Kolb, P., Liebl, J., Zahler, S., Caflisch, A. & Nevado, C. Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation. Eur J Med Chem 112, 347-66 (2016). PMID: 26907157.

Dubey, GP., Malli Mohan, GB., Dubrovsky, A., Amen, T., Tsipshtein, S., Rouvinski, A., Rosenberg, A., Kaganovich, D., Sherman, E., Medalia, O. & Ben-Yehuda, S. Architecture and Characteristics of Bacterial Nanotubes. Dev. Cell 36, 453-61 (2016). PMID: 26906740.

Zwerger, M., Eibauer, M. & Medalia, O. Insights into the gate of the nuclear pore complex. Nucleus 7, 1-7 (2016). PMID: 26902931.

Reichen, C., Madhurantakam, C., Hansen, S., Grütter, MG., Plückthun, A. & Mittl, PR. Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects. Acta Crystallogr D Struct Biol 72, 168-75 (2016). PMID: 26894544.

Klenk, C., Ehrenmann, J., Schütz, M. & Plückthun, A. A generic selection system for improved expression and thermostability of G protein-coupled receptors by directed evolution. Sci Rep 6, 21294 (2016). PMID: 26887595.

Hansen, S., Tremmel, D., Madhurantakam, C., Reichen, C., Mittl, PR. & Plückthun, A. Structure and Energetic Contributions of a Designed Modular Peptide-Binding Protein with Picomolar Affinity. J. Am. Chem. Soc. 138, 3526-32 (2016). PMID: 26878586.

Vašák, M. & Schnabl, J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 16, 259-90 (2016). PMID: 26860304.

Benke, S., Roderer, D., Wunderlich, B., Nettels, D., Glockshuber, R. & Schuler, B. Erratum: The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 7, 10650 (2016). PMID: 26830972.

Schütz, M., Batyuk, A., Klenk, C., Kummer, L., de Picciotto, S., Gülbakan, B., Wu, Y., Newby, GA., Zosel, F., Schöppe, J., Sedlák, E., Mittl, PR., Zenobi, R., Wittrup, KD. & Plückthun, A. Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools. J. Mol. Biol. 428, 1272-89 (2016). PMID: 26812208.

Xu, M., Caflisch, A. & Hamm, P. Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates. J Chem Theory Comput 12, 1393-9 (2016). PMID: 26799675.

Irobalieva, RN., Martins, B. & Medalia, O. Cellular structural biology as revealed by cryo-electron tomography. J. Cell. Sci. 129, 469-76 (2016). PMID: 26787742.

Tamir, A., Sorrentino, S., Motahedeh, S., Shai, E., Dubrovsky, A., Dahan, I., Eibauer, M., Studt, JD., Sapra, KT., Varon, D. & Medalia, O. The macromolecular architecture of platelet-derived microparticles. J. Struct. Biol. 193, 181-7 (2016). PMID: 26767592.

Niewoehner, O. & Jinek, M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA 22, 318-29 (2016). PMID: 26763118.

Roderer, D., Benke, S., Schuler, B. & Glockshuber, R. Soluble oligomers of the pore-forming toxin Cytolysin A from Escherichia coli are off-pathway products of pore assembly. J. Biol. Chem. 291, 5652-63 (2016). PMID: 26757820.

Jones, TD., Carter, PJ., Plückthun, A., Vásquez, M., Holgate, RG., Hötzel, I., Popplewell, AG., Parren, PW., Enzelberger, M., Rademaker, HJ., Clark, MR., Lowe, DC., Dahiyat, BI., Smith, V., Lambert, JM., Wu, H., Reilly, M., Haurum, JS., Dübel, S., Huston, JS., Schirrmann, T., Janssen, RA., Steegmaier, M., Gross, JA., Bradbury, AR., Burton, DR., Dimitrov, DS., Chester, KA., Glennie, MJ., Davies, J., Walker, A., Martin, S., McCafferty, J. & Baker, MP. The INNs and outs of antibody nonproprietary names. MAbs 8, 1-9 (2016). PMID: 26716992.

Bode, H., Bourquin, F., Suriyanarayanan, S., Wei, Y., Alecu, I., Othman, A., von Eckardstein, A. & Hornemann, T. HSAN1 mutations in serine palmitoyltransferase reveal a close structure-function-phenotype relationship. Hum. Mol. Genet. Hum. Mol. Genet. 25, 853-65 (2016). PMID: 26681808.

Xu, M., Unzue, A., Dong, J., Spiliotopoulos, D., Nevado, C. & Caflisch, A. Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics. J. Med. Chem. 59, 1340-9 (2016). PMID: 26125948.

Unzue, A., Xu, M., Dong, J., Wiedmer, L., Spiliotopoulos, D., Caflisch, A. & Nevado, C. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 59, 1350-6 (2016). PMID: 26043365.