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Department of Biochemistry

Publications 2018

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

Gutte, B. & Klauser, S. Design of catalytic polypeptides and proteins. Protein Eng. Des. Sel. 31, 457-470 (2018). PMID: 31241746.

Schuler, B., Szabo, A. & Wolynes, PG. Tribute to William A. Eaton. J Phys Chem B 122, 10971-10973 (2018). PMID: 30986080.

Palermo, G., Chen, JS., Ricci, CG., Rivalta, I., Jinek, M., Batista, VS., Doudna, JA. & McCammon, JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q. Rev. Biophys. 51, (2018). PMID: 30555184.

Vigano, MA., Bieli, D., Schaefer, JV., Jakob, RP., Matsuda, S., Maier, T., Plückthun, A. & Affolter, M. Correction: DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations. Biol Open 7, (2018). PMID: 30545951.

Studer, S., Hansen, DA., Pianowski, ZL., Mittl, PRE., Debon, A., Guffy, SL., Der, BS., Kuhlman, B. & Hilvert, D. Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science 362, 1285-1288 (2018). PMID: 30545884.

Holmstrom, ED., Holla, A., Zheng, W., Nettels, D., Best, RB. & Schuler, B. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Meth. Enzymol. 611, 287-325 (2018). PMID: 30471690.

Ehrenmann, J., Schöppe, J., Klenk, C., Rappas, M., Kummer, L., Doré, AS. & Plückthun, A. High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Nat. Struct. Mol. Biol. 25, 1086-1092 (2018). PMID: 30455434.

Sturzenegger, F., Zosel, F., Holmstrom, ED., Buholzer, KJ., Makarov, DE., Nettels, D. & Schuler, B. Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nat Commun 9, 4708 (2018). PMID: 30413694.

Nishimura, T., Fakim, H., Brandmann, T., Youn, JY., Gingras, AC., Jinek, M. & Fabian, MR. Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs. Nucleic Acids Res. 46, 12008-12021 (2018). PMID: 30364987.

Esposito, C. & Vitalis, A. Precise estimation of transfer free energies for ionic species between similar media. Phys Chem Chem Phys 20, 27003-27010 (2018). PMID: 30328430.

Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Adariani, SR., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., Bowen, ME., Chen, H., Cordes, T., Eilert, T., Fijen, C., Gebhardt, C., Götz, M., Gouridis, G., Gratton, E., Ha, T., Hao, P., Hanke, CA., Hartmann, A., Hendrix, J., Hildebrandt, LL., Hirschfeld, V., Hohlbein, J., Hua, B., Hübner, CG., Kallis, E., Kapanidis, AN., Kim, JY., Krainer, G., Lamb, DC., Lee, NK., Lemke, EA., Levesque, B., Levitus, M., McCann, JJ., Naredi-Rainer, N., Nettels, D., Ngo, T., Qiu, R., Robb, NC., Röcker, C., Sanabria, H., Schlierf, M., Schröder, T., Schuler, B., Seidel, H., Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, AM., Weninger, KR., Wünsch, B., Yanez-Orozco, IS., Michaelis, J., Seidel, CAM., Craggs, TD. & Hugel, T. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat. Methods 15, 984 (2018). PMID: 30327572.

Lam, AKM. & Dutzler, R. Calcium-dependent electrostatic control of anion access to the pore of the calcium-activated cloride channel TMEM16A. Elife 7 pii: e39122 (2018). PMID: 30311910.

Grotz, K., Nüesch, M., Holmstrom, E., Heinz, M., Stelzl, LS., Schuler, B. & Hummer, G. Dispersion correction alleviates dye stacking of single-stranded DNA and RNA in simulations of single-molecule fluorescence experiments. J Phys. Chem B. Oct 122, 11626-11639 (2018). PMID: 30285443.

Zheng, W., Hofmann, H., Schuler, B. & Best, RB. Origin of internal friction in disordered proteins depends on solvent quality. J Phys. Chem B. Oct 122, 11478-11487 (2018). PMID: 30277791.

Zhu, J., Dong, J., Batiste; L., Unzue, A., Dolbois, A., Pascanu, V., Śledź, P., Nevado, C. &  Caflisch, A. Binding motifs in the CBP bromodomain: an analysis of 20 crystal structures of complexes with small molecules. ACS Med Chem Lett. 9, 929-934 (2018). PMID: 39258543.
Esposito, C., Wiedmer, L. & Caflisch, A. In silico identification of JMJD3 demethylase inhibitors. J Chem inf Model 58, 2151-2163 (2018). PMID: 30226987.

Dreier, B. & Plückthun, A.Rapid selection of high-affinity antibody scFv fragments using ribosome display. Methods Mol Biol. 1827, 235-268 (2018). PMID: 30196501.

Rezaei-Ghaleh N, Parigi G, Soranno A, Holla A, Becker S, Schuler B, Luchinat C & Zweckstetter M. Local and global dynamics in intrinsically disordered synuclein. Angew Chem Int Ed Engl. 57, 15262-15266 (2018). PMID: 30184304.

Marino, J., Buholzer, KJ., Zosel, F., Nettels, D. & Schuler, B. Charge interactions can dominate coupled folding and binding on the ribosome. Biophys. J. 115, 996-1006 (2018). PMID: 30173887.

Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD & Hugel T. Precision and accuracy of single-molecule FRET measurements - a multi-laboratory benchmark study. Nat Methods. 15, 669-676 (2018). PMID: 30171252.

Best RB, Zheng W, Borgia A, Buholzer K, Borgia MB, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A & Schuler B. Comment on "innovative scattering analysis shows that hydophobic disordered proteins are expanded in water". Science 361, (2018). PMID: 30166459.

Dingfelder F, Benke S, Nettels D & Schuler B. Mapping an equilibrium folding intermediate of the cytolytic pore toxin ClyA with single-molecule FRET. J Phys Chem B. 122, 11251-11261 (2018). PMID: 30156409.

ElGamacy M, Coles M, Ernst P, Zhu H, Hartmann MD, Plückthun A & Lupas AN. An interface-driven design strategy yields a novel , corrugated protein architecture. ACS Synth Biol. 7, 2226-2253 (2018). PMID: 30148951.

Zosel F, Mercadante D, Nettels D & Schuler B. A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction. Nat Commun. 9,  3332 (2018). PMID: 30127362.

Hartmann, J., Münch, RC., Freiling, RT., Schneider, IC., Dreier, B., Samukange, W., Koch, J., Seeger, MA., Plückthun, A. &  Buchholz, CJ. A library-based screening strategy for the identification of DARPins as ligands for receptor-targeted AAV and lentiviral vectors. Mol Ther Methods Clin Dev. 10, 128-143 (2018). PMID: 30101151.

Dahan, I., Sorrentino, S., Boujemaa-Paterski, R. & Medalia, O.Troponin-protected gold nanoparticles as a potential marker for cryo-EM and tomography. Structure 26, 1408-1413 (2018). PMID: 30078643.

Marchand, JR. & Caflisch, A.In silico fragment-based drug design with SEED. Eur J Med Chem. 156, 907-917 (2018). PMID: 30064119.

Saponara, E., Visentin, M., Baschieri, F., Seleznik, G., Martinelli, P., Esposito, I., Buschmann, J., Chen, R., Parrotta, R., Borgeaud, N., Bombardo, M., Malagola, E., Caflisch, A., Farhan, H., Graf, R.&  Sonda S. Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas. J Pathol. 246, 352-365 (2018). PMID: 30058725.

Yen, HY., Hoi, KK., Liko, I., Hedger, G., Horrell, MR., Song, W., Wu, D., Heine, P., Warne, T., Lee, Y., Carpenter, B., Plückthun, A., Tate, CG., Sansom, MSP. & Robinson, CV. PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling. Nature 559, 423-427 (2018). PMID: 29995853.

Schuler, B. Perspective: chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET. J Chem Phys. 149, 010901 (2018). PMID: 29981536.

Ilie, IM. & Caflisch, A. Disorder at the tips of a disease-relevant A beta42 amyloid fibril. A molecular dynamics study. J Phys Chem B. 122, 11072-11082 (2018). PMID: 29965774.

Zhu, J., Zhou, C. & Caflisch, A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. Eur J Med Chem. 155, 337-352 (2018). PMID: 29902720.

Radom, F., Plückthun, A. & Paci, E. Assessment of ab initio models of protein complexes by molecular dynamics. PLoS Comput Biol. 14, e 1006182 (2018). PMID: 29864135.

Savic, N., Ringnalda, FC., Lindsay, H., Berk, C., Bargsten, K., Li, Y., Neri, D., Robinson, MD., Ciaudo, C., Hall, J., Jinek, M. &  Schwank, G. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife 7, (2018). PMID: 29809142.

Tatli, M. & Medalia, O. Insight into the functional organization of nuclear lamins in health and disease. Curr Opin Cell Biol. 54, 72-79 (2018). PMID: 29800922.

Swarts, D. & Jinek. M. Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. Wiley Interdiscip Rev RNA 9, e1481 (2018). PMID: 29790280.

Unzue, A., Cribiú, R., Hoffman, MM., Knehans, T., Lafleur, K., Caflisch, A. & Nevado, C. Iriomoteolides: novel chemical tools to study actin dynamics. Chem Sci. 9, 3793-3802 (2018). PMID: 29780512.

Dalle Vedove, A., Spiliotopoulos, D., D'Agostino, VG., Marchand, JR., Unzue, A., Nevado, C., Lolli, G. & Caflisch, A. Structural analysis of small molecule  binding to the BAZ2A amd BAZ2B bromodomains. ChemMedChem  13, 1479-1487 (2018). PMID: 29770599.

Deneka, D., Sawicka, M., Lam, AKM., Paulino, C. & Dutzer, R. Structure of a volume-regulated anion channel of the LRRC8 family. Nature 558, 254-259 (2018).  PMID: 29769723.

Stritt, S., Birkholz, I., Beck, S., Sorrentino, S., Sapra, KT., Viaud, J., Heck, J., Gaits-Iacovoni, F., Schulze, H., Du, X., Hartwig, JH., Braun, A., Bender, M., Medalia, O. & Nieswandt, B. Profilin 1-mediated cytoskeletal rearrangements regulate integrin function in mouse platelets. Blood Adv. 2, 1040-1045 (2018). PMID: 29739775.

Lickert, S., Sorrentino, S., Studt, JD., Medalia, O., Vogel, V. & Schoen, I. Morphometric analysis of spread platelets identifies integrin alphaIIbbeta3-specific contractile phenotype. Sci Rep. 8, 5428 (2018). PMID: 29615672.

Zheng, W., Zerze, GH., Borgia, A., Mittal, J., Schuler, B. & Best, RB. Inferring properties of disordered chains from FRET transfer efficiencies. J Chem Phys. 148, 123329 (2018). PMID: 29604882.

Makarov, DE. & Schuler, B. Preface: Special Topic on single-molecule biophysics. J Chem Phys. 148, 123001 (2018). PMID: 29604869.

Reinartz, I., Sinner, C., Nettels, D., Stucki-Buchli, B., Stockmar, F., Panek, PT., Jacob, CR., Nienhaus, GU., Schuler, B. & Schug, A. Simulation of FRET dyes allows quantitative comparison against experimental data. J Chem Phys 148, 123321 (2018). PMID: 29604831.

Clerici, M., Faini, M., Muckenfuss, LM., Aebersold, R. &  Jinek, M. Author correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat Struct Mol Biol. 25, 355 (2018). PMID: 29540792.

Schaefer, JV., Sedlák, E., Kast, F., Nemergut, M. & Plückthun, A. Modification of the kinetic stability of immunoglobulin G by solvent additives. MAbs. 10, 607-623 (2018). PMID: 29537925.

Yong, KJ., Vaid, TM., Shilling, PJ., Wu, FJ., Williams, LM., Deluigi, M., Plückthun, A., Bathgate, RA., Gooley, PR. & Scott, DJ. Determinants of ligand subtype-selectivity at alpha 1A-adrenoceptor revealed using saturation transfer difference (STD) NMR. ACS Chem Biol. 13, 1090-1102 (2018). PMID: 29537256.

Mikula, KM., Krumwiede, L., Plückthun, A. & Iwaï, H. Segmental isotopic labeling by asparaginyl endopeptidase-mediated protein ligation. J Biomol NMR 71, 225-235 (2018). PMID: 29536230.

Batiste, L., Unzue, A., Dolbois, A., Hassler, F., Wang, X., Deerain, N., Zhu, J., Spiliotopoulos, D., Nevado, C. & Caflisch, A. Chemical space expansion of bromodomain ligands guided by in silico virtual couplings (AutoCouple). ACS Cent Sci. 4, 180-188 (2018). PMID: 29532017.

Stichling, N., Suomalainen, M., Flatt, JW., Schmid, M., Pacesa, M., Hemmi, S., Jungraithmayr, W., Maler, MD., Freudenberg, MA., Plückthun, A., May, T., Köster, M., Fejer, G. & Greber, UF. Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor. PLoS Pathog. 14 (3) e1006914 (2018). PMID: 29522575.

Brandmann, T., Fakim, H., Padamsi, Z., Youn, JY., Gingras, AC., Fabian, MR. & Jinek, M. Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. EMBO J. 37(7) e97869 (2018). PMID: 29510985.

Swainston, N., Baici, A., Bakker, BM., Cornish-Bowden, A., Fitzpatrick, PF., Halling, P., Leyh, TS., O'Donovan, C., Raushel, FM., Reschel, U., Rohwer, JM., Schnell, S., Schomburg, D., Tipton, KF., Tsai, MD., Westerhoff, HV., Wittig, U., Wohlgemuth, R. & Kettner, C. STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS J. 285, 2193-2204 (2018). PMID: 29498804.

Härmä, H., Tong-Ochoa, N., van Adrichem, AJ., Jelesarov, I., Wennerberg, K. & Kopra, K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb). 54, 2910-2913 (2018) . PMID: 29498735.

Michel, E., Plückthun, A. &  Zerbe, O. Peptide-guided assembly of repeat protein fragments. Angew Chem Int Ed Engl. 574576-4579 (2018). PMID: 29480529.

Caflisch, A. & Gianni, S. Editorial overview: Folding and binding: In silico, in vitro and in cellula. Curr Opin Struct Biol. 48, iv-vii (2018). PMID: 29475490.

Borgia, A., Borgia, MB., Bugge, K., Kissling, VM., Heidarsson, PO., Fernandes, CB., Sottini, A., Soranno, A., Buholzer, KJ., Nettels, D., Kragelund, BB., Best, RB. &  Schuler, B.Extreme disorder in an ultrahigh-affinity protein complex. Nature 555, 61-66 (2018). PMID: 29466338.

Masliah, G., Maris, C., König, SL., Yulikov, M., Aeschimann, F., Malinowska, AL., Mabille, J., Weiler, J., Holla, A., Hunziker, J., Meisner-Kober, N., Schuler, B., Jeschke, G. & Allain, FH. Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains. EMBO J. 37(6), e97089 (2018). PMID: 29449323.

Chorev, DS., Volberg, T., Livne,  A., Eisenstein, M., Martins, B., Kam, Z., Jockusch, BM., Medalia, O., Sharon, M. & Geiger, B. Conformational states during vinculin unlocking differentially regulate focal adhesions properties. Sci Rep 8, 2693 (2018). PMID: 29426917.

Schmid, M., Ernst, P., Honegger, A., Suomalainen, M., Zimmermann, M., Braun, L., Stauffer, S., Thom, C., Dreier, B., Eibauer, M., Kipar, A., Vogel, V., Greber, UF., Medalia, O, & Plückthun, A. Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nat Commun 9, 450 (2018). PMID: 29386504.

Clerici, M., Faini, M., Muckenfuss, LM., Aebersold, R. & Jinek, M. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat Struct Mol Biol. 25, 135-138 (2018). PMID: 29358758.

Pott, M., Hayashi, T., Mori, T., Mittl, P., Green AP & Hilvert, D. A non-canonical proximal heme ligand affords an efficient peroxidase in a globin fold. J Am Chem Soc. 140, 1535-1543 (2018). PMID: 29309143.

Vlot, M., Houkes, J., Lochs, SJA., Swarts, DC., Zheng, P., Kunne, T., Mohanraju, P., Anders, C., Jinek, M., van der Oost, J.,  Dickman, MJ. & Brouns, SJJ. Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not type V CRISPR-Cas effector complexes. Nucleic Acids Res. 46873-885 (2018). PMID: 29253268.

Hansen, S., Ernst, P., König, SLB., Reichen, C., Ewald, C., Nettels, D., Mittl, PRE., Schuler, B. & Plückthun, A. Curvature of deignes armadillo repeat proteins allows modular peptide binding. J Struct Biol. 201 108-117 (2018). PMID: 28864298.

Śledź, P. & Caflisch, A. Protein structure-based drug design: from docking to molecular dynamics. Curr. Opin. Struct. Biol. 48, 93-102 (2018). PMID: 29149726.

Tamás, MJ., Fauvet, B., Christen, P. & Goloubinoff, P. Misfolding and aggregation of nascent proteins: a novel mode of toxic cadmium action in vivo. Curr Genet64, 177-181 (2018). PMID: 28936749.

Morger, D., Zosel, F., Bühlmann, M., Züger, S., Mittelviefhaus, M., Schuler, B., Luban, J. &  Grütter, MG.The three-fold axis of the HIV-1 capsid lattice is the species-specific binding interface for TRIM5  alpha. J. Virol. 92(5), e01541-17 (2018).  PMID: 29237846.

de Leeuw, R., Gruenbaum, Y. & Medalia, O. Nuclear lamins: thin filaments with major functions. Trends Cell Biol. 28, 34-45 (2018). PMID: 28893461.

Holmstrom, ED., Nettels, D. & Schuler, B. Conformational plasticity of hepatitis C virus core protein enables RNA-induced formation of nucleocapsid-like particles. J Mol Biol. 430, 2453-2467 (2018). PMID: 29045818.

Wu,Y., Honegger, A., Batyuk, A., Mittl, P. & Plückthun, A. Structural basis for the selective inhibition of c-Jun N-terminal kinase 1 determined by rigid DARPin-DARPin fusions. J Mol Biol 430, 2128-2138 (2018). PMID: 29126898.