Publikationen

2.

Zeitschriftenartikel

Lapolla, A.; Godec, A.: BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Computer Physics Communications 258, 107569 (2021)

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3.

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Lykke-Andersen, S.; Zumer, K.; Molska, E. Š.; Rouvière, J. O.; Wu, G.; Demel, C.; Schwalb, B.; Schmid, M.; Cramer, P.; Jensen, T. H.: Integrator is a genome-wide attenuator of non-productive transcription. Molecular Cell, in Press (2020)

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4.

Zeitschriftenartikel

Lapolla, A.; Hartich, D.; Godec, A.: Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 2 (4), 043084 (2020)

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5.

Zeitschriftenartikel

Netz, E.; Dijkstra, T. M. H.; Sachsenberg, T.; Zimmermann, L.; Walzer, M.; Monecke, T.; Ficner, R.; Dybkov, O.; Urlaub, H.; Kohlbacher, O.: OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS. Molecular and Cellular Proteomics 19 (12), S. 2157 - 2167 (2020)

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6.

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Oudelaar, A. M.; Higgs, D. R.: The relationship between genome structure and function. Nature Reviews Genetics, In Press (2020)

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7.

Zeitschriftenartikel

Lapolla, A.; Godec, A.: Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. The Journal of Chemical Physics 153 (19), 194104 (2020)

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8.

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Borodin, D.; Golibrzuch, K.; Schwarzer, M.; Fingerhut, J.; Skoulatakis, G.; Schwarzer, D.; Seelemann, T.; Wodtke, A. M.: Measuring transient reaction rates from nonstationary catalysts. ACS Catalysis 10 (23), S. 14056 - 14066 (2020)

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9.

Zeitschriftenartikel

Wu, X.; Ganzella, M.; Zhou, J.; Zhu, S.; Jahn, R.; Zhang, M.: Vesicle tethering on the surface of phase-separated active zone condensates. Molecular Cell, In Press (2020)

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10.

Zeitschriftenartikel

Bubnis, G.; Grubmüller, H.: Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal, In Press (2020)

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11.

Zeitschriftenartikel

Kohnke, B.; Kutzner, C.; Grubmüller, H.: A GPU-accelerated fast multipole method for GROMACS: Performance and accuracy. Journal of Chemical Theory and Computation 16 (11), S. 6938 - 6949 (2020)

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12.

Zeitschriftenartikel

Yip, K. M.; Fischer, N.; Paknia, E.; Chari, A.; Stark, H.: Atomic-resolution protein structure determination by cryo-EM. Nature 587 (7832), S. 157 - 161 (2020)

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13.

Zeitschriftenartikel

Rabe von Pappenheim, F.; Aldeghi, M.; Shome, B.; Begley, T.; de Groot, B. L.; Tittmann, K.: Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 16 (11), S. 1237-1245 (2020)

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14.

Zeitschriftenartikel

Korchak, S.; Jagtap, A.; Glöggler, S.: Signal-enhanced real-time magnetic resonance of enzymatic reactions at millitesla fields. Chemical Science, In Press (2020)

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15.

Zeitschriftenartikel

Geweke, J.; Wodtke, A. M.: Vibrationally inelastic scattering of HCl from Ag(111). Journal of Chemical Physics 153 (16), 164703 (2020)

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16.

Zeitschriftenartikel

Liutkute, M.; Maiti, M.; Samatova, E. N.; Enderlein, J.; Rodnina, M. V.: Gradual compaction of nascent peptide during cotranslational folding on the ribosome. eLife 9, e60895 (2020)

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17.

Zeitschriftenartikel

Reinhardt, M.; Grubmüller, H.: GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. arXiv, 2010.14193 (2020)

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18.

Zeitschriftenartikel

Liess, A. K. L.; Kucerova, A.; Schweimer, K.; Schlesinger, D.; Dybkov, O.; Urlaub, H.; Mansfeld, J.; Lorenz, S.: Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S. Science Signaling 13 (654), eaba8208 (2020)

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19.

Zeitschriftenartikel

Lau, J. A.; Schönemann, A.-M.; Schwarzer, D.; Wodtke, A. M.: The coverage dependence of the infrared absorption of CO adsorbed to NaCI(100). The Journal of Chemical Physics 153 (15), 154703 (2020)

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20.

Zeitschriftenartikel

Kohnke, B.; Kutzner, C.; Beckmann, A.; Lube, G.; Kabadshow, I.; Dachsel, H.; Grubmüller, H.: A CUDA fast multipole method with highly efficient M2L farfield evaluationfield evaluation. The International Journal of High Performance Computing Applications, In Press (2020)

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21.

Zeitschriftenartikel

Osman, S.; Cramer, P.: Structural biology of RNA polymerase II transcription: 20 years on. Annual Review of Cell and Developmental Biology 36, S. 1 - 34 (2020)

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22.

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Bertram, K.; El Ayoubi, L.; Dybkov, O.; Agafonov, D.; Will, C. L.; Hartmuth, K.; Urlaub, H.; Kastner, B.; Stark, H.; Lührmann, R.: Structural insights into the roles of metazoan-specific splicing factors in the human step 1 spliceosome. Molecular Cell 80 (1), S. 127 - 139.e6 (2020)

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23.

Zeitschriftenartikel

Reinhardt, M.; Grubmüller, H.: Variationally derived intermediates for correlated free-energy estimates between intermediate states. Physical Review E 102 (4), 043312 (2020)

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24.

Zeitschriftenartikel

Borodin, D.; Rahinov, I.; Shirhatti, P. R.; Huang, M.; Kandratsenka, A.; Auerbach, D. J.; Zhong, T.; Guo, H.; Schwarzer, D.; Kitsopoulos, T. N. et al.; Wodtke, A. M.: Following the microscopic pathway to adsorption through chemisorption and physisorption wells. Science 369 (6510), S. 1461 - 1465 (2020)

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25.

Zeitschriftenartikel

Erijman, A.; Kozlowski, L.; Sohrabi-Jahromi, S.; Fishburn, J.; Warfield, L.; Schreiber, J.; Noble, W. S.; Söding, J.; Hahn, S.: A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning (Correction). Molecular Cell 79 (6), S. 1066 (2020)

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26.

Zeitschriftenartikel

Lapolla, A.; Godec, A.: Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 125 (11), 110602 (2020)

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27.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9, e57589 (2020)

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28.

Zeitschriftenartikel

Wille, S.; Jiang, H.; Bünermann, O.; Wodtke, A. M.; Behler, J.; Kandratsenka, A.: An experimentally validated neural-network potential energy surface for H-atom on free-standing graphene in full dimensionality. Physical Chemistry Chemical Physics, In Press (2020)

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29.

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Igaev, M.; Grubmüller, H.: Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Computational Biology 16 (9), e1008132 (2020)

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30.

Zeitschriftenartikel

Langan, P. S.; Vandavasi, V. G.; Kopec, W.; Sullivan, B.; Afonne, P. V.; Weiss, K. L.; de Groot, B. L.; Coates, L.: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 7 (5), S. 835 - 843 (2020)

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31.

Zeitschriftenartikel

Maier, K. C.; Gressel, S.; Cramer, P.; Schwalb, B.: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Genome Research 30 (9), S. 1332 - 1344 (2020)

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32.

Zeitschriftenartikel

Mamone, S.; Schmidt, A. B.; Schwaderlapp, N.; Lange, T.; Elverfeldt, D. v.; Hennig, J.; Glöggler, S.: Localized singlet-filtered MRS in vivo. NMR in Biomedicine, e4400; In Press (2020)

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33.

Zeitschriftenartikel

Nagy, G.; Grubmueller, H.: How accurate is circular dichroism-based model validation? European Biophysics Journal 49 (6), S. 497 - 510 (2020)

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34.

Zeitschriftenartikel

Schubeis, T.; Le Marchand, T.; Daday, C.; Kopec, W.; Tekwani Movellan, K.; Stanek, J.; Schwarzer, T. S.; Castiglione, K.; de Groot, B. L.; Pintacuda, G. et al.; Andreas, L. B.: A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America 117 (35), S. 21014 - 21021 (2020)

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35.

Zeitschriftenartikel

Galparsoro, O.; Kaufmann, S.; Auerbach, D. J.; Kandratsenka, A.; Wodtke, A. M.: First principles rates for surface chemistry employing exact transition state theory: application to recombinative desorption of hydrogen from Cu(111). Physical Chemistry Chemical Physics 22 (31), S. 17532 - 17539 (2020)

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36.

Zeitschriftenartikel

Pape, J. K.; Stephan, T.; Balzarotti, F.; Büchner, R.; Lange, F.; Riedel, D.; Jakobs, S.; Hell, S. W.: Multicolor 3D MINFLUX nanoscopy of mitochondrial MICOS proteins. Proceedings of the National Academy of Sciences of the USA 117 (34), S. 20607 - 20614 (2020)

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37.

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Cramer, P.: Rosalind Franklin and the advent of molecular biology. Cell 182 (4), S. 787 - 789 (2020)

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38.

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Tellier, M.; Zaborowska, J.; Caizzi, L.; Mohammad, E.; Velychko, T.; Schwalb, B.; Ferrer-Vicens, I.; Blears, D.; Nojima, T.; Cramer, P. et al.; Murphy, S.: CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Research 48 (14), S. 7712 - 7727 (2020)

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39.

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Kim, K.-P.; Choi, J.; Yoon, J.; Bruder, J. M.; Shin, B.; Kim, J.; Arauzo-Bravo, M. J.; Han, D.; Wu, G.; Han, D. W. et al.; Kim, J.; Cramer, P.; Schöler, H. R.: Permissive epigenomes endow reprogramming competence to transcriptional regulators. Nature Chemical Biology, In Press (2020)

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40.

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Chan, K.-H.; Petrychenko, V.; Mueller, C.; Maracci, C.; Holtkamp, W.; Wilson, D. N.; Fischer, N.; Rodnina, M. V.: Mechanism of ribosome rescue by alternative ribosome-rescue factor B. Nature Communications 11, 4106 (2020)

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41.

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Hillen, H.; Kokic, G.; Farnung, L.; Dienemann, C.; Tegunov, D.; Cramer, P.: Structure of replicating SARS-CoV-2 polymerase. Nature 584 (7819), S. 154 - 156 (2020)

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42.

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Mercier, E.; Wintermeyer, W.; Rodnina, M. V.: Co‐translational insertion and topogenesis of bacterial membrane proteins monitored in real time. EMBO Journal 39 (15), e104054 (2020)

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43.

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Westphal, G.; Wega, J.; Dissanayake, R. E. A.; Schäfer, T.: Chirality detection of surface desorption products using photoelectron circular dichroism. The Journal of Chemical Physics 153 (5), 054707 (2020)

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44.

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O’Reilly, F. J.; Xue, L.; Graziadei, A.; Sinn, L.; Lenz, S.; Tegunov, D.; Blötz, C.; Singh, N.; Hagen, W. J. H.; Cramer, P. et al.; Stülke, J.; Mahamid, J.; Rappsilber, J.: In-cell architecture of an actively transcribing-translating expressome. Science 369 (6503), S. 554 - 557 (2020)

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45.

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Bucevicius, J.; Kostiuk, G.; Gerasimaite, R.; Gilat, T.; Lukinavicius, G.: Enhancing the biocompatibility of rhodamine fluorescent probes by a neighbouring group effect. Chemical Science 11 (28), S. 7313 - 7323 (2020)

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46.

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O'Loughlin, S.; Capece, M. C.; Klimova, M.; Wills, N. M.; Coakley, A.; Samatova, E. N.; O'Connor, P.k. B. F.; Loughran, G.; Weissman, J. S.; Baranov, P. V. et al.; Rodnina, M. V.; Puglisi, J.h. D.; Atkins, J. F.: Polysomes bypass a 50-nucleotide coding gap less efficiently than monosomes due to attenuation of a 5′ mRNA stem–loop and enhanced drop-off. Journal of Molecular Biology 432 (16), S. 4369 - 4387 (2020)

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47.

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Gerrits, N.; Geweke, J.; Smeets, E. W. F.; Voss, J.; Wodtke, A. M.; Kroes, G.-J.: Closing the gap between experiment and theory: Reactive scattering of HCl from Au(111). Journal of Physical Chemistry C 124 (29), S. 15944 - 15960 (2020)

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48.

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Ukmar-Godec, T.; Fang, P.; Ibáñez de Opakua, A.; Henneberg, F.; Godec, A.; Pan, K. T.; Cima-Omori, M.-S.; Chari, A.; Mandelkow, E.; Urlaub, H. et al.; Zweckstetter, M.: Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Science Advances 6 (30), eaba3916 (2020)

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49.

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van der Meeren, L.; Li, J.; Konrad, M.; Skirtach, A. G.; Volodkin, D.; Parakhonskiy, B. V.: Temperature window for encapsulation of an enzyme into thermally shrunk, CaCO3-templated polyelectrolyte multilayer capsules. Macromolecular Bioscience 20 (7), 2000081 (2020)

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50.

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Stephan, T.; Brüser, C.; Deckers, M.; Steyer, A. M.; Balzarotti, F.; Barbot, M.; Behr, T. S.; Heim, G.; Hübner, W.; Ilgen, P. et al.; Lange, F.; Pacheu‐Grau, D.; Pape, J. K.; Stoldt, S.; Huser, T.; Hell, S. W.; Möbius, W.; Rehling, P.; Riedel, D.; Jakobs, S.: MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO Journal 39 (14), e104105 (2020)

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51.

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Fast, A.; Meek, S. A.: Sub-ppb measurement of a fundamental band rovibrational transition in HD. Physical Review Letters 125 (2), 023001 (2020)

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52.

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Zhang, Z.; Will, C. L.; Bertram, K.; Dybkov, O.; Hartmuth, K.; Agafonov, D. E.; Hofele, R. V.; Urlaub, H.; Kastner, B.; Lührmann, R. et al.; Stark, H.: Molecular architecture of the human 17S U2 snRNP. Nature 583 (7815), S. 310 - 313 (2020)

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Jaeger, M. G.; Schwalb, B.; Mackowiak, S. D.; Velychko, T.; Hanzl, A.; Imrichova, H.; Brand, M.; Agerer, B.; Chorn, S.; Nabet, B. et al.; Ferguson, F. M.; Müller, A. C.; Bergthaler, A.; Gray, N. S.; Bradner, J. E.; Bock, C.; Hnisz, D.; Cramer, P.; Winter, G. E.: Selective Mediator dependence of cell-type-specifying transcription. Nature Genetics 52 (7), S. 719 - 727 (2020)

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54.

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Königsmann, T.; Parfentev, I.; Urlaub, H.; Riedel, D.; Schuh, R.: The bicistronic gene würmchen encodes two essential components for epithelial development in Drosophila. Developmental Biology 463 (1), S. 53 - 62 (2020)

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Linden, A.; Deckers, M.; Parfentev, I.; Pflanz, R.; Homberg, B.; Neumann, P.; Ficner, R.; Rehling, P.; Urlaub, H.: A Cross-linking mass spectrometry approach defines protein interactions in yeast mitochondria. Molecular and Cellular Proteomics 19 (7), S. 1161 - 1178 (2020)

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Stik, G.; Vidal, E.; Barrero, M.; Cuartero, S.; Vila-Casadesús, M.; Mendieta-Esteban, J.; Tian, T. V.; Choi, J.; Berenguer, C.; Abad, A. et al.; Borsari, B.; le Dily, F.; Cramer, P.; Marti-Renom, M. A.; Stadhouders, R.; Graf, T.: CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response. Nature Genetics 52 (7), S. 655 - 661 (2020)

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Vos, S. M.; Farnung, L.; Linden, A.; Urlaub, H.; Cramer, P.: Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation. Nature Structural and Molecular Biology 27 (7), S. 668 - 677 (2020)

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Schmidt, C. C.; Vasic, V.; Stein, A.: Doa10 is a membrane protein retrotranslocase in ER-associated protein degradation. eLife 9, e56945 (2020)

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Schulze, S.; Adams, Z.; Cerletti, M.; Castro, R. D.; Ferreira-Cerca, S.; Fufezan, C.; Giménez, M. I.; Hippler, M.; Jevtic, Z.; Knüppel, R. et al.; Legerme, G.; Lenz, C.; Marchfelder, A.; Maupin-Furlow, J.; Paggi, R. A.; Pfeiffer, F.; Poetsch, A.; Urlaub, H.; Pohlschroder, M.: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nature Communications 11, 3145 (2020)

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Farnung, L.; Ochmann, M.; Cramer, P.: Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations. eLife 9, e56178 (2020)

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Reinhardt, M.; Grubmüller, H.: Determining free-energy differences through variationally derived intermediates. Journal of Chemical Theory and Computation 16 (6), S. 3504 - 3512 (2020)

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Erijman, A.; Kozlowski, L. P.; Sohrabi-Jahromi, S.; Fishburn, J.; Warfield, L.; Schreiber, J.; Noble, W. S.; Söding, J.; Hahn, S.: A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning. Molecular Cell 78 (5), S. 890 - 902.e6 (2020)

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Greene, B. L.; Kang, G.; Cui, C.; Bennati, M.; Nocera, D. G.; Drennan, C. L.; Stubbe, J.: Ribonucleotide reductases: Structure, chemistry, and metabolism suggest new therapeutic targets. Annual Review of Biochemistry 89, S. 45 - 75 (2020)

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Parfentev, I.; Schilbach, S.; Cramer, P.; Urlaub, H.: An experimentally generated peptide database increases the sensitivity of XL-MS with complex samples. Journal of proteomics 220, 103754 (2020)

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ElInati, E.; Zielinska, A.; McCarthy, A.; Kubikova, N.; Maciulyte, V.; Mahadevaiah, S.; Sangrithi, M. N.; Ojarikre, O.; Wells, D.; Niakan, K. K. et al.; Schuh, M.; Turner, J. M. A.: The BCL-2 pathway preserves mammalian genome integrity by eliminating recombination-defective oocytes. Nature Communications 11, 2598 (2020)

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Bastys, T.; Gapsys, V.; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17, 13 (2020)

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Abalymov, A.; Poelvoorde, L. V.; Atkin, V.; Skirtach, A. G.; Konrad, M.; Parakhonskiy, B.: Alkaline phosphatase delivery system based on calcium carbonate carriers for acceleration of ossification. ACS Applied Bio Materials 3 (5), S. 2986 - 2996 (2020)

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Zapp, C.; Obarska-Kosinska, A.; Rennekamp, B.; Kurth, M.; Hudson, D. M.; Mercadante, D.; Barayeu, U.; Dick, T. P.; Denysenkov, V.; Prisner, T. et al.; Bennati, M.; Daday, C.; Kappl, R.; Gräter, F.: Mechanoradicals in tensed tendon collagen as a source of oxidative stress. Nature Communications 11, 2315 (2020)

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Zheng, X.; Zhang, L.; Kuang, Y.; Venkataramani, V.; Jin, F.; Hein, K.; Zafeiriou, M. P.; Lenz, C.; Moebius, W.; Kilic, E. et al.; Hermann, D. M.; Weber, M. S.; Urlaub, H.; Zimmermann, W.-H.; Bähr, M.; Doeppner, T. R.: Extracellular vesicles derived from neural progenitor cells: A preclinical evaluation for stroke treatment in mice. Translational Stroke Research, In Press (2020)

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Voit, D.; Kalentev, O.; van Zalk, M.; Joseph, A. A.; Frahm, J.: Rapid and motion-robust volume coverage using cross-sectional real-time MRI. Magnetic Resonance in Medicine 83 (5), S. 1652 - 1658 (2020)

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Dodonova, S. O.; Zhu, F.; Dienemann, C.; Taipale, J.; Cramer, P.: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 580 (7805), S. 669 - 672 (2020)

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Vahsen, B. F.; Ribas, V. T.; Sundermeyer, J.; Boecker, A.; Dambeck, V.; Lenz, C.; Shomroni, O.; Gomes, L. C.; Tatenhorst, L.; Barski, E. et al.; Roser, A.-E.; Michel, U.; Urlaub, H.; Salinas, G.; Bähr, M.; Koch, J. C.; Lingor, P.: Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo, enhances translation, and modulates splicing. Cell Death and Differentiation, In Press (2020)

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Gerasimaite, R.; Seikowski, J.; Schimpfhauser, J.; Kostiuk, G.; Gilat, T.; D'Este, E.; Schnorrenberg, S.; Lukinavicius, G.: Efflux pump insensitive rhodamine–jasplakinolide conjugates for G- and F-actin imaging in living cells. Organic Biomolecular Chemistry 18 (15), S. 2929 - 2937 (2020)

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Pierron, M.; Kalbfuss, N.; Borrego-Pinto, J.; Lenart, P.; Gönczyp, P.: Centriole foci persist in starfish oocytes despite Plk1 inactivation or loss of microtubule nucleation activity. Molecular Biology of the Cell 31 (9), S. 873 - 880 (2020)

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Fomin, M.; Seikowski, J.; Belov, V. N.; Hell, S. W.: Negatively charged red-emitting acridine dyes for facile reductive amination, separation and fluorescent detection of glycans. Analytical Chemistry 92 (7), S. 5329 - 5336 (2020)

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Levy Karin, E.; Mirdita, M.; Söding, J.: MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020)

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Favretto, F.; Baker, J.; Strohäker, T.; Andreas, L.; Blair, L.; Becker, S.; Zweckstetter, M.: Molecular basis of the interaction of cyclophilin A with alpha-synuclein. Angewandte Chemie International Edition 132 (14), S. 5692 - 5695 (2020)

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Singh, K.; Graf, B.; Linden, A.; Sautner, V.; Urlaub, H.; Tittmann, K.; Stark, H.; Chari, A.: Discovery of a regulatory subunit of the yeast fatty acid synthase. Cell 180 (6), S. 1130 - 1143.e20 (2020)

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Wagner, F. R; Dienemann, C.; Wang, H.; Stützer, A.; Tegunov, D.; Urlaub, H.; Cramer, P.: Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Nature 579 (7799), S. 448 - 451 (2020)

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