Publications of the Institute | Max Planck Institute of Biophysics

1.

Journal Article

Sim, S. I.; von Bülow, S.; Hummer, G.; Park, E.: Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 81, pp. 4635 - 4649 (2021)

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2.

Journal Article

Zhao, J.; Xie, H.; Mehdipour, A. R.; Safarian, S.; Ermler, U.; Münke, C.; Thielmann, Y.; Hummer, G.; Ebersberger, I.; Wang, J. et al.; Michel, H.: The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily. Proceedings of the National Academy of Sciences of the United States of America 118 (46), e2107335118 (2021)

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3.

Journal Article

Zimmerli, C. E.; Allegretti, M.; Rantos, V.; Goetz, S. K.; Obarska-Kosinska, A.; Zagoriy, I.; Halavatyi, A.; Hummer, G.; Mahamid, J.; Kosinski, J. et al.; Beck, M.: Nuclear pores dilate and constrict in cellulo. Science, eabd9776 (2021)

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4.

Journal Article

Müller, D. J.; Dumitru, A. C.; Lo Giudice, C.; Gaub, H. E.; Hinterdorfer, P.; Hummer, G.; De Yoreo, J. J.; Dufrêne, Y. F.; Alsteens, D.: Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 121 (19), pp. 11701 - 11725 (2021)

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5.

Journal Article

Reggio, A.; Buonomo, V.; Berkane, R.; Bhaskara, R.; Tellechea, M.; Peluso, I.; Polishchuk, E.; Di Lorenzo, G.; Cirillov, C.; Esposito, M. et al.; Hussain, A.; Huebner, A. K.; Hübner, C. A.; Settembre, C.; Hummer, G.; Grumati, P.; Stolz, A.: Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 22 (9), e52289 (2021)

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6.

Journal Article

Safarian, S.; Opel-Reading, H. K.; Wu, D.; Mehdipour, A. R.; Hards, K.; Harold, L. H.; Radloff, M.; Stewart, I.; Welsch, S.; Hummer, G. et al.; Cook, G. M.; Krause, K. L.; Michel, H.: The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nature Communications 12 (1), 5236 (2021)

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7.

Journal Article

Väth, K.; Mattes, C.; Reinhard, J.; Covino, R.; Stumpf, H.; Hummer, G.; Ernst, R.: Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 220 (8), e202011078 (2021)

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8.

Journal Article

Mukherjee, R.; Bhattacharya, A.; Bojkova, D.; Mehdipour, A. R.; Shin, D.; Khan, K. S.; Hei-Yin Cheung, H.; Wong, K.-B.; Ng, W.; Cinatl, J. et al.; Geurink, P. P.; van der Heden van Noort, G. J.; Rajalingam, K.; Ciesek, S.; Hummer, G.; Dikic, I.: Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 297 (2), 100925 (2021)

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9.

Journal Article

Schaefer, S. L.; Jung, H.; Hummer, G.: Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B 125 (28), pp. 7732 - 7741 (2021)

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10.

Journal Article

Bullerjahn, J. T.; Hummer, G.: Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 154 (23), 234105 (2021)

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11.

Journal Article

Mehdipour, A. R.; Hummer, G.: Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2100425118 (2021)

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12.

Journal Article

Ho, N. T.; Siggel, M.; Camacho, K. V.; Bhaskara, R.; Hicks, J. M.; Yao, Y.-C.; Zhang, Y.; Köfinger, J.; Hummer, G.; Noy, A.: Membrane fusion and drug delivery with carbon nanotube porins. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2016974118 (2021)

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13.

Journal Article

Sikora, M.; von Bülow, S.; Blanc, F. E. C.; Gecht, M.; Covino, R.; Hummer, G.: Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 17 (4), e1008790 (2021)

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14.

Journal Article

Siggel, M.; Bhaskara, R.; Moesser, M. K.; Đikić, I.; Hummer, G.: FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 12 (7), pp. 1926 - 1931 (2021)

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15.

Journal Article

Benayad, Z.; von Bülow, S.; Stelzl, L. S.; Hummer, G.: Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 17 (1), pp. 525 - 537 (2021)

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16.

Journal Article

Bárcena, M.; Barnes, C. O.; Beck, M.; Bjorkman, P. J.; Canard, B.; Gao, G. F.; Gao, Y.; Hilgenfeld, R.; Hummer, G.; Patwardhan, A. et al.; Santoni, G.; Saphire, E. O.; Schaffitzel, C.; Schendel, S. L.; Smith, J. L.; Thorn, A.; Veesler, D.; Zhang, P.; Zhou, Q.: Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 28 (1), pp. 2 - 7 (2021)

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17.

Journal Article

Klionsky, D. J.; Abdel-Aziz, A. K.; Abdelfatah, S.; Hummer, G.; 2295 other, A.: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 17 (1), pp. 1 - 382 (2021)

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18.

Journal Article

Collauto, A.; von Bülow, S.; Gophane, D.; Saha, S.; Stelzl, L. S.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 59, pp. 23025 - 23029 (2020)

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19.

Journal Article

Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G. et al.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Müller, S.; Knobeloch, K.-P.; Rajalingam, K.; Schulman, B.; Cinatl, J.; Hummer, G.; Ciesek, S.; Đikić, I.: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587 (7835), pp. 657 - 662 (2020)

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20.

Journal Article

Shin, D.; Bhattacharya, A.; Cheng, Y.-L.; Alonso, M. C.; Mehdipour, A. R.; van der Heden van Noort, G. J.; Ovaa, H.; Hummer, G.; Dikic, I.: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 9 (2020)

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21.

Journal Article

Sikora, M.; Ermel, U. H.; Seybold, A.; Kunz, M.; Calloni, G.; Reitz, J.; Vabulas, R. M.; Hummer, G.; Frangakis, A. S.: Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 117 (44), pp. 27132 - 27140 (2020)

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22.

Journal Article

Turoňová, B.; Sikora, M.; Schürmann, C.; Hagen, W. J. H.; Welsch, S.; Blanc, F. E. C.; von Bülow, S.; Gecht, M.; Bagola, K.; Hörner, C. et al.; van Zandbergen, G.; Landry, J.; de Azevedo, N. T. D.; Mosalaganti, S.; Schwarz, A.; Covino, R.; Mühlebach, M. D.; Hummer, G.; Krijnse Locker, J.; Beck, M.: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 370 (6513), pp. 203 - 208 (2020)

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23.

Journal Article

Gebel, J.; Tuppi, M.; Chaikuad, A.; Hötte, K.; Schröder, M.; Schulz, L.; Löhr, F.; Gutfreund, N.; Finke, F.; Henrich, E. et al.; Mezhyrova, J.; Lehnert, R.; Pampaloni, F.; Hummer, G.; Stelzer, E. H.K.; Knapp, S.; Dötsch, V.: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 16 (10), pp. 1078 - 1086 (2020)

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24.

Journal Article

Gecht, M.; Siggel, M.; Linke, M.; Hummer, G.; Köfinger, J.: MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 153 (14), 144105 (2020)

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25.

Journal Article

Sawa-Makarska, J.; Baumann, V.; Coudevylle, N.; von Bülow, S.; Nogellova, V.; Abert, C.; Schuschnig, M.; Graef, M.; Hummer, G.; Martens, S.: Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 369 (6508), eaaz7714 (2020)

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26.

Journal Article

Ortiz , S.; Stanisic, L.; Rodriguez , B. A.; Rampp, M.; Hummer, G.; Cossio, P.: Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 4, 100032 (2020)

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27.

Journal Article

Bullerjahn, J. T.; von Bülow, S.; Hummer, G.: Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 153 (2), 024116 (2020)

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28.

Journal Article

von Bülow, S.; Bullerjahn, J. T.; Hummer, G.: Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 153 (2), 021101 (2020)

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29.

Journal Article

Jost Lopez, A.; Quoika, P. K.; Linke, M.; Hummer, G.; Köfinger, J.: Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 124 (23), pp. 4673 - 4685 (2020)

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30.

Journal Article

Wu, X.; Siggel, M.; Ovchinnikov, S.; Mi, W.; Svetlov, V.; Nudler, E.; Liao, M.; Hummer, G.; Rapoport, T. A.: Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 368 (6489), eaaz2449, p. 385 (2020)

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31.

Journal Article

Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.: Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation. Proceedings of the National Academy of Sciences of the United States of America 117 (10), pp. 5109 - 5110 (2020)

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32.

Journal Article

Ballweg, S.; Sezgin, E.; Doktorova, M.; Covino, R.; Reinhard, J.; Wunnicke, D.; Hänelt, I.; Levental, I.; Hummer, G.; Ernst, R.: Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 11, 756 (2020)

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33.

Journal Article

Heinz, M.; Erlenbach, N.; Stelzl, L. S.; Thierolf, G.; Kamble, N. R.; Sigurdsson, S. T. H.; Prisner, T. F.; Hummer, G.: High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research 48 (2), pp. 924 - 933 (2020)

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34.

Journal Article

Warnau, J.; Wöhlert, D.; Okazaki, K.-I.; Yildiz, Ö.; Gamiz-Hernandez, A. P.; Kaila, V. R. I.; Kühlbrandt, W.; Hummer, G.: Ion Binding and Selectivity of the Na⁺/H⁺ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B 124 (2), pp. 336 - 344 (2020)

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35.

Journal Article

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 16 (1), pp. 725 - 737 (2020)

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36.

Journal Article

Shin, D.; Mukherjee, R.; Liu, Y.; Gonzalez, A.; Bonn, F.; Liu, Y.; Rogov, V. V.; Heinz, M.; Stolz, A.; Hummer, G. et al.; Dötsch, V.; Luo, Z.-Q.; Bhogaraju, S.; Đikić, I.: Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 77 (1), pp. 164 - 179 (2020)

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External

37.

Journal Article

Berman, H. M.; Adams, P. D.; Bonvin, A. A.; Burley, S. K.; Carragher, B.; Chiu, W.; DiMaio, F.; Ferrin, T. E.; Gabanyi, M. J.; Goddard, T. D. et al.; Griffin, P. R.; Haas, J.; Hanke, C. A.; Hoch, J. C.; Hummer, G.; Kurisu, G.; Lawson, C. L.; Leitner, A.; Markley, J. L.; Meiler, J.; Montelione, G. T.; Phillips, G. N.; Prisner, T.; Rappsilber, J.; Schriemer, D. C.; Schwede, T.; Seidel, C. A. M.; Strutzenberg, T. S.; Svergun, D. I.; Tajkhorshid, E.; Trewhella, J.; Vallat, B.; Velankar, S.; Vuister, G. W.; Webb, B.; Westbrook, J. D.; White, K. L.; Sali, A.: Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 27 (12), pp. 1745 - 1759 (2019)

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38.

Journal Article

Baldering, T. N.; Bullerjahn, J. T.; Hummer, G.; Heilemann, M.; Malkusch, S.: Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 52 (47), 474002 (2019)

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39.

Journal Article

Herhaus, L.; Bhaskara, R.; Lystad, A. H.; Gestal-Mato, U.; Covarrubias-Pinto, A.; Bonn, F.; Simonsen, A.; Hummer, G.; Đikić, I.: TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 21 (1), e48317 (2019)

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40.

Journal Article

Covino, R.; Woodside, M. T.; Hummer, G.; Szabo, A.; Cossio, P.: Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 151 (15), 154115 (2019)

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41.

Journal Article

Linker, S. M.; Magarkar, A.; Köfinger, J.; Hummer, G.; Seeliger, D.: Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation 15 (9), pp. 4974 - 4981 (2019)

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42.

Journal Article

Nishimura, T.; Gecht, M.; Covino, R.; Hummer, G.; Surma, M. A.; Klose, C.; Arai, H.; Kono, N.; Stefan, C. J.: Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P₂ Synthesis. Molecular Cell 75 (5), pp. 1043 - 1057 (2019)

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43.

Journal Article

Hofmann, S.; Januliene, D.; Mehdipour, A. R.; Thomas, C.; Stefan, E.; Brüchert, S.; Kuhn, B. T.; Geertsma, E. R.; Hummer, G.; Tampé, R. et al.; Möller, A.: Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 571 (7766), pp. 580 - 583 (2019)

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44.

Journal Article

Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.: Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America 116 (27), pp. 13352 - 13357 (2019)

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45.

Journal Article

Vögele, M.; Köfinger, J.; Hummer, G.: Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 123 (24), pp. 5099 - 5106 (2019)

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46.

Journal Article

Zakrzewska, S.; Mehdipour, A. R.; Malviya, V. N.; Nonaka, T.; Koepke, J.; Muenke, C.; Hausner, W.; Hummer, G.; Safarian, S.; Michel, H.: Inward-facing conformation of a multidrug resistance MATE family transporter. Proceedings of the National Academy of Sciences of the United States of America 116 (25), pp. 12275 - 12284 (2019)

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47.

Journal Article

Bhaskara, R.; Grumati, P.; Garcia-Pardo, J.; Kalayil, S.; Covarrubias-Pinto, A.; Chen, W.; Kudryashev, M.; Đikić, I.; Hummer, G.: Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 10, 2370 (2019)

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48.

Journal Article

Köfinger, J.; Stelzl, L. S.; Reuter, K.; Allande, C.; Reichel, K.; Hummer, G.: Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 15 (5), pp. 3390 - 3409 (2019)

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49.

Journal Article

von Bülow, S.; Siggel, M.; Linke, M.; Hummer, G.: Dynamic cluster formation determines viscosity and diffusion in dense protein solutions. Proceedings of the National Academy of Sciences of the United States of America 116 (20), pp. 9843 - 9852 (2019)

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50.

Journal Article

Chang, Y.-N.; Jaumann, E. A.; Reichel, K.; Hartmann, J.; Oliver, D.; Hummer, G.: Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications 10, 2032 (2019)

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51.

Journal Article

Okazaki, K.-i.; Wöhlert, D.; Warnau, J.; Jung, H.; Yildiz, Ö.; Kühlbrandt, W.; Hummer, G.: Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 10, 1742 (2019)

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52.

Journal Article

Perez, C.; Mehdipour, A. R.; Hummer, G.; Locher, K. P.: Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation. Structure 27 (4), pp. 669 - 678.e5 (2019)

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53.

Journal Article

von Domaros, M.; Bratko, D.; Kirchner, B.; Hummer, G.; Luzar, A.: Multifaceted Water Dynamics in Spherical Nanocages. The Journal of Physical Chemistry C 123 (10), pp. 5989 - 5998 (2019)

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54.

Journal Article

Chang, C.; Young, L. N.; Morris, K. L.; Bülow, S. v.; Schöneberg, J.; Yamamoto-Imoto, H.; Oe, Y.; Yamamoto, K.; Nakamura, S.; Stjepanovic, G. et al.; Hummer, G.; Yoshimori, T.; Hurley, J. H.: Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Molecular Cell 73 (2), pp. 339 - 353 (2019)

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55.

Journal Article

Böger, C.; Baldering, T. N.; Krüger, C. L.; Harwardt, M.-L. I. E.; Mertinkus, K. R.; Schröder, M. S.; Karathanasis, C.; Deußner-Helfmann, N. S.; Barth, H.-D.; Malkusch, S. et al.; Dietz, M. S.; Hummer, G.; Wohland, T.; Heilemann, M.: Quantification of membrane receptor complexes with single-molecule localization microscopy. Proceedings of SPIE 10884, 108840T (2019)

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56.

Journal Article

Schöneberg, J.; Pavlin, M. R.; Yan, S.; Righini, M.; Lee, I.-H.; Carlson, L.-A.; Bahrami, A. H.; Goldman, D. H.; Ren, X.; Hummer, G. et al.; Bustamante, C.; Hurley, J. H.: ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 362 (6421), pp. 1423 - 1428 (2018)

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57.

Journal Article

Grotz, K. K.; Nueesch, M. F.; Holmstrom, E. D.; Heinz, M.; Stelzl, L. S.; Schuler, B.; Hummer, G.: Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. The Journal of Physical Chemistry B 122 (49), pp. 11626 - 11639 (2018)

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58.

Journal Article

Seyfried, P.; Heinz, M.; Pintér, G.; Klötzner, D.-P.; Becker, Y.; Bolte, M.; Jonker, H. R. A.; Stelzl, L. S.; Hummer, G.; Schwalbe, H. et al.; Heckel, A.: Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal 24 (66), pp. 17568 - 17576 (2018)

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59.

Journal Article

Bock, C.; Löhr, F.; Tumulka, F.; Reichel, K.; Würz, J.; Hummer, G.; Schäfer, L.; Tampé, R.; Joseph, B.; Bernhard, F. et al.; Dötsch, V.; Abele, R.: Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL. Scientific Reports 8, 15662 (2018)

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60.

Journal Article

Rossini, E.; Gajewski, J.; Klaus, M.; Hummer, G.; Grininger, M.: Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs). Chemical Communications 54 (82), pp. 11606 - 11609 (2018)

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61.

Journal Article

Reichel, K.; Stelzl, L. S.; Köfinger, J.; Hummer, G.: Precision DEER Distances from Spin-Label Ensemble Refinement. The Journal of Physical Chemistry Letters 9 (18), pp. 5748 - 5752 (2018)

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62.

Journal Article

Cossio, P.; Allegretti, M.; Mayer, F.; Müller, V.; Vonck, J.; Hummer, G.: Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 67 (5), pp. 266 - 273 (2018)

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63.

Journal Article

Warnau, J.; Sharma, V.; Gamiz-Hernandez, A. P.; Di Luca, A.; Haapanen, O.; Vattulainen, I.; Wilkström, M.; Hummer, G.; Kaila, V. R. I.: Redox-coupled quinone dynamics in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 115 (36), pp. E8413 - E8420 (2018)

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64.

Journal Article

Hofbauer, H. F.; Gecht, M.; Fischer, S. C.; Seybert, A.; Frangakis, A. S.; Stelzer, E. H. K.; Covino, R.; Hummer, G.; Ernst, R.: The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. The Journal of Cell Biology: JCB 217 (9), pp. 3109 - 3126 (2018)

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65.

Journal Article

Vögele, M.; Köfinger, J.; Hummer, G.: Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 209, pp. 341 - 358 (2018)

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66.

Journal Article

Covino, R.; Hummer, G.; Ernst, R.: Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response. Molecular Cell 71 (3), pp. 458 - 467 (2018)

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67.

Journal Article

Vögele, M.; Köfinger, J.; Hummer, G.: Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 120 (26), 268104 (2018)

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68.

Journal Article

De Vos, O.; Venable, R. M.; Van Hecke, T.; Hummer, G.; Pastor, R. W.; Ghysels, A.: Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model. Journal of Chemical Theory and Computation 14 (7), pp. 3811 - 3824 (2018)

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69.

Journal Article

Linke, M.; Köfinger, J.; Hummer, G.: Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters 9 (11), pp. 2874 - 2878 (2018)

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70.

Journal Article

Linke, M.; Köfinger, J.; Hummer, G.: Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 122 (21), pp. 5630 - 5639 (2018)

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71.

Journal Article

Ardevol, A.; Hummer, G.: Retinal isomerization and water-pore formation in channelrhodopsin-2. Proceedings of the National Academy of Sciences of the United States of America 115 (14), pp. 3557 - 3562 (2018)

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72.

Journal Article

Cossio, P.; Hummer, G.: Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 49, pp. 162 - 168 (2018)

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73.

Journal Article

Cossio, P.; Hummer, G.; Szabo, A.: Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 148 (12), 123309 (2018)

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74.

Journal Article

Ramírez, A. S.; Boilevin, J.; Mehdipour, A. R.; Hummer, G.; Darbre, T.; Reymond, J.-L.; Locher, K. P.: Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nature Communications 9, 445 (2018)

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75.

Journal Article

D'Imprima, E.; Salzer, R.; Bhaskara, R. M.; Sánchez, R.; Rose, I.; Kirchner, L.; Hummer, G.; Kühlbrandt, W.; Vonck, J.; Averhoff, B.: Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 6, 10.7554/eLife.30483 (2017)

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76.

Journal Article

Stelzl, L. S.; Kells, A.; Rosta, E.; Hummer, G.: Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations. Journal of Chemical Theory and Computation 13 (12), pp. 6328 - 6342 (2017)

MPG.PuRe

DOI

77.

Journal Article

Lazaridis, T.; Hummer, G.: Classical Molecular Dynamics with Mobile Protons. Journal of Chemical Information and Modeling 57 (11), pp. 2833 - 2845 (2017)

MPG.PuRe

DOI

78.

Journal Article

Bahrami, A. H.; Lin, M. G.; Ren, X.; Hurley, J. H.; Hummer, G.: Scaffolding the cup-shaped double membrane in autophagy. PLoS Computational Biology 13 (10), e1005817 (2017)

MPG.PuRe

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79.

Journal Article

Jung, H.; Okazaki, K.-i.; Hummer, G.: Transition path sampling of rare events by shooting from the top. The Journal of Chemical Physics 147 (15), 152716 (2017)

MPG.PuRe

DOI

80.

Journal Article

Leahy, C. T.; Kells, A.; Hummer, G.; Buchete, N.-V.; Rosta, E.: Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics 147 (15), 152725 (2017)

MPG.PuRe

DOI

81.

Journal Article

Martini, L.; Covino, R.; Hummer, G.; Buchete, N.-V.; Rosta, E.: Variational Identification of Markovian Transition States. Physical Review X 7 (3), 031060 (2017)

MPG.PuRe

DOI

82.

Journal Article

Bahrami, A. H.; Hummer, G.: Formation and Stability of Lipid Membrane Nanotubes. ACS Nano 11 (9), pp. 9558 - 9565 (2017)

MPG.PuRe

DOI

83.

Journal Article

Sharma, V.; Belevich, G.; Gamiz-Hernandez, A. P.; Róg, T.; Vattulainen, I.; Verkhovskaya, M. L.; Wikström, M.; Hummer, G.; Kaila, V. R.I.: Redox-induced activation of the proton pump in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 112 (37), pp. 11571 - 11576 (2017)

MPG.PuRe

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84.

Journal Article

Stelzl, L. S.; Erlenbach, N.; Heinz, M.; Prisner, T. F.; Hummer, G.: Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics. Journal of the American Chemical Society 139 (34), pp. 11674 - 11677 (2017)

MPG.PuRe

DOI

85.

Journal Article

Halbleib, K.; Pesek, K.; Covino, R.; Hofbauer, H. F.; Wunnicke, D.; Hänelt, I.; Hummer, G.; Ernst, R.: Activation of the Unfolded Protein Response by Lipid Bilayer Stress. Molecular Cell 67 (4), pp. 673 - 684 (2017)

MPG.PuRe

DOI

86.

Journal Article

Stelzl, L. S.; Hummer, G.: Kinetics from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 13 (8), pp. 3927 - 3935 (2017)

MPG.PuRe

DOI

87.

Journal Article

Chiavazzo, E.; Covino, R.; Coifman, R. R.; Gear, C. W.; Georgiou, A. S.; Hummer, G.; Kevrekidis, I. G.: Intrinsic map dynamics exploration for uncharted effective free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America 114 (28), pp. E5494 - E5503 (2017)

MPG.PuRe

DOI

88.

Journal Article

Malinverni, D.; Jost-Lopez, A.; De Los Rios, P.; Hummer, G.; Barducci, A.: Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. eLife 6, e23471 (2017)

MPG.PuRe

DOI

89.

Journal Article

Ghysels, A.; Venables, R. M.; Pastor, R. W.; Hummer, G.: Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes. Journal of Chemical Theory and Computation 13 (6), pp. 2962 - 2976 (2017)

MPG.PuRe

DOI

90.

Journal Article

Reichel, K.; Fisette, O.; Braun, T.; Lange, O.; Hummer, G.; Schäfer, L. V.: Systematic evaluation of CS‐Rosetta for membrane protein structure prediction with sparse NOE restraints. Proteins: Structure, Function, and Bioinformatics 85 (5), pp. 812 - 826 (2017)

MPG.PuRe

DOI

91.

Journal Article

Hummer, G.; Szabo, A.: Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer. The Journal of Physical Chemistry B 121 (15), pp. 3331 - 3339 (2017)

MPG.PuRe

DOI

92.

Journal Article

Karathanasis, C.; Frick, F.; Hummer, G.; Heilemann, M.: Molecule Counts in Localization Microscopy with Organic Fluorophores. ChemPhysChem 18 (8), pp. 942 - 948 (2017)

MPG.PuRe

DOI

93.

Journal Article

Bhaskara, R.; Linker, S. M.; Vögele, M.; Köfinger, J.; Hummer, G.: Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano 11 (2), pp. 1273 - 1280 (2017)

MPG.PuRe

DOI

94.

Journal Article

Simonson, T.; Hummer, G.; Roux, B.: Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry A 121 (7), pp. 1525 - 1530 (2017)

MPG.PuRe

DOI

95.

Journal Article

Nöll, A.; Christoph, T.; Herbring, V.; Zollmann, T.; Barth, K.; Mehdipour, A. R.; Tomasiak, T. M.; Brüchert, S.; Joseph, B.; Abele, R. et al.; Oliéric, V.; Wang, M.; Diederichs, K.; Hummer, G.; Stroud, R. M.; Pos, K. M.; Tampé, R.: Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP. Proceedings of the National Academy of Sciences of the United States of America 114 (4), pp. E438 - E447 (2017)

MPG.PuRe

DOI

96.

Journal Article

Cossio, P.; Rohr, D.; Baruffa, F.; Rampp, M.; Lindenstruth, V.; Hummer, G.: BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications 210 (01), pp. 163 - 171 (2017)

MPG.PuRe

DOI

97.

Journal Article

Diskowski, M.; Mehdipour, A. R.; Wunnicke, D.; Mills, D. J.; Mikusevic, V.; Bärland, N.; Hoffmann, J.; Morgner, N.; Steinhoff, H.-J.; Hummer, G.: Helical jackknives control the gates of the double-pore K⁺ uptake system KtrABs. eLife, pp. 1 - 21 (2017)

MPG.PuRe

DOI

98.

Journal Article

Hummer, G.; Fricke, F.; Heilemann, M.: Model-independent counting of molecules in single-molecule localization microscopy. Molecular Biology of the Cell 27 (22), pp. 3637 - 3644 (2016)

MPG.PuRe

DOI

99.

Journal Article

Lehnert, E.; Mao, J.; Mehdipour, A. R.; Hummer, G.; Abele, R.; Glaubitz, C.; Tampé, R.: Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy. Journal of the American Chemical Society 138 (42), pp. 13967 - 13974 (2016)

MPG.PuRe

DOI

100.

Journal Article

Vögele, M.; Hummer, G.: Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. The Journal of Physical Chemistry B 25 (33), pp. 8722 - 8732 (2016)

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Publications of Gerhard Hummer

Journal Article (308)