Gerhard Hummer Publications

2019

Journal Article

Siggel, M.; Bhaskara, R. M.; Hummer, G.: Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters 10 (20), pp. 6351 - 6354 (2019)

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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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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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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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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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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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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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Full

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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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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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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Full

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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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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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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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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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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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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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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2018

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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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2017

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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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)

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Journal Article

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

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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)

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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)

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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)

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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)

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Journal Article

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

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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2016

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)

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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)

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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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Journal Article

Cossio, P.; Hummer, G.; Szabo, A.: Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophysical Journal 111 (4), pp. 832 - 840 (2016)

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Journal Article

Mehdipour, A. R.; Hummer, G.: Cardiolipin puts the seal on ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 113 (31), pp. 8568 - 8570 (2016)

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Journal Article

Leahy, C. T.; Murphy, R. D.; Hummer, G.; Rosta, E.; Buchete, N.-V.: Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters 7 (14), pp. 2676 - 2682 (2016)

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Journal Article

Covino, R.; Ballweg, S.; Stordeur, C.; Michaelis, J. B.; Puth, K.; Wernig, F.; Bahrami, A. H.; Ernst, A. M.; Hummer, G.; Ernst, R.: A Eukaryotic Sensor for Membrane Lipid Saturation. Molecular Cell 63 (1), pp. 49 - 59 (2016)

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Journal Article

Hummer, G.; Wikström, M.: Molecular simulation and modeling of complex I. Biochimica et Biophysica Acta, Bioenergetics 1857 (7), pp. 915 - 921 (2016)

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Journal Article

Sugawa, M.; Okazaki, K.-i.; Kobayashi, M.; Matsui, T.; Hummer, G.; Masaike, T.; Nishizaka, T.: F₁-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements. Proceedings of the National Academy of Sciences of the United States of America 113 (21), pp. E2916 - E2924 (2016)

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Journal Article

Best, R.; Hummer, G.: Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proceedings of the National Academy of Sciences of the United States of America 113 (12), pp. 3263 - 3268 (2016)

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2015

Journal Article

Hummer, G.; Köfinger, J.: Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 143 (24), pp. 243150-1 - 243150-14 (2015)

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Journal Article

Blees, A.; Reichel, K.; Trowitzsch, S.; Fisette, O.; Bock, C.; Abele, R.; Hummer, G.; Schäfer, L. V.; Tampé, R.: Assembly of the MHC I peptideloading complex determined by a conserved ionic lock-switch. Scientific Reports 5, 17341 (2015)

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Journal Article

Cossio, P.; Hummer, G.; Szabo, A.: On artifacts in single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 112 (46), pp. 14248 - 14253 (2015)

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Journal Article

Barends, T. R.M.; Foucar, L.; Ardevol, A.; Nass, K.; Aquila, A.; Botha, S.; Doak, R. B.; Falahati, K.; Hartmann, E.; Hilpert, M. et al.; Heinz, M.; Hoffmann, M. C.; Köfinger, J.; Koglin, J. E.; Kovacsova, G.; Liang, M.; Milathianaki, D.; Lemke, H. T.; Reinstein, J.; Roome, C. M.; Shoeman, R. L.; Williams, G. J.; Burghardt, I.; Hummer, G.; Boutet, S.; Schlichting, I.: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350 (6259), pp. 445 - 450 (2015)

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Journal Article

Mantsyzov, A. B.; Shen, Y.; Lee, J. H.; Hummer, G.; Bax, A.: MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data. Journal of Biomolecular NMR 63 (1), pp. 85 - 95 (2015)

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Journal Article

Okazaki, K.-i.; Hummer, G.: Elasticity, friction, and pathway of γ-subunit rotation in F_oF₁-ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 112 (34), pp. 10720 - 10725 (2015)

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Journal Article

Hummer, G.; Szabo, A.: Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models. The Journal of Physical Chemistry B 119 (29), pp. 9029 - 9037 (2015)

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Journal Article

Sali, A.; Berman, H. M.; Schwede, T.; Trewhella, J.; Kleywegt, G.; Burley, S. K.; Markley, J.; Nakamura, H.; Adams, P.; Bonvin, A. M.J.J. et al.; Chiu, W.; Dal Peraro, M.; Di Maio, F.; Ferrin, T. E.; Grünewald, K.; Gutmanas, A.; Henderson, R.; Hummer, G.; Iwasaki, K.; Johnson, G.; Lawson, C. L.; Meiler, J.; Marti-Renom, M. A.; Montelione, G. T.; Nilges, M.; Nussinov, R.; Patwardhan, A.; Rappsilber, J.; Read, R. J.; Saibil, H.; Schröder, G. F.; Schwieters, C. D.; Seidel, C. A.M.; Svergun, D.; Topf, M.; Ulrich, E. L.; Velankar, S.; Westbrook, J. D.: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23 (7), pp. 1156 - 1167 (2015)

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Journal Article

Kmita, K.; Wirth, C.; Warnau, J.; Guerrero-Castillo, S.; Hunte, C.; Hummer, G.; Kaila, V. R.I.; Zwicker, K.; Brandt, U.; Zickermann, V.: Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proceedings of the National Academy of Sciences of the United States of America 112 (18), pp. 5685 - 5690 (2015)

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Journal Article

Köfinger, J.; Ragusa, M. J.; Lee, I.-H.; Hummer, G.; Hurley, J. H.: Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site. Structure 23 (5), pp. 809 - 818 (2015)

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Journal Article

Wikström, M.; Sharma, V.; Kaila, V. R.I.; Hosler, J. P.; Hummer, G.: New Perspectives on Proton Pumping in Cellular Respiration. Chemical Reviews 115 (5), pp. 2045 - 2222 (2015)

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Journal Article

Gamiz-Hernandez, A. P.; Magomedov, A.; Hummer, G.; Kaila, V. R.I.: Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer. The Journal of Physical Chemistry B 119 (6), pp. 2611 - 2619 (2015)

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Journal Article

Rosta, E.; Hummer, G.: Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model. Journal of Chemical Theory and Computation 11 (1), pp. 276 - 285 (2015)

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2014

Journal Article

Nedialkova, L. V.; Amat, M. A.; Kevrekidis, I. G.; Hummer, G.: Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. The Journal of Chemical Physics 141 (11), pp. 114102 - 114117 (2014)

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Journal Article

Hummer, G.: Potassium ions line up. Do K⁺ ions move in single file through potassium channels? Science Magazine 346 (6207), p. 303 - 303 (2014)

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Journal Article

Johnson, M. E.; Hummer, G.: Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 4 (3), pp. 031037 - 031058 (2014)

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Journal Article

Mantsyzov, A. B.; Maltsev, A. S.; Ying, J.; Shen, Y.; Hummer, G.; Bax, A.: A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein. Protein Science 23 (9), pp. 1275 - 1290 (2014)

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Journal Article

Kaila, V. R.I.; Wikström, M.; Hummer, G.: Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 111 (19), pp. 6988 - 6993 (2014)

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Journal Article

Kaila, V. R.I.; Schotte, F.; Cho, H. S.; Hummer, G.; Anfinrud, P. A.: Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nature Chemistry 6 (4), pp. 258 - 259 (2014)

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Journal Article

Rosta, E.; Yang, W.; Hummer, G.: Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis. Journal of the American Chemical Society 136 (8), pp. 3137 - 3144 (2014)

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Journal Article

Hummer, G.; Dellago, C.: Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 16 (1), pp. 41 - 61 (2014)

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2013

Journal Article

Cossio, P.; Hummer, G.: Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Journal of Structural Biology 184 (3), pp. 427 - 437 (2013)

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Journal Article

Best, R. B.; Hummer, G.; Eaton, W. A.: Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 110 (44), pp. 17874 - 17879 (2013)

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Johnson, M. E.; Hummer, G.: Evolutionary pressure on the topology of protein interface interaction networks. The Journal of Physical Chemistry B 117 (42), pp. 13098 - 13106 (2013)

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Journal Article

Okazaki, K.-i.; Hummer, G.: Phosphate release coupled to rotary motion of F₁-ATPase. Proceedings of the National Academy of Sciences of the United States of America 110 (41), pp. 16468 - 16473 (2013)

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Johnson, M. E.; Hummer, G.: Interface-resolved network of protein-protein interactions. PLoS Computational Biology 9 (5), e1003065 (2013)

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Köfinger, J.; Hummer, G.: Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical Review E 87, 052712 (2013)

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Grigoriu, S.; Bond, R.; Cossio, P.; Chen, J. A.; Ly, N.; Hummer, G.; Page, R.; Cyert, M. S.; Peti, W.: The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biology 11 (2), e1001492 (2013)

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2012

Journal Article

Lans, I.; Medina, M.; Rosta, E.; Hummer, G.; Garcia-Viloca, M.; Lluch, J. M.; González-Lafont, À.: Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP⁺ reductase and NADP⁺: the role of Tyr303. Journal of the American Chemical Society 134 (50), pp. 20544 - 20553 (2012)

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Journal Article

Schotte, F.; Cho, H. S.; Kaila, V. R. I.; Kamikubo, H.; Dashdorj, N.; Henry, E. R.; Graber, T. J.; Henning, R.; Wulff, M.; Hummer, G. et al.; Kataoka, M.; Anfinrud, P. A.: Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America 109 (47), pp. 19256 - 19261 (2012)

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Journal Article

Zhu, F.; Hummer, G.: Theory and simulation of ion conduction in the pentameric GLIC channel. Journal of Chemical Theory and Computation 8 (10), pp. 3759 - 3768 (2012)

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Publications of Gerhard Hummer

Journal Article (370)