Gerhard Hummer

2024

Journal Article

Heidari, M.; Sikora, M.; Hummer, G.: Refined Protein-Sugar Interactions in the Martini Force Field. Journal of Chemical Theory and Computation (2024)

MPG.PuRe

DOI

Full

Journal Article

Poveda-Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R. M.: Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy. Proceedings of the National Academy of Sciences of the United States of America 121 (44), e2408071121 (2024)

MPG.PuRe

DOI

Full

Journal Article

Mandal, T.; Brandt, N.; Tempra, C.; Javanainen, M.; Fábián, B.; Chiantia, S.: A comparison of lipid diffusive dynamics in monolayers and bilayers in the context of interleaflet coupling. Biochimica et Biophysica Acta: BBA 186 (1), 184388 (2024)

MPG.PuRe

DOI

Journal Article

Nüesch, M. F.; Pietrek, L.; Holmstrom, E. D.; Nettels, D.; von Roten, V.; Kronenberg-Tenga, R.; Medalia, O.; Hummer, G.; Schuler, B.: Nanosecond chain dynamics of single-stranded nucleic acids. Nature Communications 15 (1), 6010 (2024)

MPG.PuRe

DOI

Full

Journal Article

Eerlapally, R.; Vechalapu, S. K.; Duraisamy, S.; Hareendran, D. L.; Debnath, J.; Allimuthu, D.; Draksharapu, A.: A Cu(ii) pseudopeptide complex: a surrogate to a formal Cu(iii) species in water and an inhibitor of cancer cell proliferation. Inorganic Chemistry Frontiers (2024)

MPG.PuRe

DOI

Journal Article

Ri, K.; Weng, T.-H.; Claveras Cabezudo, A.; Jösting, W.; Zhang, Y.; Bazzone, A.; Leong, N. C. P.; Welsch, S.; Doty, R. T.; Gursu, G. et al.; Lim, T. J. Y.; Schmidt, S. L.; Abkowitz, J. L.; Hummer, G.; Wu, D.; Nguyen, L. N.; Safarian, S.: Molecular mechanism of choline and ethanolamine transport in humans. Nature 630, pp. 501 - 508 (2024)

MPG.PuRe

DOI

Full

Journal Article

Gauger, M.; Heinz, M.; Halbritter, A.-L. J.; Stelzl, L. S.; Erlenbach, N.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Structure and internal dynamics of short RNA duplexes determined by a combination of pulsed EPR methods and MD simulations. Angewandte Chemie, International Edition in English 63, e202402498 (2024)

MPG.PuRe

DOI

Full

Journal Article

Fábián, B.; Javanainen, M.: Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch. The Journal of Physical Chemistry Letters 15 (20), pp. 5344 - 5349 (2024)

MPG.PuRe

DOI

Full

Journal Article

Wang, J.; Heinz, M.; Han, K.; Shah, V. J.; Hasselbeck, S.; Schwalm, M. P.; Rathore, R.; Hummer, G.; Zhou, J.; Dikic, I. et al.; Cheng, X.: Thalidomide derivatives degrade BCL-2 by reprogramming the binding surface of CRBN. Cell Reports Physical Science 5 (5) (2024)

MPG.PuRe

DOI

Full

Journal Article

Cruz-León, S.; Majtner, T.; Hoffmann, P. C.; Kreysing, J. P.; Kehl, S.; Tuijtel, M.; Schaefer, S. L.; Geißler, K.; Beck, M.; Turoňová, B. et al.; Hummer, G.: High-confidence 3D template matching for cryo-electron tomography. Nature Communications 15, 3992 (2024)

MPG.PuRe

DOI

Full

Journal Article

Tuijtel, M.; Cruz-León, S.; Kreysing, J. P.; Welsch, S.; Hummer, G.; Beck, M.; Turoňová, B.: Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances 10 (17), eadk6285 (2024)

MPG.PuRe

DOI

Full

Journal Article

Bullerjahn, J. T.; Hanson, S. M.: Extracting thermodynamic properties from van ’t Hoff plots with emphasis on temperature-sensing ion channels. Temperature 11 (1), pp. 60 - 71 (2024)

MPG.PuRe

DOI

Full

Journal Article

Johnson, A. G.; Mayer, M. L.; Schaefer, S. L.; McNamara-Bordewick, N. K.; Hummer, G.; Kranzusch, P. J.: Structure and assembly of a bacterial gasdermin pore. Nature 628 (8008), pp. 657 - 663 (2024)

MPG.PuRe

DOI

Journal Article

Köfinger, J.; Hummer, G.: Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics 160, 114111 (2024)

MPG.PuRe

DOI

Full

Journal Article

Vallat, B.; Webb, B. M.; Westbrook, J. D.; Goddard, T. D.; Hanke, C. A.; Graziadei, A.; Peisach, E.; Zalevsky, A.; Sagendorf, J.; Tangmunarunkit, H. et al.; Voinea, S.; Sekharan, M.; Yu, J.; A M J J Bonvin, A.; DiMaio, F.; Hummer, G.; Meiler, J.; Tajkhorshid, E.; Ferrin, T. E.; Lawson, C. L.; Leitner, A.; Rappsilber, J.; Seidel, C. A. M.; Jeffries, C. M.; Burley, S. K.; Hoch, J. C.; Kurisu, G.; Morris, K.; Patwardhan, A.; Velankar, S.; Schwede, T.; Trewhella, J.; Kesselman, C.; Berman, H. M.; Sali, A.: IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology, 168546 (2024)

MPG.PuRe

DOI

Journal Article

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Hierarchical Assembly of Single-Stranded RNA. Journal of Chemical Theory and Computation 20 (5), pp. 2246 - 2260 (2024)

MPG.PuRe

DOI

Full

Journal Article

Blanc, F. E. C.; Hummer, G.: Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. PNAS 121 (11), e2314199121 (2024)

MPG.PuRe

DOI

Full

Journal Article

Tsai, Y.-X.; Chang, N.-E.; Reuter, K.; Chang, H.-T.; Yang, T.-J.; von Bülow, S.; Sehrawat, V.; Zerrouki, N.; Tuffery, M.; Gecht, M. et al.; Grothaus, I. L.; Colombi Ciacchi, L.; Wang, Y.-S.; Hsu, M.-F.; Khoo, K.-H.; Hummer, G.; Hsu, S.-T. D.; Hanus, C.; Sikora, M.: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 187 (5), pp. 1296 - 1311.e26 (2024)

MPG.PuRe

DOI

Full

Journal Article

Shukla, S.; Chen, W.; Rao, S.; Yang, S.; Ou, C.; Larsen, K. P.; Hummer, G.; Hanson, P. I.; Hurley, J. H.: Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca²⁺-sensor ALG-2. Proceedings of the National Academy of Sciences of the United States of America 121 (9), e2318046121 (2024)

MPG.PuRe

DOI

Full

Journal Article

Vögele, M.; Köfinger, J.; Hummer, G.: Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials 7 (2), pp. 528 - 534 (2024)

MPG.PuRe

DOI

Full

Journal Article

Bjarnason, S.; McIvor, J. A. P.; Prestel, A.; Demény, K. S.; Bullerjahn, J. T.; Kragelund, B. B.; Mercadante, D.; Heidarsson, P. O.: DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nature Communications 15, 1445 (2024)

MPG.PuRe

DOI

Full

Journal Article

Rao, S.; Skulsuppaisarn, M.; Strong, L. M.; Ren, X.; Lazarou, M.; Hurley, J. H.; Hummer, G.: Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Science Advances 10 (6), eadj8027 (2024)

MPG.PuRe

DOI

Full

Journal Article

Gambelli, L.; McLaren, M.; Conners, R.; Sanders, K.; Gaines, M. C.; Clark, L.; Gold, V. A. M.; Kattnig, D.; Sikora, M.; Hanus, C. et al.; Isupov, M. N.; Daum, B.: Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 13, e84617 (2024)

MPG.PuRe

DOI

Full

Journal Article

Gewering, T.; Waghray, D.; Parey, K.; Jung, H.; Tran, N. N. B.; Zapata, J.; Zhao, P.; Chen, H.; Januliene, D.; Hummer, G. et al.; Urbatsch, I.; Moeller, A.; Zhang, Q.: Tracing the substrate translocation mechanism in P-glycoprotein. eLife 12, RP90174 (2024)

MPG.PuRe

DOI

Full

Journal Article

Ugrina, M.; Burkhart, I.; Müller, D.; Schwalbe, H.; Schwierz, N.: RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Research 52 (1), gkad1065, pp. 87 - 100 (2024)

MPG.PuRe

DOI

Full

2023

Journal Article

Lazzeri, G.; Jung, H.; Bolhuis, P. G.; Covino, R.: Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations. Journal of Chemical Theory and Computation 19 (24), pp. 9060 - 9076 (2023)

MPG.PuRe

DOI

Full

Journal Article

Kim, H.; Fábián, B.; Hummer, G.: Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 19 (23), pp. 8919 - 8929 (2023)

MPG.PuRe

DOI

Full

Journal Article

Pandi, A.; Adam, D.; Zare, A.; Trinh, V. T.; Schaefer, S. L.; Burt, M.; Klabunde, B.; Bobkova, E.; Kushwaha, M.; Foroughijabbari, Y. et al.; Braun, P.; Spahn, C.; Preußer, C.; Pogge von Strandmann, E.; Bode, H. B.; von Buttlar, H.; Bertrams, W.; Jung, A. L.; Abendroth, F.; Schmeck, B.; Hummer, G.; Vázquez, O.; Erb, T. J.: Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. Nature Communications 14 (1), 7197 (2023)

MPG.PuRe

DOI

Full

Journal Article

Ibrahim, M.; Wenzel, C.; Lallemang, M.; Balzer, B. N.; Schwierz, N.: Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. Langmuir 39 (44), pp. 15553 - 15562 (2023)

MPG.PuRe

DOI

Journal Article

Oosterheert, W.; Blanc, F. E. C.; Roy, A.; Belyy, A.; Sanders, M. B.; Hofnagel, O.; Hummer, G.; Bieling, P.; Raunser, S.: Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology 30 (11), pp. 1774 - 1785 (2023)

MPG.PuRe

DOI

Full

Journal Article

Borges-Araújo, L.; Borges-Araújo, A. C.; Ozturk, T. N.; Ramirez-Echemendia, D. P.; Fábián, B.; Carpenter, T. S.; Thallmair, S.; Barnoud, J.; Ingólfsson, H. I.; Hummer, G. et al.; Tieleman, D. P.; Marrink, S. J.; Souza, P. C. T.; Melo, M. N.: Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation 19 (20), pp. 7387 - 7404 (2023)

MPG.PuRe

DOI

Journal Article

Flores-Solis, D.; Lushpinskaia, I. P.; Polyansky, A. A.; Changiarath, A.; Boehning, M.; Mirkovic, M.; Walshe, J.; Pietrek, L. M.; Cramer, P.; Stelzl, L. S. et al.; Zagrovic, B.; Zweckstetter, M.: Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications 14, 5979 (2023)

MPG.PuRe

DOI

Full

Journal Article

Nguyen, H.; Nguyen, H. L.; Lan, P. D.; Thai, N. Q.; Sikora, M.; Li, M. S.: Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chemical Society Reviews 52 (18), pp. 6497 - 6553 (2023)

MPG.PuRe

DOI

Journal Article

Bullerjahn, J. T.; Fábián, B.; Hummer, G.: Efficient generation of random rotation matrices in four dimensions. Physical Review E 108 (3), 035307 (2023)

MPG.PuRe

DOI

Full

Journal Article

Hanson, S. M.; Scholüke, J.; Liewald, J.; Sharma, R.; Ruse, C.; Engel, M.; Schüler, C.; Klaus, A.; Arghittu, S.; Baumbach, F. et al.; Seidenthal, M.; Dill, H.; Hummer, G.; Gottschalk, A.: Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB 33 (16), pp. 3423 - 3435.e5 (2023)

MPG.PuRe

DOI

Journal Article

Wu, D.; Mehdipour, A. R.; Finke, F.; Goojani, H. G.; Groh, R. R.; Grund, T. N.; Reichhart, T. M. B.; Zimmermann, R.; Welsch, S.; Bald, D. et al.; Shepherd, M.; Hummer, G.; Safarian, S.: Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 19 (8), pp. 992 - 1003 (2023)

MPG.PuRe

DOI

Full

Journal Article

Goretzki, B.; Wiedemann, C.; McCray, B. A.; Schäfer, S. L.; Jansen, J.; Tebbe, F.; Mitrovic, S.-A.; Nöth, J.; Cabezudo, A. C.; Donohue, J. K. et al.; Jeffries, C. M.; Steinchen, W.; Stengel, F.; Sumner, C. J.; Hummer, G.; Hellmich, U. A.: Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications 14, 4165 (2023)

MPG.PuRe

DOI

Full

Journal Article

Ibrahim, M.; Gilbert, J.; Heinz, M.; Nylander, T.; Schwierz, N.: Structural insights on ionizable Dlin-MC3-DMA lipids in DOPC layers by combining accurate atomistic force fields, molecular dynamics simulations and neutron reflectivity. Nanoscale 15 (27), pp. 11647 - 11656 (2023)

MPG.PuRe

DOI

Full

Journal Article

Bullerjahn, J. T.; von Bülow, S.; Heidari, M.; Hénin, J.; Hummer, G.: Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation 19, pp. 3406 - 3417 (2023)

MPG.PuRe

DOI

Full

Journal Article

Foronda, H.; Fu, Y.; Covarrubias-Pinto, A.; Bocker, H. T.; González, A.; Seemann, E.; Franzka, P.; Bock, A.; Bhaskara, R. M.; Liebmann, L. et al.; Hoffmann, M. E.; Katona, I.; Koch, N.; Weis, J.; Kurth, I.; Gleeson, J. G.; Reggiori, F.; Hummer, G.; Kessels, M. M.; Qualmann, B.; Mari, M.; Dikić, I.; Hübner, C. A.: Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 618 (7964), pp. 402 - 410 (2023)

MPG.PuRe

DOI

Full

Journal Article

González, A.; Covarrubias-Pinto, A.; Bhaskara, R. M.; Glogger, M.; Kuncha, S. K.; Xavier, A.; Seemann, E.; Misra, M.; Hoffmann, M. E.; Bräuning, B. et al.; Balakrishnan, A.; Qualmann, B.; Dötsch, V.; Schulman, B. A.; Kessels, M. M.; Hübner, C. A.; Heilemann, M.; Hummer, G.; Dikić, I.: Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature 618 (7964), pp. 394 - 401 (2023)

MPG.PuRe

DOI

Full

Journal Article

Valko, A.; Fracchiolla, D.: “Autophagic landscapes: on the paradox of survival through self-degradation” – A science-inspired exhibition. Autophagy 19 (9), pp. 2601 - 2606 (2023)

MPG.PuRe

DOI

Full

Journal Article

Cai, W.; Jäger, M.; Bullerjahn, J. T.; Hugel, T.; Wolf, S.; Balzer, B. N.: Anisotropic Friction in a Ligand-Protein Complex. Nano Letters 23 (10), pp. 4111 - 4119 (2023)

MPG.PuRe

DOI

Full

Journal Article

Lettl, C.; Schindele, F.; Mehdipour, A. R.; Steiner, T.; Ring, D.; Brack-Werner, R.; Stecher, B.; Eisenreich, W.; Bilitewski, U.; Hummer, G. et al.; Witschel, M.; Fischer, W.; Haas, R.: Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 30 (5), pp. 499 - 512 (2023)

MPG.PuRe

DOI

Journal Article

Yu, M.; Heidari, M.; Mikhaleva, S.; Tan, P. S.; Mingu, S.; Ruan, H.; Reinkemeier, C. D.; Obarska-Kosinska, A.; Siggel, M.; Beck, M. et al.; Hummer, G.; Lemke, E. A.: Visualizing the disordered nuclear transport machinery in situ. Nature 617 (7959), pp. 162 - 169 (2023)

MPG.PuRe

DOI

Full

Journal Article

Jung, H.; Covino, R.; Arjun, A.; Leitold, C.; Dellago, C.; Bolhuis, P. G.; Hummer, G.: Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 3 (4), pp. 334 - 345 (2023)

MPG.PuRe

DOI

Full

Journal Article

Fábián, B.; Thallmair, S.; Hummer, G.: Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 19 (5), pp. 1592 - 1601 (2023)

MPG.PuRe

DOI

Full

Journal Article

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 78, 102501 (2023)

MPG.PuRe

DOI

Full

Journal Article

von Bülow, S.; Sikora, M.; Blanc, F. E. C.; Covino, R.; Hummer, G.: Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 19 (1), e1010822 (2023)

MPG.PuRe

DOI

Full

Journal Article

Honti, B.; Fábián, B.; Idrissi, A.; Jedlovszky, P.: Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations. The Journal of Physical Chemistry B 127 (4), pp. 1050 - 1062 (2023)

MPG.PuRe

DOI

Full

2022

Journal Article

Zhu, R.; Canena, D.; Sikora, M.; Klausberger, M.; Seferovic, H.; Mehdipour, A. R.; Hain, L.; Laurent, E.; Monteil, V.; Wirnsberger, G. et al.; Wieneke, R.; Tampé, R.; Kienzl, N. F.; Mach, L.; Mirazimi, A.; Oh, Y. J.; Penninger, J. M.; Hummer, G.; Hinterdorfer, P.: Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 13 (1), 7926 (2022)

MPG.PuRe

DOI

Full

Journal Article

Jensen, L. E.; Rao, S.; Schuschnig, M.; Cada, A. K.; Martens, S.; Hummer, G.; Hurley, J. H.: Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 8 (50), eadd1436 (2022)

MPG.PuRe

DOI

Full

Journal Article

Linke, M.; Quoika, P. K.; Bramas, B.; Köfinger, J.; Hummer, G.: Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 157 (20), 204802 (2022)

MPG.PuRe

DOI

Full

Journal Article

Schaefer, S. L.; Hummer, G.: Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022)

MPG.PuRe

DOI

Full

Journal Article

Siggel, M.; Kehl, S.; Reuter, K.; Köfinger, J.; Hummer, G.: TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 157 (17), 174801 (2022)

MPG.PuRe

DOI

Full

Journal Article

Cruz-León, S.; Schwierz, N.: RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B (2022)

MPG.PuRe

DOI

Full

Journal Article

Bieber, A.; Capitanio, C.; Erdmann, P. S.; Fiedler, F.; Beck, F.; Lee, C.-W.; Li, D.; Hummer, G.; Schulman, B. A.; Baumeister, W. et al.; Wilfling, F.: In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America 119 (39), e2209823119 (2022)

MPG.PuRe

DOI

Full

Journal Article

Khera, R.; Mehdipour, A. R.; Bolla, J. R.; Kahnt, J.; Welsch, S.; Ermler, U.; Münke, C.; Robinson, C. V.; Hummer, G.; Xie, H. et al.; Michel, H.: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 41 (18), e109990 (2022)

MPG.PuRe

DOI

Full

Journal Article

Mikolajczyk, K.; Sikora, M.; Hanus, C.; Kaczmarek, R.; Czerwinski, M.: One of the two N-glycans on the human Gb3/CD77 synthase is essential for its activity and allosterically regulates its function. Biochemical and Biophysical Research Communications (Orlando, FL) 617, pp. 36 - 41 (2022)

MPG.PuRe

DOI

Journal Article

Palacio-Rodriguez, K.; Vroylandt, H.; Stelzl, L. S.; Pietrucci, F.; Hummer, G.; Cossio, P.: Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 13 (32), pp. 7490 - 7496 (2022)

MPG.PuRe

DOI

Journal Article

Sušac, L.; Vuong, M. T.; Thomas, C.; von Bülow, S.; O'Brien-Ball, C.; Santos, A. M.; Fernandes, R. A.; Hummer, G.; Tampé, R.; Davis, S. J.: Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 185 (17), pp. 3201 - 3213 (2022)

MPG.PuRe

DOI

publisher-version

Journal Article

Bullerjahn, J. T.; Hummer, G.: Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 4 (3), 033097 (2022)

MPG.PuRe

DOI

Full

Journal Article

Fábián, B.; Thallmair, S.; Hummer, G.: Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 157 (3), 034101 (2022)

MPG.PuRe

DOI

Full

Journal Article

Cruz-León, S.; Vanderlinden, W.; Müller, P.; Forster, T.; Staudt, G.; Lin, Y.-Y.; Lipfert, J.; Schwierz, N.: Twisting DNA by salt. Nucleic Acids Research (London) 50 (10), pp. 5726 - 5739 (2022)

MPG.PuRe

DOI

Full

Journal Article

Mosalaganti, S.; Obarska-Kosinska, A.; Siggel, M.; Taniguchi, R.; Turoňová, B.; Zimmerli, C. E.; Buczak, K.; Schmidt, F. H.; Margiotta, E.; Mackmull, M.-T. et al.; Hagen, W. J. H.; Hummer, G.; Kosinski, J.; Beck, M.: AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 376 (6598), eabm9506 (2022)

MPG.PuRe

DOI

Full

Journal Article

Cullati, S. N.; Chaikuad, A.; Chen, J.-S.; Gebel, J.; Tesmer, L.; Zhubi, R.; Navarrete-Perea, J.; Guillen, R. X.; Gygi, S. P.; Hummer, G. et al.; Dötsch, V.; Knapp, S.; Gould, K. L.: Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 82 (11), pp. 2006 - 2020.e8 (2022)

MPG.PuRe

DOI

Journal Article

Ochoa, R.; Lunardelli, V. A. S.; Rosa, D. S.; Laio, A.; Cossio, P.: Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Frontiers in immunology 13, 862851 (2022)

MPG.PuRe

DOI

Journal Article

Cai, W.; Bullerjahn, J. T.; Lallemang, M.; Kroy, K.; Balzer, B. N.; Hugel, T.: Angle-dependent strength of a single chemical bond by stereographic force spectroscopy. Chemical Science 13 (19), pp. 5734 - 5740 (2022)

MPG.PuRe

DOI

Full

Journal Article

Fuks, C.; Falkner, S.; Schwierz, N.; Hengesbach, M.: Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Frontiers in Molecular Biosciences 9, 826505 (2022)

MPG.PuRe

DOI

Full

Journal Article

Grotz, K. K.; Schwierz, N.: Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E. The Journal of Chemical Physics 156 (11), 114501 (2022)

MPG.PuRe

DOI

Full

Journal Article

Seidel, M.; Becker, A.; Pereira, F.; Landry, J. J. M.; de Azevedo, N. T. D.; Fusco, C. M.; Kaindl, E.; Romanov, N.; Baumbach, J.; Langer, J. D. et al.; Schuman, E. M.; Patil, K. R.; Hummer, G.; Benes, V.; Beck, M.: Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 13, 1224 (2022)

MPG.PuRe

DOI

Full

Journal Article

Stelzl, L. S.; Pietrek, L. M.; Holla, A.; Oroz, J.; Sikora, M.; Köfinger, J.; Schuler, B.; Zweckstetter, M.; Hummer, G.: Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 2 (3), pp. 673 - 686 (2022)

MPG.PuRe

DOI

Full

Journal Article

Lambert, E.; Mehdipour, A. R.; Schmidt, A.; Hummer, G.; Perez, C.: Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 13 (1), 1022 (2022)

MPG.PuRe

DOI

Journal Article

Slováková, J.; Sikora, M.; Arslan, F. N.; Caballero-Mancebo, S.; Krens, S. F. G.; Kaufmann, W. A.; Merrin, J.; Heisenberg, C.-P.: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America 119 (8), e2122030119 (2022)

MPG.PuRe

DOI

Journal Article

Neumann, J.; Schwierz, N.: Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA. Journal of Chemical Theory and Computation 18 (2), pp. 1202 - 1212 (2022)

MPG.PuRe

DOI

Journal Article

Gruijs da Silva, L. A.; Simonetti, F.; Hutten, S.; Riemenschneider, H.; Sternburg, E. L.; Pietrek, L. M.; Gebel, J.; Dötsch, V.; Edbauer, D.; Hummer, G. et al.; Stelzl, L. S.; Dormann, D.: Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 41 (3), e108443 (2022)

MPG.PuRe

DOI

Full

Journal Article

Grotz, K. K.; Schwierz, N.: Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. Journal of Chemical Theory and Computation 18 (1), pp. 526 - 537 (2022)

MPG.PuRe

DOI

Full

Journal Article

Heerde, T.; Rennegarbe, M.; Biedermann, A.; Savran, D.; Pfeiffer, P. B.; Hitzenberger, M.; Baur, J.; Puscalau-Girtu, I.; Zacharias, M.; Schwierz, N. et al.; Haupt, C.; Schmidt, M.; Fändrich, M.: Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding. Nature Communications 13 (1), 85 (2022)

MPG.PuRe

DOI

2021

Journal Article

Köfinger, J.; Hummer, G.: Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 94 (12), 245 (2021)

MPG.PuRe

DOI

Full

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 374 (6573), eabd9776 (2021)

MPG.PuRe

DOI

Full

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

Journal Article

Rocha-Roa, C.; Orjuela, J. D.; Leidy, C.; Cossio, P.; Aponte-Santamaría, C.: Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Letters 595 (21), pp. 2701 - 2714 (2021)

MPG.PuRe

DOI

Journal Article

Klaus, M.; Rossini, E.; Linden, A.; Paithankar, K. S.; Zeug, M.; Ignatova, Z.; Urlaub, H.; Khosla, C.; Köfinger, J.; Hummer, G. et al.; Grininger, M.: Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 1 (12), pp. 2162 - 2171 (2021)

MPG.PuRe

DOI

Full

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

Journal Article

Falkner, S.; Schwierz, N.: Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field. The Journal of Chemical Physics 155 (8), 084503 (2021)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

Journal Article

Giraldo-Barreto, J.; Ortiz, S.; Thiede, E. H.; Palacio-Rodriguez, K.; Carpenter, B.; Barnett, A. H.; Cossio, P.: A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Scientific Reports 11 (1), 13657 (2021)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

Full

Journal Article

Cruz-León, S.; Grotz, K. K.; Schwierz, N.: Extended magnesium and calcium force field parameters for accurate ion–nucleic acid interactions in biomolecular simulations. The Journal of Chemical Physics 154 (17), 171102 (2021)

MPG.PuRe

DOI

Full

Journal Article

Grotz, K. K.; Cruz-León, S.; Schwierz, N.: Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties. Journal of Chemical Theory and Computation 17 (4), pp. 2530 - 2540 (2021)

MPG.PuRe

DOI

Full

Journal Article

Nome, R. A.; Cossio, P.; Z, Y.: Editorial: Integrating Timescales From Molecules Up. Frontiers in Chemistry 9, 680533 (2021)

MPG.PuRe

DOI

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)

MPG.PuRe

DOI

Full

Gerhard Hummer: Theoretical Biophysics – Department Publications

Journal Article (243)