Gerhard Hummer: Theoretical Biophysics – Department Publications

Rosas Jiménez, J. G.; Fábián, B.; Hummer, G.: Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water. Journal of Chemical Theory and Computation 20 (24), pp. 11068 - 11081 (2024)

Heidari, M.; Sikora, M.; Hummer, G.: Refined Protein-Sugar Interactions in the Martini Force Field. Journal of Chemical Theory and Computation 20 (22), pp. 10259 - 10265 (2024)

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)

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 436 (17), 168546 (2024)

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)

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 11, pp. 5172 - 5184 (2024)

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)

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)

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)

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), 101960 (2024)

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)

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)

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)

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)

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

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)

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

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)

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)

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)

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)

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)

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)

Martinez-Mayorga, K.; Rosas-Jiménez, J. G.; Gonzalez-Ponce, K.; López-López, E.; Neme, A.; Medina-Franco, J. L.: The pursuit of accurate predictive models of the bioactivity of small molecules. Chemical Science 15 (6), pp. 1938 - 1952 (2024)

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)

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)

Jung, H.: Machine Learning for Biomolecular Simulations. Dissertation, 251 pp., FachbereichnPhysik Johann Wolfgang Goethe-Universität, Frankfurt am Main (2024)

Pietrek, L.: Modeling Ensembles of Disordered Biomolecules. Dissertation, 69 pp., Fachbereich Biochemie, Chemie und Pharmazie, Johann Wolfgang Goethe-Universität, Frankfurt am Main (2024)

Paikert, E.: TRPV4 regulation by Intrinsically Disordered Regions. Bachelor, 81 pp., Department of Physics, Goethe-University Frankfurt, Frankfurt am Main (2024)