Publications of the Max Planck Institute of Biophysics 1947 – present

2024

Journal Article

Lyratzakis, A.; Daskalakis, V.; Xie, H.; Tsiotis, G.: The synergy between the PscC subunits for electron transfer to the P₈₄₀ special pair in Chlorobaculum tepidum. Photosynthesis Research (2024)

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Schulz, V.; Steinhilper, R.; Oltmanns, J.; Freibert, S.-A.; Krapoth, N.; Linne, U.; Welsch, S.; Hoock, M. H.; Schünemann, V.; Murphy, B. J. et al.; Lill, R.: Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2. Nature Communications 15, 3269 (2024)

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Aziz, I.; Kayastha, K.; Kaltwasser, S.; Vonck, J.; Welsch, S.; Murphy, B. J.; Kahnt, J.; Wu, D.; Wagner, T.; Shima, S. et al.; Ermler, U.: Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. PNAS 121 (14), e2315568121 (2024)

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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)

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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)

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Adolph, C.; Cheung, C.-Y.; McNeil, M. B.; Jowsey, W. J.; Williams, Z. C.; Hards, K.; Harold, L. K.; Aboelela, A.; Bujaroski, R. S.; Buckley, B. J. et al.; Tyndall, J. D. A.; Li, Z.; Langer, J. D.; Preiss, L.; Meier, T.; Steyn, A. J. C.; Rhee, K. Y.; Berney, M.; Kelso, M. J.; Cook, G. M.: A dual-targeting succinate dehydrogenase and F₁F_o-ATP synthase inhibitor rapidly sterilizes replicating and non-replicating Mycobacterium tuberculosis. Cell Chemical Biology 31 (2024)

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

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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 (2024)

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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)

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

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Lasham, J.; Djurabekova, A.; Zickermann, V.; Vonck, J.; Sharma, V.: Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. The Journal of Physical Chemistry B (2024)

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Hoyer, M. J.; Capitanio, C.; Smith, I. R.; Paoli, J. C.; Bieber, A.; Jiang, Y.; Paulo, J. A.; Gonzalez-Lozano, M. A.; Baumeister, W.; Wilfling, F. et al.; Schulman, B. A.; Harper, J. W.: Combinatorial selective ER-phagy remodels the ER during neurogenesis. Nature Cell Biology (2024)

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Laube, E.; Schiller, J.; Zickermann, V.; Vonck, J.: Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallographica Section D: Structural Biology (2024)

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Schumacher, M.; Bamann, C.; Steinhoff, H.-J.: Time-Resolved EPR Spectroscopy of Channelrhodopsin-2 Helix B Movements. Applied Magnetic Resonance 55, pp. 207 - 218 (2024)

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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)

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Vlasova, A. D.; Bukhalovich, S. M.; Bagaeva, D. F.; Polyakova, A. P.; Ilyinsky, N. S.; Nesterov, S. V.; Tsybrov, F. M.; Bogorodskiy, A. O.; Zinovev, E. V.; Mikhailov, A. E. et al.; Vlasov, A. V.; Kuklin, A. I.; Borshchevskiy, V. I.; Bamberg, E.; Uversky, V. N.; Gordeliy, V. I.: Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling. Chemical Society Reviews 53 (7), pp. 3327 - 3349 (2024)

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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)

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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)

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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)

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

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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)

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Arnold, B.; Riegger, R. J.; Okuda, E. K.; Slišković, I.; Keller, M.; Bakisoglu, C.; McNicoll, F.; Zarnack, K.; Müller-McNicoll, M.: hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. Journal of Cell Biology 223 (2), e202304030 (2024)

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Liu, J.; Corroyer-Dulmont, S.; Pražák, V.; Khusainov, I.; Bahrami, K.; Welsch, S.; Vasishtan, D.; Obarska-Kosińska, A.; Thorkelsson, S. R.; Grünewald, K. et al.; Quemin, E. R. J.; Turoňová, B.; Locker, J. K.: The palisade layer of the poxvirus core is composed of flexible A10 trimers. Nature Structural & Molecular Biology (2024)

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Asgari, N.; Baaske, M. D.; Ton, J.; Orrit, M.: Exploring Rotational Diffusion with Plasmonic Coupling. ACS Photonics 11, pp. 634 - 641 (2024)

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Beck, M.; Covino, R.; Hänelt, I.; Müller-McNicoll, M.: Understanding the cell: Future views of structural biology. Cell 187 (3), pp. 545 - 562 (2024)

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Campbell, E. A.; Walden, H.; Walter, J. C.; Shukla, A. K.; Beck, M.; Passmore, L. A.; Xu, H. E.: AlphaFold: Research accelerator and hypothesis generator. Molecular Cell 84 (3), pp. 404 - 408 (2024)

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Centola, M.; Poppleton, E.; Ray, S.; Centola, M.; Welty, R.; Valero, J.; Walter, N. G.; Šulc, P.; Famulok, M.: A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. Nature Nanotechnology 19 (2), pp. 226 - 236 (2024)

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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)

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Jeppsson, K.; Pradhan, B.; Sutani, T.; Sakata, T.; Umeda Igarashi, M.; Berta, D. G.; Kanno, T.; Nakato, R.; Shirahige, K.; Kim, E. et al.; Björkegren, C.: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils. Molecular Cell (2024)

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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)

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Altincekic, N.; Jores, N.; Löhr, F.; Richter, C.; Ehrhardt, C.; Blommers, M. J. J.; Berg, H.; Öztürk, S.; Gande, S. L.; Linhard, V. et al.; Orts, J.; Abi Saad, M. J.; Bütikofer, M.; Kaderli, J.; Karlsson, B. G.; Brath, U.; Hedenström, M.; Gröbner, G.; Sauer, U. H.; Perrakis, A.; Langer, J. D.; Banci, L.; Cantini, F.; Fragai, M.; Grifagni, D.; Barthel, T.; Wollenhaupt, J.; Weiss, M. S.; Robertson, A.; Bax, A.; Sreeramulu, S.; Schwalbe, H.: Targeting the Main Protease (M^pro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies. ACS Chemical Biology (2024)

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Bapat, O.; Purimetla, T.; Kruessel, S.; Shah, M.; Fan, R.; Thum, C.; Rupprecht, F. A.; Langer, J. D.; Rangaraju, V.: VAP spatially stabilizes dendritic mitochondria to locally support synaptic plasticity. Nature Communications 15 (1), 205 (2024)

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Eria-Oliveira, A.-S.; Folacci, M.; Chassot, A. A.; Fedou, S.; Thézé, N.; Zabelskii, D.; Alekseev, A.; Bamberg, E.; Gordeliy, V.; Sandoz, G. et al.; Vivaudou, M.: Hijacking of internal calcium dynamics by intracellularly residing viral rhodopsins. Nature Communications 15 (1), 65 (2024)

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Asido, M.; Boumrifak, C.; Weissbecker, J.; Bamberg, E.; Wachtveitl, J.: Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality. Journal of Molecular Biology, 168447 (2024)

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Braun, H.-P.; Klusch, N.: Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases? Trends in Plant Science 29 (1), pp. 64 - 71 (2024)

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Schmidt, F. V.; Schulz, L.; Zarzycki, J.; Prinz, S.; Oehlmann, N. N.; Erb, T. J.; Rebelein, J. G.: Structural insights into the iron nitrogenase complex. Nature Structural & Molecular Biology 31 (1), pp. 150 - 158 (2024)

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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)

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Publications of the Max Planck Institute of Biophysics 1947 – present

Journal Article (37)