Max Planck Institute of Biophysics

Publications of the Max Planck Institute of Biophysics

Publications of the Max Planck Institute of Biophysics

Journal Article (42)

2025

Journal Article

Stautz, J.; Griwatz, D.; Kaltwasser, S.; Mehdipour, A. R.; Ketter, S.; Thiel, C.; Wunnicke, D.; Schrecker, M.; Mills, D. J.; Hummer, G. et al.; Vonck, J.; Hänelt, I.: A short intrinsically disordered region at KtrB’s N-terminus facilitates allosteric regulation of K⁺ channel KtrAB. Nature Communications 16, 4252 (2025)

MPG.PuRe

Journal Article

Stuke, J. F. M.; Hummer, G.: AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy. Autophagy (2025)

MPG.PuRe

Journal Article

Kühlbrandt, W.; Carreira, L. A. M.; Yildiz, Ö.: Cryo-EM of Mitochondrial Complex I and ATP Synthase. Annual Review of Biophysics 54, pp. 209 - 226 (2025)

MPG.PuRe

Journal Article

Bukhdruker, S.; Gushchin, I.; Shevchenko, V.; Kovalev, K.; Polovinkin, V.; Tsybrov, F.; Astashkin, R.; Alekseev, A.; Mikhaylov, A.; Bukhalovich, S. et al.; Bratanov, D.; Ryzhykau, Y.; Kuklina, D.; Caramello, N.; Rokitskaya, T.; Antonenko, Y.; Rulev, M.; Stoev, C.; Zabelskii, D.; Round, E.; Rogachev, A.; Borshchevskiy, V.; Ghai, R.; Bourenkov, G.; Zeghouf, M.; Cherfils, J.; Engelhard, M.; Chizhov, I.; Rodriguez-Valera, F.; Bamberg, E.; Gordeliy, V.: Proteorhodopsin insights into the molecular mechanism of vectorial proton transport. Science Advances 11 (16), eadu5303 (2025)

MPG.PuRe

Journal Article

Ros, U.; Martinez-Osorio, V.; Valiente, P. A.; Abdelwahab, Y.; Gojkovic, M.; Shalaby, R.; Zanna, S.; Saggau, J.; Wachsmuth, L.; Nemade, H. N. et al.; Zoeller, J.; Lottermoser, H.; Chen, Y.-G.; Ibrahim, M.; Kelepouras, K.; Vasilikos, L.; Bedoya, P.; Espiritu, R. A.; Müller, S.; Altmannova, V.; Tieleman, D. P.; Weir, J.; Langer, J. D.; Adam, M.; Walczak, H.; Wong, W. W.-L.; Liccardi, G.; Mollenhauer, M.; Pasparakis, M.; Peltzer, N.; García-Sáez, A. J.: MLKL activity requires a splicing-regulated, druggable intramolecular interaction. Molecular Cell 85 (2025)

MPG.PuRe

Journal Article

Zaghbani, S.; Faber, L.; Garcia Saez, A. J.: Convolutional Neural Network approach to classify mitochondrial morphologies. Computational Biology and Chemistry 118, 108477 (2025)

MPG.PuRe

Journal Article

Cook, A. S. I.; Chen, M.; Nguyen, T. N.; Cabezudo, A. C.; Khuu, G.; Rao, S.; Garcia, S. N.; Yang, M.; Iavarone, A. T.; Ren, X. et al.; Lazarou, M.; Hummer, G.; Hurley, J. H.: Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Science 388 (6743), eadl3787 (2025)

MPG.PuRe

Journal Article

Taniguchi, R.; Orniacki, C.; Kreysing, J. P.; Zila, V.; Zimmerli, C. E.; Böhm, S.; Turoňová, B.; Kräusslich, H.-G.; Doye, V.; Beck, M.: Nuclear pores safeguard the integrity of the nuclear envelope. Nature Cell Biology (2025)

MPG.PuRe

Journal Article

Zabelskii, D.; Bukhdruker, S.; Bukhalovich, S.; Tsybrov, F.; Lamm, G. H. U.; Astashkin, R.; Doroginin, D.; Matveev, G.; Sudarev, V.; Kuzmin, A. et al.; Zinovev, E.; Vlasova, A.; Ryzhykau, Y.; Ilyinsky, N.; Gushchin, I.; Bourenkov, G.; Alekseev, A.; Round, A.; Wachtveitl, J.; Bamberg, E.; Gordeliy, V.: Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states. Nature Structural & Molecular Biology (2025)

MPG.PuRe

Journal Article

Fuchs, J.; Fernández-Arévalo, U.; Demmer, U.; Díaz, E.; Ullmann, G. M.; Pierik, A. J.; Ermler, U.; Boll, M.: Enzymatic Birch reduction via hydrogen atom transfer at [4Fe-4S]-OH₂ and [8Fe-9S] clusters. Nature Communications 16, 3236 (2025)

MPG.PuRe

Journal Article

Amaro, R. E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P. C.; Bonomi, M.; Bowman, G. R.; Bryce, R. A. et al.; Bussi, G.; Carloni, P.; Case, D. A.; Cavalli, A.; Chang, C.-E. A.; Cheatham, T. E.; Cheung, M. S.; Chipot, C.; Chong, L. T.; Choudhary, P.; Cisneros, G. A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T. D.; Dal Peraro, M.; de Groot, B. L.; Delemotte, L.; De Vivo, M.; Essex, J. W.; Fraternali, F.; Gao, J.; Gelpí, J. L.; Gervasio, F. L.; González-Nilo, F. D.; Grubmüller, H.; Guenza, M. G.; Guzman, H. V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J. H.; Jha, S.; Jiao, W.; Jorgensen, W. L.; Kamerlin, S. C. L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y. L.; Luque, F. J.; Lynch, C. I.; MacKerell, A. D.; Magistrato, A.; Marrink, S. J.; Martin, H.; McCammon, J. A.; Merz, K.; Moliner, V.; Mulholland, A. J.; Murad, S.; Naganathan, A. N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O'Mara, M. L.; Ondrechen, M. J.; Onuchic, J. N.; Onufriev, A.; Osuna, S.; Palermo, G.; Panchenko, A. R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J. R.; Pettitt, B. M.; Pietropaolo, A.; Piquemal, J.-P.; Poma, A. B.; Praprotnik, M.; Ramos, M. J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Rothlisberger, U.; Sanbonmatsu, K. Y.; Schlick, T.; Shaytan, A. K.; Simmerling, C.; Smith, J. C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tieleman, D. P.; Tikhonova, I. G.; Tirado-Rives, J.; Tuñón, I.; van der Kamp, M. W.; van der Spoel, D.; Velankar, S.; Voth, G. A.; Wade, R.; Warshel, A.; Welborn, V. V.; Wetmore, S. D.; Wheeler, T. J.; Wong, C. F.; Yang, L.-W.; Zacharias, M.; Orozco, M.: The need to implement FAIR principles in biomolecular simulations. Nature Methods (2025)

MPG.PuRe

Journal Article

Roeck, B. F.; Lotfipour Nasudivar, S.; Vorndran, M. R. H.; Schueller, L.; Yapici, F. I.; Rübsam, M.; von Karstedt, S.; Niessen, C. M.; Garcia-Saez, A. J.: Ferroptosis spreads to neighboring cells via plasma membrane contacts. Nature Communications 16, 2951 (2025)

MPG.PuRe

Journal Article

Eerlapally, R.; Hareendran, D. L.; Velasco, L.; Charisiadis, A.; Sauvan, M.; Debnath, J.; Moonshiram, D.; Draksharapu, A.: Impact of Lewis Acids on the Reactivity of a High-Valent Cu(III) Complex. Inorganic Chemistry (2025)

MPG.PuRe

Journal Article

Licheva, M.; Babic, R.; Pflaum, J.; Mancilla, H.; Wilfling, F.; Kraft, C.: To degrade or not to degrade: how phase separation modulates selective autophagy. Autophagy (2025)

MPG.PuRe

Journal Article

Zimmann, F.; McNicoll, F.; Thakur, P. K.; Blažíková, M.; Kubovčiak, J.; Hernández Cañás, M. C.; Nováková, Z.; Bařinka, C.; Kolář, M.; Staněk, D. et al.; Müller-McNicoll, M.; Cvačková, Z.: Retinitis pigmentosa-linked mutations impair the snRNA unwinding activity of SNRNP200 and reduce pre-mRNA binding of PRPF8. Cellular and Molecular Life Sciences 82, 103 (2025)

MPG.PuRe

Journal Article

Klumpe, S.; Senti, K. A.; Beck, F.; Sachweh, J.; Hampoelz, B.; Ronchi, P.; Oorschot, V.; Brandstetter, M.; Yeroslaviz, A.; Briggs, J. A. G. et al.; Brennecke, J.; Beck, M.; Plitzko, J. M.: In-cell structure and snapshots of copia retrotransposons in intact tissue by cryoelectron tomography. Cell 188 (2025)

MPG.PuRe

Journal Article

Cortés Rodríguez, F. J.; Frattini, G.; Phloi-Montri, S.; Pinto Meireles, F. T.; Terrien, D. A.; Cruz-León, S.; Dal Peraro, M.; Schier, E.; Lindorff-Larsen, K.; Limpanuparb, T. et al.; Moreno, D. M.; Abriata, L. A.: MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality. Journal of Molecular Graphics and Modelling 135, 108932 (2025)

MPG.PuRe

Journal Article

Poveda Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R.: Janus-like behavior of intrinsically disordered regions in reticulophagy. Autophagy 21 (3), pp. 681 - 683 (2025)

MPG.PuRe

Journal Article

Zaghbani, S.; Pranti, R. K.; Faber, L.; Garcia-Saez, A. J.: MitoSkel: AI tool for semantic segmentation and quantification of mitochondria from light microscopy images. Biomedical Signal Processing and Control 106, 107762 (2025)

MPG.PuRe

Journal Article

Smarduch, S.; Moreno-Velasquez, S. D.; Ilic, D.; Dadsena, S.; Morant, R.; Ciprinidis, A.; Pereira, G.; Binder, M.; García-Sáez, A. J.; Acebrón, S. P.: A novel biosensor for the spatiotemporal analysis of STING activation during innate immune responses to dsDNA. The EMBO Journal (2025)

MPG.PuRe

Journal Article

Bailey, H. J.; Eisert, J.; Kazi, R.; Gerhartz, J.; Pieńkowska, D. E.; Dressel, I.; Vollrath, J.; Kondratov, I.; Matviyuk, T.; Tolmachova, N. et al.; Shah, V. J.; Giuliani, G.; Mosler, T.; Geiger, T. M.; Esteves, A. M.; Santos, S. P.; Sousa, R. L.; Bandeiras, T. M.; Leibrock, E.-M.; Bauer, U.; Leuthner, B.; Langer, J. D.; Wegener, A. A.; Nowak, R. P.; Sorrell, F. J.; Đikić, I.: An engineered cereblon optimized for high throughput screening and molecular glue discovery. Cell Chemical Biology 32 (2), pp. 363 - 376.e10 (2025)

MPG.PuRe

Journal Article

Kreysing, J. P.; Heidari, M.; Zila, V.; Cruz-León, S.; Obarska-Kosinska, A.; Laketa, V.; Rohleder, L.; Welsch, S.; Köfinger, J.; Turoňová, B. et al.; Hummer, G.; Kräusslich, H.-G.; Beck, M.: Passage of the HIV capsid cracks the nuclear pore. Cell 188 (4), pp. 930 - 943.e21 (2025)

MPG.PuRe

Journal Article

Kutzner, C.; Miletić, V.; Palacio Rodríguez, K.; Rampp, M.; Hummer, G.; de Groot, B. L.; Grubmüller, H.: Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. Journal of Computational Chemistry 46 (5), e70059 (2025)

MPG.PuRe

Journal Article

Lee, Y.; Jin, C.; Ohgaki, R.; Xu, M.; Ogasawara, S.; Warshamanage, R.; Yamashita, K.; Murshudov, G.; Nureki, O.; Murata, T. et al.; Kanai, Y.: Structural basis of anticancer drug recognition and amino acid transport by LAT1. Nature Communications 16, 1635 (2025)

MPG.PuRe

Journal Article

Hoffmann, P. C.; Kim, H.; Obarska-Kosinska, A.; Kreysing, J. P.; Andino-Frydman, E.; Cruz-León, S.; Margiotta, E.; Cernikova, L.; Kosinski, J.; Turoňová, B. et al.; Hummer, G.; Beck, M.: Nuclear pore permeability and fluid flow are modulated by its dilation state. Molecular Cell 85 (3), pp. 537 - 554.e11 (2025)

MPG.PuRe

Journal Article

Cutts, E. E.; Tetiker, D.; Kim, E.; Aragon, L.: Molecular mechanism of condensin I activation by KIF4A. The EMBO Journal 44 (3), pp. 682 - 704 (2025)

MPG.PuRe

Journal Article

Licheva, M.; Pflaum, J.; Babic, R.; Mancilla, H.; Elsässer, J.; Boyle, E.; Hollenstein, D. M.; Jimenez-Niebla, J.; Pleyer, J.; Heinrich, M. et al.; Wieland, F.-G.; Brenneisen, J.; Eickhorst, C.; Brenner, J.; Jiang, S.; Hartl, M.; Welsch, S.; Hunte, C.; Timmer, J.; Wilfling, F.; Kraft, C.: Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy. Nature Cell Biology 27 (2), pp. 283 - 297 (2025)

MPG.PuRe

Journal Article

Rutkauskas, M.; Kim, E.: In vitro dynamics of DNA loop extrusion by structural maintenance of chromosomes complexes. Current Opinion in Genetics & Development 90, 102284 (2025)

MPG.PuRe

Journal Article

Yin, M. D.; Lemaire, O. N.; Rosas Jiménez, J. G.; Belhamri, M.; Shevchenko, A.; Hummer, G.; Wagner, T.; Murphy, B. J.: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Science 387 (6733), pp. 498 - 504 (2025)

MPG.PuRe

Journal Article

Hayashi, K.; Hummer, G.; Joseph, J. A.; Li, R.; Nagai, T.; Onami, S.; Zhang, F.: A round table at IUPAB Congress in Kyoto 2024: Dreaming the next 50 years in our biophysics. Biophysics and Physicobiology 21 (Supplemental2), e212012 (2025)

MPG.PuRe

Journal Article

Pedrera, L.; Prieto Clemente, L.; Dahlhaus, A.; Lotfipour Nasudivar, S.; Tishina, S.; Olmo González, D.; Stroh, J.; Yapici, F. I.; Singh, R. P.; Grotehans, N. et al.; Langer, T.; García-Sáez, A. J.; von Karstedt, S.: Ferroptosis triggers mitochondrial fragmentation via Drp1 activation. Cell Death and Disease 16, 40 (2025)

MPG.PuRe

Journal Article

Introini, B.; Hahn, A.; Kühlbrandt, W.: Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea. Nature Structural & Molecular Biology (2025)

MPG.PuRe

Journal Article

Xing, H.; Rosenkranz, R. R. E.; Rodriguez-Aliaga, P.; Lee, T.-T.; Majtner, T.; Böhm, S.; Turoňová, B.; Frydman, J.; Beck, M.: In situ analysis reveals the TRiC duty cycle and PDCD5 as an open-state cofactor. Nature 637 (8047), pp. 983 - 990 (2025)

MPG.PuRe

Journal Article

Kraus, F.; He, Y.; Swarup, S.; Overmyer, K. A.; Jiang, Y.; Brenner, J.; Capitanio, C.; Bieber, A.; Jen, A.; Nightingale, N. M. et al.; Anderson, B. J.; Lee, C.; Paulo, J. A.; Smith, I. R.; Plitzko, J. M.; Gygi, S. P.; Schulman, B. A.; Wilfling, F.; Coon, J. J.; Harper, J. W.: Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST. Science Advances 11 (4), eadu5787 (2025)

MPG.PuRe

Journal Article

Münick, P.; Strubel, A.; Balourdas, D.-I.; Funk, J. S.; Mernberger, M.; Osterburg, C.; Dreier, B.; Schaefer, J. V.; Tuppi, M.; Yüksel, B. et al.; Schäfer, B.; Knapp, S.; Plückthun, A.; Stiewe, T.; Joerger, A. C.; Dötsch, V.: DARPin-induced reactivation of p53 in HPV-positive cells. Nature Structural & Molecular Biology (2025)

MPG.PuRe

Journal Article

Catapano, C.; Dietz, M. S.; Kompa, J.; Jang, S.; Freund, P.; Johnsson, K.; Heilemann, M.: Long-term single-molecule tracking in living cells using weak-affinity protein labeling. Angewandte Chemie, International Edition in English 64 (1), e202413117 (2025)

MPG.PuRe

Journal Article

Oo, J. A.; Warwick, T.; Pálfi, K.; Lam, F.; McNicoll, F.; Prieto-Garcia, C.; Günther, S.; Cao, C.; Zhou, Y.; Gavrilov, A. A. et al.; Razin, S. V.; Cabrera-Orefice, A.; Wittig, I.; Pullamsetti, S. S.; Kurian, L.; Gilsbach, R.; Schulz, M. H.; Dikic, I.; Müller-McNicoll, M.; Brandes, R. P.; Leisegang, M. S.: Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers. Nature Communications 16, 131 (2025)

MPG.PuRe

Journal Article

Pradhan, B.; Deep, A.; König, J.; Baaske, M. D.; Corbett, K. D.; Kim, E.: Loop-extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex. Molecular Cell 85 (2025)

MPG.PuRe

Journal Article

Etxebeste-Mitxeltorena, M.; Flores-Romero, H.; Ramos-Inza, S.; Masiá, E.; Nenchova, M.; Montesinos, J.; Martinez-Gonzalez, L.; Porras, G.; Orzáez, M.; Vicent, M. J. et al.; Gil, C.; Area-Gomez, E.; Garcia-Saez, A. J.; Martinez, A.: Modulation of Mitochondria-Endoplasmic Reticulum Contacts (MERCs) by Small Molecules as a New Strategy for Restoring Lipid Metabolism in an Amyotrophic Lateral Sclerosis Model. Journal of Medicinal Chemistry 68 (2), pp. 1179 - 1194 (2025)

MPG.PuRe

Journal Article

Karimi, K.; Zöller, J.; Hofmann, T.; Zangl, R.; Schulte, J.; Langer, J. D.; Schmidt, C.; Morgner, N.: MS SIEVE – Pushing the Limits for Biomolecular Mass Spectrometry. Journal of the American Society for Mass Spectrometry 36 (1), pp. 91 - 99 (2025)

MPG.PuRe

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 1867, 184388 (2025)

MPG.PuRe

Journal Article

Periasamy, A.; Ornelas, P.; Bausewein, T.; Mitchell, N.; Zhao, J.; Quinn, L. M.; Kuehlbrandt, W.; Gulbis, J. M.: Structure of an ex vivoDrosophila TOM complex determined by single-particle cryoEM. IUCrJ 12 (1) (2025)

MPG.PuRe

Book Chapter (1)

2025

Book Chapter

Krasnoselska, G. O.; Meier, T.: Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. In: Springer Protocols: Methods in Molecular Biology: Molecular Motors, Vol. 2881, pp. 65 - 86 (Eds. Lavelle, C.; Le Gall , A.) (2025)

MPG.PuRe

Thesis - Bachelor (2)

2025

Thesis - Bachelor

Ho, C. X. Y.: Improving Low-Dose EELS Spectral Analysis: A Combined Mathematical and Machine Learning Approach. Bachelor, 126 pp., Technical University of Munich, München (2025)

MPG.PuRe

Thesis - Bachelor

Przybylek, L.: Inducing mRNA accumulation in the nuclei of mammalian cells. Bachelor, 85 pp., Frankfurt University of Applied Science, Frankfurt am Main (2025)

MPG.PuRe