Publications of the Max Planck Institute of Biophysics 1947

2024

Journal Article

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 80, pp. 159 - 173 (2024)

MPG.PuRe

DOI

Full

Journal Article

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)

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

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)

MPG.PuRe

DOI

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

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 19 (2), pp. 563 - 574 (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

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)

MPG.PuRe

DOI

Full

Journal Article

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

MPG.PuRe

DOI

Full

Journal Article

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

MPG.PuRe

DOI

Full

Journal Article

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)

MPG.PuRe

DOI

Journal Article

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)

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

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)

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

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)

MPG.PuRe

DOI

Full

Journal Article

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)

MPG.PuRe

DOI

Full

Journal Article

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)

MPG.PuRe

DOI

Full

Journal Article

Lasham, J.; Djurabekova, A.; Kolypetris, G.; Zickermann, V.; Vonck, J.; Sharma, V.: Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1866 (1), 149512 (2024)

MPG.PuRe

DOI

Full

Journal Article

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)

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

Trebino, T. E.; Markusic, B.; Nan, H.; Banerjee, S.; Wang, Z.: Unveiling the domain-specific and RAS isoform-specific details of BRAF kinase regulation. eLife 12, RP88836 (2023)

MPG.PuRe

DOI

Full

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

Marchal, D. G.; Schulz, L.; Schuster, I.; Ivanovska, J.; Paczia, N.; Prinz, S.; Zarzycki, J.; Erb, T. J.: Machine Learning-Supported Enzyme Engineering toward Improved CO₂-Fixation of Glycolyl-CoA Carboxylase. ACS Synthetic Biology 12 (12), pp. 3521 - 3530 (2023)

MPG.PuRe

DOI

Full

Journal Article

Jagtap, P. K. A.; Müller, M.; Kiss, A. E.; Thomae, A. W.; Lapouge, K.; Beck, M.; Becker, P. B.; Hennig, J.: Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless. Molecular Cell 83, pp. 4318 - 4333 (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

Wilfling, F.; Kaksonen, M.; Stachowiak, J.: Protein condensates as flexible platforms for membrane traffic. Current Opinion in Cell Biology 85, 102258 (2023)

MPG.PuRe

DOI

Journal Article

van Oostrum, M.; Blok, T. M.; Giandomenico, S. L.; tom Dieck, S.; Tushev, G.; Fürst, N.; Langer, J. D.; Schuman, E. M.: The proteomic landscape of synaptic diversity across brain regions and cell types. Cell 186 (24), pp. 5411 - 5427.e23 (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

Boyle, E.; Wilfling, F.: Autophagy as a caretaker of nuclear integrity. FEBS Letters 597, pp. 2728 - 2738 (2023)

MPG.PuRe

DOI

Full

Journal Article

Gul, M.; Yuksel, B.; Bulut, H.; DeMirci, H.: Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography. Acta Crystallographica Section D: Structural Biology 79 (11), pp. 1010 - 1017 (2023)

MPG.PuRe

DOI

Full

Journal Article

Hau, J.-L.; Kaltwasser, S.; Muras, V.; Casutt, M. S.; Vohl, G.; Claußen, B.; Steffen, W.; Leitner, A.; Bill, E.; Cutsail, G. E. et al.; DeBeer, S.; Vonck, J.; Steuber, J.; Fritz, G.: Conformational coupling of redox-driven Na⁺-translocation in Vibrio cholerae NADH:quinone oxidoreductase. Nature Structural & Molecular Biology 30 (11), pp. 1686 - 1694 (2023)

MPG.PuRe

DOI

Full

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

Demmer, U.; Lemaire, O.; Belhamri, M.; Ermler, U.: Ethoxylate Polymer-Based 96-Well Screen for Protein Crystallization. Crystals 13, 1519 (2023)

MPG.PuRe

DOI

Full

Journal Article

Balyschew, N.; Yushkevich, A.; Mikirtumov, V.; Sanchez, R. M.; Sprink, T.; Kudryashev, M.: Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR. Nature Communications 14, 6543 (2023)

MPG.PuRe

DOI

Full

Journal Article

Bühl, E.; Resler, T.; Lam, R. S.; Asido, M.; Bamberg, E.; Schlesinger, R.; Bamann, C.; Heberle, J.; Wachtveitl, J.: Assessing the Role of R120 in the Gating of Cr ChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds. Journal of the American Chemical Society 145 (40), pp. 21832 - 21840 (2023)

MPG.PuRe

DOI

Journal Article

Mello-Vieira, J.; Bopp, T.; Đikić, I.: Ubiquitination and cell-autonomous immunity. Current Opinion in Immunology 84, 102368 (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

Vaculík, O.; Chalupová, E.; Grešová, K.; Majtner, T.; Alexiou, P.: Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes. Biology 12 (10), 1276 (2023)

MPG.PuRe

DOI

Full

Journal Article

Sanchez Carrillo, I. B.; Hoffmann, P. C.; Barff, T.; Beck, M.; Germain, H.: Preparing Arabidopsis thaliana root protoplasts for cryo electron tomography. Frontiers in Plant Science 14, 1261180 (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

Gehl, M.; Demmer, U.; Ermler, U.; Shima, S.: Crystal structure of FAD-independent methylene-tetrahydrofolate reductase from Mycobacterium hassiacum. Proteins: Structure, Function, and Bioinformatics 91 (9), pp. 1329 - 1340 (2023)

MPG.PuRe

DOI

Full

Journal Article

Deák, G.; Wapenaar, H.; Sandoval, G.; Chen, R.; Taylor, M. D.; Burdett, H.; Watson, J.; Tuijtel, M. W.; Webb, S.; Wilson, M.: Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Nucleic Acids Research 51 (15), gkad577, pp. 7882 - 7899 (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. M.; 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

Jang, S.; Narayanasamy, K. K.; Rahm, J. V.; Saguy, A.; Kompa, J.; Dietz, M. S.; Johnsson, K.; Shechtman, Y.; Heilemann, M.: Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag. Biophysical Reports 3 (3), 100123 (2023)

MPG.PuRe

DOI

Full

Journal Article

Meier-Credo, J.; Heiniger, B.; Schori, C.; Rupprecht, F.; Michel, H.; Ahrens, C. A.; Langer, J. D.: Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics. Analytical Chemistry 95, pp. 11892 - 11900 (2023)

MPG.PuRe

DOI

Full

Journal Article

Ornelas, P.; Bausewein, T.; Martin, J.; Morgner, N.; Nussberger, S.; Kühlbrandt, W.: Two conformations of the Tom20 preprotein receptor in the TOM holo complex. Proceedings of the National Academy of Sciences of the United States of America 120 (34), e2301447120 (2023)

MPG.PuRe

DOI

Full

Journal Article

Brenner, J.; Klumpe, S.; Wilfling, F.; Plitzko, J. M.: Towards Temporal Resolution in Correlative Cryo-electron Tomography. Microscopy and Microanalysis 29 (Supplement\1), pp. 1937 - 1938 (2023)

MPG.PuRe

DOI

Journal Article

Castillo Duque de Estrada, N. M.; Thoms, M.; Flemming, D.; Hammaren, H. M.; Buschauer, R.; Ameismeier, M.; Baßler, J.; Beck, M.; Beckmann, R.; Hurt, E.: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways. Nature Structural and Molecular Biology 30, pp. 1119 - 1131 (2023)

MPG.PuRe

DOI

Full

Journal Article

Gorriti, M. F.; Bamann, C.; Alonso-Reyes, D. G.; Wood, P. G.; Bamberg, E.; Farías, M. E.; Gärtner, W.; Albarracín, V. H.: Functional characterization of xanthorhodopsin in Salinivibrio socompensis, a novel halophile isolated from modern stromatolites. Photochemical & Photobiological Sciences 22 (8), pp. 1809 - 1823 (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

Saguy, A.; Alalouf, O.; Opatovski, N.; Jang, S.; Heilemann, M.; Shechtman, Y.: DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning. Nature Methods 20 (12), pp. 1939 - 1948 (2023)

MPG.PuRe

DOI

Journal Article

Chang, S.-Y. S.; Dijkman, P. M.; Wiessing, S. A.; Kudryashev, M.: Determining the structure of the bacterial voltage-gated sodium channel NaChBac embedded in liposomes by cryo electron tomography and subtomogram averaging. Scientific Reports 13, 11523 (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

Reislöhner, S.; Schermann, G.; Kilian, M.; Santamaría-Muñoz, D.; Zimmerli, C.; Kellner, N.; Baßler, J.; Brunner, M.; Hurt, E.: Identification and characterization of sugar-regulated promoters in Chaetomium thermophilum. BMC Biotechnology 23, 19 (2023)

MPG.PuRe

DOI

Full

Journal Article

Xing, H.; Taniguchi, R.; Khusainov, I.; Kreysing, J. P.; Welsch, S.; Turoňová, B.; Beck, M.: Translation dynamics in human cells visualized at high resolution reveal cancer drug action. Science 381 (6653), pp. 70 - 75 (2023)

MPG.PuRe

DOI

Full

Journal Article

Kovalev, K.; Tsybrov, F.; Alekseev, A.; Shevchenko, V.; Soloviov, D.; Siletsky, S.; Bourenkov, G.; Agthe, M.; Nikolova, M.; von Stetten, D. et al.; Astashkin, R.; Bukhdruker, S.; Chizhov, I.; Royant, A.; Kuzmin, A.; Gushchin, I.; Rosselli, R.; Rodriguez-Valera, F.; Ilyinskiy, N.; Rogachev, A.; Borshchevskiy, V.; Schneider, T. R.; Bamberg, E.; Gordeliy, V.: Mechanisms of inward transmembrane proton translocation. Nature Structural and Molecular Biology 30 (7), pp. 970 - 979 (2023)

MPG.PuRe

DOI

Journal Article

Schmitt, D.; Bozkurt, S.; Henning-Domres, P.; Huesmann, H.; Eimer, S.; Bindila, L.; Behrends, C.; Boyle, E.; Wilfling, F.; Tascher, G. et al.; Münch, C.; Behl, C.; Kern, A.: FACS-mediated isolation of native autophagic vesicles. Autophagy 19 (7), pp. 2146 - 2147 (2023)

MPG.PuRe

DOI

Full

Journal Article

Thielmann, Y.; Luft, T.; Zint, N.; Koepke, J.: Crystal search - feasibility study of a real-time deep learning process for crystallization well images. Acta Crystallographica Section A: Foundations and Advances A79 (Part 4), pp. 331 - 338 (2023)

MPG.PuRe

DOI

Full

Journal Article

Asgari, N.; Baaske, M. D.; Orrit, M.: Burst-by-Burst Measurement of Rotational Diffusion at Nanosecond Resolution Reveals Hot-Brownian Motion and Single-Chain Binding. ACS Nano 17 (13), pp. 12684 - 12692 (2023)

MPG.PuRe

DOI

Full

Journal Article

Fuss, M. F.; Wieferig, J.-P.; Corey, R. A.; Hellmich, Y.; Tascón, I.; Sousa, J. S.; Stansfeld, P. J.; Vonck, J.; Hänelt, I.: Cyclic di-AMP traps proton-coupled K⁺ transporters of the KUP family in an inward-occluded conformation. Nature Communications 14, 3683 (2023)

MPG.PuRe

DOI

Full

Journal Article

Drakonaki, A.; Mathioudaki, E.; Geladas, E. D.; Konsolaki, E.; Vitsaxakis, N.; Chaniotakis, N.; Xie, H.; Tsiotis, G.: Production of Polyhydroxybutyrate by Genetically Modified Pseudomonas sp. phDV1: A Comparative Study of Utilizing Wine Industry Waste as a Carbon Source. Microorganisms 11 (16), 1592 (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

Seidel, M.; Romanov, N.; Obarska-Kosinska, A.; Becker, A.; Trevisan Doimo de Azevedo, N.; Provaznik, J.; Nagaraja, S. R.; Landry, J. J. M.; Benes, V.; Beck, M.: Co-translational binding of importins to nascent proteins. Nature Communications 14, 3418 (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

Kim, E.; Barth, R.; Dekker, C.: Looping the Genome with SMC Complexes. Annual Review of Biochemistry 92, pp. 15 - 41 (2023)

MPG.PuRe

DOI

Full

Journal Article

Winiarska, A.; Ramírez-Amador, F.; Hege, D.; Gemmecker, Y.; Prinz, S.; Hochberg, G.; Heider, J.; Szaleniec, M.; Schuller, J. M.: A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. Science Advances 9, eadg6689 (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

Last, M. G. F.; Tuijtel, M.; Voortman, L. M.; Sharp, T. H.: Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy. Scientific Reports 13, 8270 (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

Capitanio, C.; Bieber, A.; Wilfling, F.: How Membrane Contact Sites Shape the Phagophore. Contact 6 (2023)

MPG.PuRe

DOI

Full

Journal Article

Ehr, J. v.; Korn, S. M.; Weiß, L.; Schlundt, A.: ¹H, ¹³C, ¹⁵N backbone chemical shift assignments of the extended ARID domain in human AT-rich interactive domain protein 5a (Arid5a). Biomolecular NMR Assignments 17 (1), pp. 121 - 127 (2023)

MPG.PuRe

DOI

Full

Journal Article

Okhrimenko, I. S.; Kovalev, K.; Petrovskaya, L. E.; Ilyinsky, N. S.; Alekseev, A. A.; Marin, E.; Rokitskaya, T. I.; Antonenko, Y. N.; Siletsky, S. A.; Popov, P. A. et al.; Zagryadskaya, Y. A.; Soloviov, D. V.; Chizhov, I. V.; Zabelskii, D. V.; Ryzhykau, Y. L.; Vlasov, A. V.; Kuklin, A. I.; Bogorodskiy, A. O.; Mikhailov, A. E.; Sidorov, D. V.; Bukhalovich, S.; Tsybrov, F.; Bukhdruker, S.; Vlasova, A. D.; Borshchevskiy, V. I.; Dolgikh, D. A.; Kirpichnikov, M. P.; Bamberg, E.; Gordeliy, V. I.: Mirror proteorhodopsins. Communications Chemistry 6, 88 (2023)

MPG.PuRe

DOI

Full

Journal Article

Bhattacharya, A.; Mukherjee, R.; Kuncha, S. K.; Brunstein, M. E.; Rathore, R.; Junek, S.; Münch, C.; Đikić, I.: A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins. Nature Cell Biology 25 (5), pp. 685 - 698 (2023)

MPG.PuRe

DOI

Full

Journal Article

Lyratzakis, A.; Meier-Credo, J.; Langer, J. D.; Tsiotis, G.: Insights into the sulfur metabolism of Chlorobaculum tepidum by label-free quantitative proteomics. Proteomics 23 (10), 2200138 (2023)

MPG.PuRe

DOI

Full

Journal Article

Sun, C.; Desch, K.; Nassim-Assir, B.; Giandomenico, S. L.; Nemcova, P.; Langer, J. D.; Schuman, E. M.: An abundance of free regulatory (19S) proteasome particles regulates neuronal synapses. Science 380 (6647), eadf2018 (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

Kalavacherla, T.; Buschmann, S.; Schleker, E. S. M.; Michel, H.; Reinhart, C.: Purification and characterization of eukaryotic ATP-dependent transporters homologously expressed in Pichia pastoris for structural studies by cryo-electron microscopy. Protein Expression and Purification 204, 106230 (2023)

MPG.PuRe

DOI

Journal Article

Lambertz, J.; Meier-Credo, J.; Kucher, S.; Bordignon, E.; Langer, J. D.; Nowaczyk, M. M.: Isolation of a novel heterodimeric PSII complex via strep-tagged PsbO. Biochimica et Biophysica Acta, Bioenergetics 1864 (2), 148953 (2023)

MPG.PuRe

DOI

Journal Article

Pradhan, B.; Kanno, T.; Umeda Igarashi, M.; Loke, M. S.; Baaske, M. D.; Wong, J. S. K.; Jeppsson, K.; Björkegren, C.; Kim, E.: The Smc5/6 complex is a DNA loop-extruding motor. Nature 616 (7958), pp. 843 - 848 (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

Li, M.; Tripathi-Giesgen, I.; Schulman, B. A.; Baumeister, W.; Wilfling, F.: In situ snapshots along a mammalian selective autophagy pathway. Proceedings of the National Academy of Sciences of the United States of America 120 (12), e2221712120 (2023)

MPG.PuRe

DOI

Full

Journal Article

Hegemann, P.; Michel, H.: Dieter Oesterhelt (1940-2022): Life with light and color, pioneer of membrane protein research. Biophysics and Physicobiology 20 (Supplemental), e201010 (2023)

MPG.PuRe

DOI

Journal Article

Sprankel, L.; Vizaragga, D.; Martín, J.; Manger, S.; Meier-Credo, J.; Marcos, M.; Julve, J.; Rotllan, N.; Scheffer, M. P.; Escolà-Gil, J. C. et al.; Langer, J. D.; Piñol, J.; Fita, I.; Frangakis, A. S.: Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Nature Structural and Molecular Biology 30 (3), pp. 321 - 329 (2023)

MPG.PuRe

DOI

Full

Journal Article

Korn, S. M.; Ehr, J. v.; Dhamotharan, K.; Tants, J.-N.; Abele, R.; Schlundt, A.: Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein. International Journal of Molecular Sciences 24 (4), 3286 (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

Hegemann, P.; Michel, H.: Dieter Oesterhelt (1940–2022). Science 379 (6630), p. 337 (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

Xie, H.; Lyratzakis, A.; Khera, R.; Koutantou, M.; Welsch, S.; Michel, H.; Tsiotis, G.: Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum. Proceedings of the National Academy of Sciences of the United States of America 120 (5), e2216734120 (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

Journal Article (3181)