Publications of the Institute | Max Planck Institute of Biophysics

2021

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

Nikolaev, A.; Safarian, S.; Thesseling, A.; Wohlwend, D.; Friedrich, T.; Michel, H.; Kusumoto, T.; Sakamoto, J.; Melin, F.; Hellwig, P.: Electrocatalytic evidence of the diversity of the oxygen reaction in the bacterial bd oxidase from different organisms. Biochimica et Biophysica Acta, Bioenergetics 1862 (8), e148436 (2021)

MPG.PuRe

DOI

Journal Article

Armstrong, L. A.; Lange, S. M.; Dee Cesare, V.; Matthews, S. P.; Nirujogi, R. S.; Cole, I.; Hope, A.; Cunningham, F.; Toth, R.; Mukherjee, R. et al.; Bojkova, D.; Gruber, F.; Gray, D.; Wyatt, P. G.; Cinatl, J.; Đikić, I.; Davies, P.; Kulathu, Y.: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One 16 (7), e0253364 (2021)

MPG.PuRe

DOI

Journal Article

Chicano, T. M.; Dietrich, L.; de Almeida, N. M.; Akram, M.; Hartmann, E.; Leidreiter, F.; Leopoldus, D.; Mueller, M.; Sanchez, R. M.; Nuijten, G. H. L. et al.; Reimann, J.; Seifert, K.-A.; Schlichting, I.; van Niftrik, L.; Jetten, M. S. M.; Dietl, A.; Kartal, B.; Parey, K.; Barends, T. R. M.: Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nature Microbiology 6 (2021)

MPG.PuRe

DOI

Journal Article

Kannt, A.; Đikić, I.: Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chemical Biology 28 (7), pp. 1014 - 1031 (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

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 (2021)

MPG.PuRe

DOI

Journal Article

Sabinina, V. J.; Hossain, M. J.; Hériché, J.-K.; Hoess, P.; Nijmeijer, B.; Mosalaganti, S.; Kueblbeck, M.; Callegari, A.; Szymborska, A.; Beck, M. et al.; Ries, J.; Ellenberg, J.: 3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex. Molecular Biology of the Cell, mbcE20110728 (2021)

MPG.PuRe

DOI

Journal Article

Zabelskii, D.; Dmitrieva, N.; Volkov, O.; Shevchenko, V.; Kovalev, K.; Balandin, T.; Soloviov, D.; Astashkin, R.; Zinovev, E.; Alekseev, A. et al.; Round, E.; Polovinkin, V.; Chizhov, I.; Rogachev, A.; Okhrimenko, I.; Borshchevskiy, V.; Chupin, V.; Büldt, G.; Yutin, N.; Bamberg, E.; Koonin, E.; Gordeliy, V.: Structure-based insights into evolution of rhodopsins. Communications Biology 4 (1), 821 (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, 100925 (2021)

MPG.PuRe

DOI

Journal Article

Feyh, R.; Waeber, N. B.; Prinz, S.; Giammarinaro, P. I.; Bange, G.; Hochberg, G.; Hartmann, R. K.; Altegoer, F.: Structure and mechanistic features of the prokaryotic minimal RNase P. eLife 10, e70160 (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

Dijkman, P. M.; Marzluf, T.; Zhang, Y.; Chang, S.-Y. S.; Helm, D.; Lanzer, M.; Bujard, H.; Kudryashev, M.: Structure of the merozoite surface protein 1 from Plasmodium falciparum. Science Advances 7 (23), eabg0465 (2021)

MPG.PuRe

DOI

Journal Article

Becker-Baldus, J.; Leeder, A.; Brown, L. J.; Brown, R. C. D.; Bamann, C.; Glaubitz, C.: The Desensitized Channelrhodopsin-2 Photointermediate Contains 13-cis,15-syn Retinal Schiff Base. Angewandte Chemie, International Edition in English 60 (2021)

MPG.PuRe

DOI

Journal Article

Mathioudaki, E.; Arvaniti, K.; Münke, C.; Drakonaki, A.; Vranakis, I.; Koutantou, M.; Psaroulaki, A.; Xie, H.; Tsiotis, G.: Expression, purification and characterization of the IcmG and IcmK proteins of the Type IVB secretion system from Coxiella burnetii. Protein Expression and Purification, e105905 (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

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

Staritzbichler, R.; Sarti, E.; Yaklich, E.; Aleksandrova, A.; Stamm, M.; Khafizov, K.; Forrest, L. R.: Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. plos one 16 (4), e0239881 (2021)

MPG.PuRe

DOI

Journal Article

Floris, D.; Kühlbrandt, W.: Molecular landscape of etioplast inner membranes in higher plants. Nature Plants 7 (4), pp. 514 - 523 (2021)

MPG.PuRe

DOI

Journal Article

Kayastha, K.; Vitt, S.; Buckel, W.; Ermler, U.: Flavins in the electron bifurcation process. Archives of Biochemistry and Biophysics 701, 108796 (2021)

MPG.PuRe

DOI

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

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

Zabret, J.; Bohn, S.; Schuller, S. K.; Arnolds, O.; Möller, M.; Meier-Credo, J.; Liauw, P.; Chan, A.; Tajkhorshid, E.; Langer, J. D. et al.; Stoll, R.; Krieger-Liszkay, A.; Engel, B. D.; Rudack , T.; Schuller, J. M.; Nowaczyk , M. M.: Structural insights into photosystem II assembly. Nature Plants (2021)

MPG.PuRe

DOI

Journal Article

Appel, L.; Willistein, M.; Dahl, C.; Ermler, U.; Boll, M.: Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond. Biochimica et Biophysica Acta, Bioenergetics 1862 (4), 148379 (2021)

MPG.PuRe

DOI

Journal Article

Gubas, A.; Karantanou, C.; Popovic, D.; Tascher, G.; Hoffmann, M. E.; Platzek, A.; Dawe, N.; Dikic, I.; Krause, D. S.; McEwan, D. G.: The endolysosomal adaptor PLEKHM1 is a direct target for both mTOR and MAPK pathways. FEBS Letters 595 (7), pp. 864 - 880 (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

Journal Article

Ochoa, R.; Laskowski, R. A.; Thornton, J. M.; Cossio, P.: Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Frontiers in Molecular Biosciences 8, 636562 (2021)

MPG.PuRe

DOI

Journal Article

Klusch, N.; Senkler, J.; Yildiz, Ö.; Kühlbrandt, W.; Braun, H.-P.: A ferredoxin bridge connects the two arms of plant mitochondrial complex I. The Plant Cell (2021)

MPG.PuRe

DOI

Journal Article

Gubas, A.; Đikić, I.: A Guide To… The regulation of selective autophagy receptors. The FEBS Journal 288, pp. 1 - 15 (2021)

MPG.PuRe

DOI

Journal Article

Ochoa, R.; Cossio, P.: PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 26 (6), 1664 (2021)

MPG.PuRe

DOI

Journal Article

Jakdetchai, O.; Eberhardt, P.; Asido, M.; Kaur, J.; Kriebel, C. N.; Mao, J.; Leeder, A. J.; Brown, L. J.; Brown, R. C. D.; Becker-Baldus, J. et al.; Bamann, C.; Wachtveitl, J.; Glaubitz, C.: Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR. Science Advances 7 (11), eabf4213 (2021)

MPG.PuRe

DOI

Journal Article

D'Imprima, E.; Kühlbrandt, W.: Current limitations to high-resolution structure determination by single-particle cryoEM. Quarterly Reviews of Biophysics 54, e4 (2021)

MPG.PuRe

DOI

Journal Article

Berger, C.; Ravelli, R. B. G.; López-Iglesias, C.; Kudryashev, M.; Diepold, A.; Peters, P. J.: Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography. Journal of Structural Biology 213 (1), 107701 (2021)

MPG.PuRe

DOI

Journal Article

Ernst, C.; Kayastha, K.; Koch , T.; Venceslau, S. S.; Pereira, I. A.C.; Demmer, U.; Ermler, U.; Dahl, C.: Structural and spectroscopic characterization of a HdrA‐like subunit from Hyphomicrobium denitrificans. The FEBS Journal 288 (5), pp. 1664 - 1678 (2021)

MPG.PuRe

DOI

Journal Article

Wiefering, J.-P.; Mills, D. J.; Kühlbrandt, W.: Devitrification reduces beam-induced movement in cryo-EM. IUCrJ 8 (Pt 2), pp. 186 - 194 (2021)

MPG.PuRe

DOI

Journal Article

Siggel, M.; Bhaskara, R.; Moesser, M. K.; Đikić, I.; Hummer, G.: FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 12 (7), pp. 1926 - 1931 (2021)

MPG.PuRe

DOI

Journal Article

Gorgulla, C.; Padmanabha Das, K. M.; Leigh, K. E.; Cespugli, M.; Fischer, P. D.; Wang, Z.-F.; Tesseyre, G.; Pandita, S.; Shnapir, A.; Calderaio, A. et al.; Gechev, M.; Rose, A.; Lewis, N.; Hutcheson, C.; Yaffe, E.; Luxenburg, R.; Herce, H. D.; Durmaz, V.; Halazonetis, T. D.; Fackeldey, K.; Patten, J. J.; Chuprina, A.; Dziuba, I.; Plekhova, A.; Moroz, Y.; Radchenko, D.; Tarkhanova, O.; Yavnyuk, I.; Gruber, C.; Yust, R.; Payne, D.; Näär, A. M.; Namchuk, M. N.; Davey, R. A.; Wagner, G.; Kinney, J.; Arthanari, H.: A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 24 (2), 102021 (2021)

MPG.PuRe

DOI

Journal Article

Zila, V.; Margiotta, E.; Turoňová, B.; Müller, T. G.; Zimmerli, C. E.; Mattei, S.; Allegretti, M.; Börner, K.; Rada, J.; Müller, B. et al.; Lusic, M.; Kräusslich, H.-G.; Beck, M.: Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Cell 184 (4), pp. 1032 - 1046 (2021)

MPG.PuRe

DOI

Journal Article

Zhang, Y.; Dijkman, P. M.; Zou, R.; Zandl-Lang, M.; Sanchez, R. M.; Eckhardt-Strelau, L.; Köfeler, H.; Vogel, H.; Yuan, S.; Kudryashev, M.: Asymmetric opening of the homopentameric 5-HT3A serotonin receptor in lipid bilayers. Nature Communications 12 (1), 1074 (2021)

MPG.PuRe

DOI

Journal Article

Eberhardt, P.; Slavov, C.; Sörmann, J.; Bamann, C.; Braun, M.; Wachtveitl, J.: Temperature Dependence of the Krokinobacter rhodopsin 2 Kinetics. Biophysical Journal (Annual Meeting Abstracts) 120 (3), pp. 568 - 575 (2021)

MPG.PuRe

DOI

Journal Article

Riedel, R.; Frese, N.; Yang, F.; Wortmann, M.; Dalpke, R.; Rhinow, D.; Hampp, N.; Gölzhäuser, A.: Fusion of purple membranes triggered by immobilization on carbon nanomembranes. Beilstein Journal of Nanotechnology 12, pp. 93 - 101 (2021)

MPG.PuRe

DOI

Journal Article

Benayad, Z.; von Bülow, S.; Stelzl, L. S.; Hummer, G.: Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 17 (1), pp. 525 - 537 (2021)

MPG.PuRe

DOI

Journal Article

Tiku, V.; Kofoed, E. M.; Yan, D.; Kang, J.; Xu, M.; Reichelt, M.; Dikic, I.; Tan, M.-W.: Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii. Scientific Reports 11 (1), 618 (2021)

MPG.PuRe

DOI

Journal Article

Cunha, E. S.; Chen, X.; Sanz-Gaitero, M.; Mills, D. J.; Luecke, H.: Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution. Nature Communications 12 (1), 230 (2021)

MPG.PuRe

DOI

Journal Article

Mills, D. J.: Setting up and operating a cryo-EM laboratory. Quarterly Reviews of Biophysics 54, e2 (2021)

MPG.PuRe

DOI

Journal Article

Ross, A. B.; Langer, J. D.; Jovanovic, M.: Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Molecular and Cellular Proteomics 20, 100016 (2021)

MPG.PuRe

DOI

Journal Article

Bárcena, M.; Barnes, C. O.; Beck, M.; Bjorkman, P. J.; Canard, B.; Gao, G. F.; Gao, Y.; Hilgenfeld, R.; Hummer, G.; Patwardhan, A. et al.; Santoni, G.; Saphire, E. O.; Schaffitzel, C.; Schendel, S. L.; Smith, J. L.; Thorn, A.; Veesler, D.; Zhang, P.; Zhou, Q.: Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 28 (1), pp. 2 - 7 (2021)

MPG.PuRe

DOI

Journal Article

Klionsky, D. J.; Abdel-Aziz, A. K.; Abdelfatah, S.; Hummer, G.; 2295 other, A.: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 17 (1), pp. 1 - 382 (2021)

MPG.PuRe

DOI

Journal Article

Lyratzakis, A.; Valsamidis, G.; Kanavaki, I.; Nikolaki , A.; Rupprecht, F. A.; Langer, J. D.; Tsiotis, G.: Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds. Proteomics 21 (2), e2000003 (2021)

MPG.PuRe

DOI

Journal Article

Wells, C. I.; Al-Ali, H.; Andrews, D. M.; Asquith, C. R. M.; Axtman, A. D.; Dikic, I.; Ebner, D.; Ettmayer, P.; Fischer, C.; Frederiksen, M. et al.; Futrell, R. E.; Gray, N. S.; Hatch, S. B.; Knapp, S.; Lücking, U.; Michaelides, M.; Mills, C. E.; Müller, S.; Owen, D.; Picado, A.; Saikatendu, K. S.; Schröder, M.; Stolz, A.; Tellechea, M.; Turunen, B. J.; Vilar, S.; Wang, J.; Zuercher, W. J.; Willson, T. M.; Drewry, D. H.: The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification. International Journal of Molecular Sciences 22 (2), 566 (2021)

MPG.PuRe

DOI

Journal Article

Zhu, G.; Zeng, H.; Zhang, S.; Juli, J.; Tai, L.; Zhang, D.; Pang , X.; Zhang, Y.; Lam, S. M.; Zhu, Y. et al.; Peng, G.; Michel, H.; Sun, F.: The unusual homodimer of a heme‐copper terminal oxidase allows itself to utilize two electron donors. Angewandte Chemie, International Edition in English 60 (2021)

MPG.PuRe

DOI

2020

Journal Article

Ochoa, R.; Magnitov, M.; Laskowski, R. A.; Cossio, P.; Thornton, J. M.: An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics 21 (1), 586 (2020)

MPG.PuRe

DOI

Journal Article

Ebenhoch, R.; Prinz, S.; Kaltwasser, S.; Mills, D. J.; Meinecke, R.; Rübbelke, M.; Reinert, D.; Bauer, M.; Weixler, L.; Zeeb, M. et al.; Vonck, J.; Nar, H.: A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I. Proceedings of the National Academy of Sciences of the United States of America 117 (50), pp. 31838 - 31849 (2020)

MPG.PuRe

DOI

Journal Article

Collauto, A.; von Bülow, S.; Gophane, D.; Saha, S.; Stelzl, L. S.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 59, pp. 23025 - 23029 (2020)

MPG.PuRe

DOI

Journal Article

Oda, K.; Lee, Y.; Wiriyasermkul, P.; Tanaka, Y.; Takemoto, M.; Yamashita, K.; Nagamori, S.; Nishizawa, T.; Nureki, O.: Consensus mutagenesis approach improves the thermal stability of system x_c- transporter, xCT, and enables cryo-EM analyses. Protein Science 29, pp. 2398 - 2407 (2020)

MPG.PuRe

DOI

Journal Article

Yadav, S.; Centola, M.; Yildiz, Ö.; Pogoryelov, D.; Rai, L. C.; Schleiff, E.: Purification and Preliminary X-Ray Crystallographic Analysis of the Peptidyl-Prolyl cis-trans Isomerase Alr5059 from Anabaena sp. PCC 7120. Crystallography Reports 65 (7), pp. 1226 - 1230 (2020)

MPG.PuRe

DOI

Journal Article

Galemou Yoga, E.; Parey, K.; Djurabekova, A.; Haapanen, O.; Siegmund, K.; Zwicker, K.; Sharma, V.; Zickermann, V.; Angerer, H.: Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Nature Communications 11, 6008 (2020)

MPG.PuRe

DOI

Journal Article

Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G. et al.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Müller, S.; Knobeloch, K.-P.; Rajalingam, K.; Schulman, B.; Cinatl, J.; Hummer, G.; Ciesek, S.; Đikić, I.: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587 (7835), pp. 657 - 662 (2020)

MPG.PuRe

DOI

Journal Article

Shin, D.; Bhattacharya, A.; Cheng, Y.-L.; Alonso, M. C.; Mehdipour, A. R.; van der Heden van Noort, G. J.; Ovaa, H.; Hummer, G.; Dikic, I.: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 9 (2020)

MPG.PuRe

DOI

Journal Article

Zabelskii, D.; Alekseev, A.; Kovalev, K.; Rankovic, V.; Balandin, T.; Soloviov, D.; Bratanov, D.; Savelyeva, E.; Podolyak, E.; Volkov, D. et al.; Vaganova, S.; Astashkin, R.; Chizhov, I.; Yutin, N.; Rulev, M.; Popov, A.; Eria-Oliveira, A.-S.; Rokitskaya, T.; Mager, T.; Antonenko, Y.; Rosselli, R.; Armeev, G.; Shaitan, K.; Vivaudou, M.; Büldt, G.; Rogachev, A.; Rodriguez-Valera, F.; Kirpichnikov, M.; Moser, T.; Offenhäusser, A.; Willbold, D.; Koonin, E.; Bamberg, E.; Gordeliy, V.: Viral rhodopsins 1 are an unique family of light-gated cation channels. Nature Communications 11, 5707 (2020)

MPG.PuRe

DOI

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 (2020)

MPG.PuRe

DOI

Journal Article

Januliene, D.; Moeller, A.: Cryo-EM of ABC transporters: an ice-cold solution to everything? FEBS Letters 594, pp. 3776 - 3789 (2020)

MPG.PuRe

DOI

Journal Article

Schulte, L.; Mao, J.; Reitz, J.; Sreeramulu, S.; Kudlinzki, D.; Hodirnau, V.-V.; Meier-Credo, J.; Saxena, K.; Buhr, F.; Langer, J. D. et al.; Blackledge, M.; Frangakis, A. S.; Glaubitz, C.; Schwalbe, H.: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications 11 (1), 5569 (2020)

MPG.PuRe

DOI

Journal Article

Sikora, M.; Ermel, U. H.; Seybold, A.; Kunz, M.; Calloni, G.; Reitz, J.; Vabulas, R. M.; Hummer, G.; Frangakis, A. S.: Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 117 (44), pp. 27132 - 27140 (2020)

MPG.PuRe

DOI

Journal Article

Golubev, A.; Fatkhullin, B.; Khusainov, I.; Jenner, L.; Gabdulkhakov, A.; Validov, S.; Yusupova, G.; Yusupov, M.; Usachev, K.: Cryo-EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 Å resolution. FEBS Letters 594 (21), pp. 3551 - 3567 (2020)

MPG.PuRe

DOI

Journal Article

Ngo, G.; Centola, M.; Krasnoselska, G.; Pogoryelov, D.; Yildiz, Ö.; Schleiff, E.: LptC from Anabaena sp. PCC 7120: Expression, purification and crystallization. Protein Expression and Purification 175, 105689 (2020)

MPG.PuRe

DOI

Journal Article

Allegretti, M.; Zimmerli, C. E.; Rantos, V.; Wilfling, F.; Ronchi, P.; Fung, H. K. H.; Lee, C.-W.; Hagen, W.; Turoňová, B.; Karius, K. et al.; Börmel, M.; Zhang, X.; Müller, C. W.; Schwab, Y.; Mahamid, J.; Pfander, B.; Kosinski, J.; Beck, M.: In-cell architecture of the nuclear pore and snapshots of its turnover. Nature 586 (7831), pp. 796 - 800 (2020)

MPG.PuRe

DOI

Journal Article

Chowdhury, N. P.; Alberti, L.; Linder, M.; Müller, V.: Exploring Bacterial Microcompartments in the Acetogenic Bacterium Acetobacterium woodii. Frontiers in Microbiology 11, 593467 (2020)

MPG.PuRe

DOI

Journal Article

Turoňová, B.; Sikora, M.; Schürmann, C.; Hagen, W. J. H.; Welsch, S.; Blanc, F. E. C.; von Bülow, S.; Gecht, M.; Bagola, K.; Hörner, C. et al.; van Zandbergen, G.; Landry, J.; de Azevedo, N. T. D.; Mosalaganti, S.; Schwarz, A.; Covino, R.; Mühlebach, M. D.; Hummer, G.; Krijnse Locker, J.; Beck, M.: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 370 (6513), pp. 203 - 208 (2020)

MPG.PuRe

DOI

Journal Article

Gebel, J.; Tuppi, M.; Chaikuad, A.; Hötte, K.; Schröder, M.; Schulz, L.; Löhr, F.; Gutfreund, N.; Finke, F.; Henrich, E. et al.; Mezhyrova, J.; Lehnert, R.; Pampaloni, F.; Hummer, G.; Stelzer, E. H.K.; Knapp, S.; Dötsch, V.: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 16 (10), pp. 1078 - 1086 (2020)

MPG.PuRe

DOI

Journal Article

Gecht, M.; Siggel, M.; Linke, M.; Hummer, G.; Köfinger, J.: MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 153 (14), 144105 (2020)

MPG.PuRe

DOI

Journal Article

Gewering, T.; Möller, A.: Neue Möglichkeiten für die Strukturbestimmung von Membranproteinen. Biospektrum 26 (6), pp. 615 - 617 (2020)

MPG.PuRe

DOI

Journal Article

Lans, I.; Palacio-Rodríguez, K.; Cavasotto, C. N.; Cossio, P.: Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. Journal of Computer-Aided Molecular Design 34 (10), pp. 1063 - 1077 (2020)

MPG.PuRe

DOI

Journal Article

Shvarev, D.: Kryo-EM-Einzelpartikelanalyse eines Membrantransporters in Liposomen. Biospektrum 26, p. 650 - 650 (2020)

MPG.PuRe

DOI

Journal Article

Bayer, N. J.; Januliene, D.; Zocher, G.; Stehle, T.; Möller, A.; Blaum, B. S.: Structure of Merkel cell polyomavirus capsid and interaction with its glycosaminoglycan attachment receptor. Journal of Virology 94 (20), e01664-19 (2020)

MPG.PuRe

DOI

Journal Article

Psaroulaki, A.; Mathioudaki, E.; Vranakis, I.; Chochlakis, D.; Yachnakis, E.; Kokkini , S.; Xie, H.; Tsiotis, G.: In the Search of Potential Serodiagnostic Proteins to Discriminate Between Acute and Chronic Q Fever in Humans. Some Promising Outcomes. Frontiers in Cellular and Infection Microbiology 10, 557027 (2020)

MPG.PuRe

DOI

Journal Article

Buczak, K.; Kirkpatrick, J. M.; Truckenmueller, F.; Santinha, D.; Ferreira, L.; Roessler, S.; Singer, S.; Beck, M.; Ori, A.: Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry. Nature Protocols 15 (9), pp. 2956 - 2979 (2020)

MPG.PuRe

DOI

Journal Article

Mykuliak, V. V.; Sikora, M.; Booth, J. J.; Cieplak, M.; Shalashilin, D. V.; Hytönen, V. P.: Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular Dynamics Study. Biophysical Journal 119, pp. 939 - 949 (2020)

MPG.PuRe

DOI

Journal Article

Sawa-Makarska, J.; Baumann, V.; Coudevylle, N.; von Bülow, S.; Nogellova, V.; Abert, C.; Schuschnig, M.; Graef, M.; Hummer, G.; Martens, S.: Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 369 (6508), eaaz7714 (2020)

MPG.PuRe

DOI

Journal Article

Wu, D.; Grund, T. N.; Welsch, S.; Mills, D.; Michel, M.; Safarian, S.; Michel, H.: Structural basis for amino acid exchange by a human heteromeric amino acid transporter. Proceedings of the National Academy of Sciences of the United States of America 117 (35), 202008111, pp. 21281 - 21287 (2020)

MPG.PuRe

DOI

Journal Article

Reyer, A.; Häßler, M.; Scherzer, S.; Huang, S.; Pedersen, J. T.; Al-Rascheid, K. A. S.; Bamberg, E.; Palmgren, M.; Dreyer, I.; Nagel, G. et al.; Hedrich, R.; Becker, D.: Channelrhodopsin-mediated optogenetics highlights a central role of depolarization-dependent plant proton pumps. Proceedings of the National Academy of Sciences of the United States of America 117 (34), pp. 20920 - 20925 (2020)

MPG.PuRe

DOI

Journal Article

Scherr, J.; Tang, Z.; Küllmer, M.; Balser, S.; Scholz, A. S.; Winter, A.; Parey, K.; Rittner, A.; Grininger, M.; Zickermann, V. et al.; Rhinow, D.; Terfort, A.; Turchanin, A.: Smart Molecular Nanosheets for Advanced Preparation of Biological Samples in Electron Cryo-Microscopy. ACS Nano 14 (8), pp. 9972 - 9978 (2020)

MPG.PuRe

DOI

Journal Article

Lans, I.; Anoz-Carbonell, E.; Palacio-Rodríguez, K.; Aínsa, J. A.; Medina, M.; Cossio, P.: In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Computational Biology 16 (8), e1007898 (2020)

MPG.PuRe

DOI

Journal Article

Lee, B.-G.; Merkel, F.; Allegretti, M.; Hassler, M.; Cawood, C.; Lecomte, L.; O'Reilly, F. J.; Sinn, L. R.; Gutierrez-Escribano, P.; Kschonsak, M. et al.; Bravo, S.; Nakane, T.; Rappsilber, J.; Aragon, L.; Beck, M.; Löwe, J.; Haering, C. H.: Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism. Nature Structural and Molecular Biology 27 (8), pp. 743 - 751 (2020)

MPG.PuRe

DOI

Journal Article

Parey, K. K.; Wirth, C.; Vonck, J.; Zickermann, V.: Respiratory complex I - structure, mechanism and evolution. Current Opinion in Structural Biology 63 (2020)

MPG.PuRe

DOI

Journal Article

Rhinow, D.; Hampp, N.: Electron beam-induced electrostatic charging causes spectral changes of an insulating electrochromic material. Applied Physics Letters 117 (8), 083701 (2020)

MPG.PuRe

DOI

Journal Article

Sanchez, R. M.; Zhang, Y.; Chen, W.; Dietrich, L.; Kudryashev, M.: Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM. Nature Communications 11, 3709 (2020)

MPG.PuRe

DOI

Journal Article

Ortiz , S.; Stanisic, L.; Rodriguez , B. A.; Rampp, M.; Hummer, G.; Cossio, P.: Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 4, 100032 (2020)

MPG.PuRe

DOI

Journal Article

Elamri, I.; Radloff, M.; Hohmann, K. F.; Nimbarte, V. D.; Nasiri, H. R.; Bolte, M.; Safarian, S.; Michel, H.; Schwalbe, H.: Synthesis and Biological Screening of new Lawson Derivatives as selective substrate‐based Inhibitors of Cytochrome bo₃ Ubiquinol Oxidase from Escherichia coli. ChemMedChem 15 (14), pp. 1262 - 1271 (2020)

MPG.PuRe

DOI

Journal Article

Bullerjahn, J. T.; von Bülow, S.; Hummer, G.: Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 153 (2), 024116 (2020)

MPG.PuRe

DOI

Journal Article

von Bülow, S.; Bullerjahn, J. T.; Hummer, G.: Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 153 (2), 021101 (2020)

MPG.PuRe

DOI

Journal Article

Zeng, H.; Zhu, G.; Zhang, S.; Li, X.; Martin, J.; Morgner, N.; Sun, F.; Peng, G.; Xie, H.; Michel, H.: Isolated Heme A Synthase from Aquifex aeolicus Is a Trimer. mBio 11 (3), e02615-19 (2020)

MPG.PuRe

DOI

Journal Article

Dasbach, M.; Pyschik, M.; Lehmann, V.; Parey, K.; Rhinow, D.; Reinhardt, H. M.; Hampp, N. A.: Assembling Carbon Nanotube Architectures. ACS Nano 14 (7), pp. 8181 - 8190 (2020)

MPG.PuRe

DOI

Journal Article

Schwierz, N.: Kinetic pathways of water exchange in the first hydration shell of magnesium. The Journal of Chemical Physics 152 (22), 224106 (2020)

MPG.PuRe

DOI

Journal Article

Jost Lopez, A.; Quoika, P. K.; Linke, M.; Hummer, G.; Köfinger, J.: Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 124 (23), pp. 4673 - 4685 (2020)

MPG.PuRe

DOI

Journal Article

Cruz-León, S.; Schwierz, N.: Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics. Langmuir 36 (21), pp. 5979 - 5989 (2020)

MPG.PuRe

DOI

Journal Article

Cossio, P.: Need for Cross-Validation of Single Particle Cryo-EM. Journal of Chemical Information and Modeling 60 (5), pp. 2413 - 2418 (2020)

MPG.PuRe

DOI

Journal Article

Neuhaus, A.; Selvaraj, M.; Salzer, R.; Langer, J. D.; Kruse, K.; Kirchner, L.; Sanders, K.; Daum, B.; Averhoff, B.; Gold, V.: Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Nature Communications 11, 2231 (2020)

MPG.PuRe

DOI

Publications of the Max Planck Institute of Biophysics

Journal Article (2380)