Publications of the Max Planck Institute of Biophysics
Institute Publications Ernst Bamberg Martin Beck Ulrich Ermler Gerhard Hummer Misha Kudryashev Werner Kühlbrandt Julian Langer Hartmut Michel Bonnie Murphy Nadine Schwierz Sonja Welsch Search YearbooksPublications Gerhard Hummer
Journal Article (361)
2024
Journal Article
15 (1), 6010 (2024)
Nanosecond chain dynamics of single-stranded nucleic acids. Nature Communications
Journal Article
630, pp. 501 - 508 (2024)
Molecular mechanism of choline and ethanolamine transport in humans. Nature
Journal Article
63, e202402498 (2024)
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
Journal Article
5 (5) (2024)
Thalidomide derivatives degrade BCL-2 by reprogramming the binding surface of CRBN. Cell Reports Physical Science
Journal Article
15, 3992 (2024)
High-confidence 3D template matching for cryo-electron tomography. Nature Communications
Journal Article
10 (17), eadk6285 (2024)
Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances
Journal Article
628 (8008), pp. 657 - 663 (2024)
Structure and assembly of a bacterial gasdermin pore. Nature
Journal Article
160, 114111 (2024)
Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics
Journal Article
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology, 168546 (2024)
Journal Article
20 (5), pp. 2246 - 2260 (2024)
Hierarchical Assembly of Single-Stranded RNA. Journal of Chemical Theory and Computation
Journal Article
121 (11), e2314199121 (2024)
Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. PNAS
Journal Article
187 (5), pp. 1296 - 1311.e26 (2024)
Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell
Journal Article
121 (9), e2318046121 (2024)
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
Journal Article
7 (2), pp. 528 - 534 (2024)
Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials
Journal Article
10 (6), eadj8027 (2024)
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Science Advances
Journal Article
12, RP90174 (2024)
Tracing the substrate translocation mechanism in P-glycoprotein. eLife 2023
Journal Article
19 (23), pp. 8919 - 8929 (2023)
Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation
Journal Article
14 (1), 7197 (2023)
Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. Nature Communications
Journal Article
30 (11), pp. 1774 - 1785 (2023)
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology
Journal Article
19 (20), pp. 7387 - 7404 (2023)
Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation
Journal Article
108 (3), 035307 (2023)
Efficient generation of random rotation matrices in four dimensions. Physical Review E
Journal Article
33 (16), pp. 3423 - 3435.e5 (2023)
Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB
Journal Article
19 (8), pp. 992 - 1003 (2023)
Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology
Journal Article
14, 4165 (2023)
Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications
Journal Article
19, pp. 3406 - 3417 (2023)
Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation
Journal Article
618 (7964), pp. 402 - 410 (2023)
Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature
Journal Article
618 (7964), pp. 394 - 401 (2023)
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature
Journal Article
30 (5), pp. 499 - 512 (2023)
Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology
Journal Article
617 (7959), pp. 162 - 169 (2023)
Visualizing the disordered nuclear transport machinery in situ. Nature
Journal Article
3 (4), pp. 334 - 345 (2023)
Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science
Journal Article
19 (5), pp. 1592 - 1601 (2023)
Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation
Journal Article
78, 102501 (2023)
Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology
Journal Article
19 (1), e1010822 (2023)
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 2022
Journal Article
13 (1), 7926 (2022)
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications
Journal Article
8 (50), eadd1436 (2022)
Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances
Journal Article
157 (20), 204802 (2022)
Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics
Journal Article
11, e81432 (2022)
Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife
Journal Article
157 (17), 174801 (2022)
TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics
Journal Article
119 (39), e2209823119 (2022)
In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
41 (18), e109990 (2022)
Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal
Journal Article
13 (32), pp. 7490 - 7496 (2022)
Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters
Journal Article
185 (17), pp. 3201 - 3213 (2022)
Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell
Journal Article
4 (3), 033097 (2022)
Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research
Journal Article
157 (3), 034101 (2022)
Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics
Journal Article
376 (6598), eabm9506 (2022)
AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science
Journal Article
82 (11), pp. 2006 - 2020.e8 (2022)
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell
Journal Article
13, 1224 (2022)
Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications
Journal Article
2 (3), pp. 673 - 686 (2022)
Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au
Journal Article
13 (1), 1022 (2022)
Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications
Journal Article
41 (3), e108443 (2022)
Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 2021
Journal Article
94 (12), 245 (2021)
Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics
Journal Article
374 (6573), eabd9776 (2021)
Nuclear pores dilate and constrict in cellulo. Science
Journal Article
81, pp. 4635 - 4649 (2021)
Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell
Journal Article
118 (46), e2107335118 (2021)
The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
1 (12), pp. 2162 - 2171 (2021)
Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au
Journal Article
121 (19), pp. 11701 - 11725 (2021)
Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews
Journal Article
22 (9), e52289 (2021)
Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports
Journal Article
12 (1), 5236 (2021)
The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nature Communications
Journal Article
220 (8), e202011078 (2021)
Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology
Journal Article
297 (2), 100925 (2021)
Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry
Journal Article
125 (28), pp. 7732 - 7741 (2021)
Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B
Journal Article
154 (23), 234105 (2021)
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics
Journal Article
118 (19), e2100425118 (2021)
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
Journal Article
118 (19), e2016974118 (2021)
Membrane fusion and drug delivery with carbon nanotube porins. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
17 (4), e1008790 (2021)
Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology
Journal Article
12 (7), pp. 1926 - 1931 (2021)
FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters
Journal Article
17 (1), pp. 525 - 537 (2021)
Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation
Journal Article
28 (1), pp. 2 - 7 (2021)
Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology
Journal Article
17 (1), pp. 1 - 382 (2021)
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 2020
Journal Article
59, pp. 23025 - 23029 (2020)
Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English
Journal Article
587 (7835), pp. 657 - 662 (2020)
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature
Journal Article
9 (2020)
Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife
Journal Article
117 (44), pp. 27132 - 27140 (2020)
Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
370 (6513), pp. 203 - 208 (2020)
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science
Journal Article
16 (10), pp. 1078 - 1086 (2020)
p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology
Journal Article
153 (14), 144105 (2020)
MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics
Journal Article
369 (6508), eaaz7714 (2020)
Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science
Journal Article
4, 100032 (2020)
Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X
Journal Article
153 (2), 024116 (2020)
Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics
Journal Article
153 (2), 021101 (2020)
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics
Journal Article
124 (23), pp. 4673 - 4685 (2020)
Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B
Journal Article
368 (6489), eaaz2449, p. 385 (2020)
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science
Journal Article
117 (10), pp. 5109 - 5110 (2020)
Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
11, 756 (2020)
Regulation of lipid saturation without sensing membrane fluidity. Nature Communications
Journal Article
48 (2), pp. 924 - 933 (2020)
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research
Journal Article
124 (2), pp. 336 - 344 (2020)
Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B
Journal Article
16 (1), pp. 725 - 737 (2020)
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation
Journal Article
77 (1), pp. 164 - 179 (2020)
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 2019
Journal Article
27 (12), pp. 1745 - 1759 (2019)
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure
Journal Article
52 (47), 474002 (2019)
Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics
Journal Article
21 (1), e48317 (2019)
TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports
Journal Article
10 (20), pp. 6351 - 6354 (2019)
Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters
Journal Article
151 (15), 154115 (2019)
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics
Journal Article
15 (9), pp. 4974 - 4981 (2019)
Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation
Journal Article
75 (5), pp. 1043 - 1057 (2019)
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell
Journal Article
571 (7766), pp. 580 - 583 (2019)
Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature
Journal Article
116 (27), pp. 13352 - 13357 (2019)
Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
123 (24), pp. 5099 - 5106 (2019)
Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. The Journal of Physical Chemistry B
Journal Article
116 (25), pp. 12275 - 12284 (2019)
Inward-facing conformation of a multidrug resistance MATE family transporter. Proceedings of the National Academy of Sciences of the United States of America