Gerhard Hummer: Theoretical Biophysics – Department Publications
Journal Article (213)
2023
Journal Article
14, 5979 (2023)
Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications
Journal Article
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology (2023)
Journal Article
Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chemical Society Reviews (2023)
Journal Article
Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB (2023)
Journal Article
14, 4165 (2023)
Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications
Journal Article
15 (2023)
Structural insights on ionizable Dlin-MC3-DMA lipids in DOPC layers by combining accurate atomistic force fields, molecular dynamics simulations and neutron reflectivity. Nanoscale
Journal Article
Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation (2023)
Journal Article
19 (9), pp. 2601 - 2606 (2023)
“Autophagic landscapes: on the paradox of survival through self-degradation” – A science-inspired exhibition. Autophagy
Journal Article
23 (10), pp. 4111 - 4119 (2023)
Anisotropic Friction in a Ligand-Protein Complex. Nano Letters
Journal Article
Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature (2023)
Journal Article
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, pp. 1 - 8 (2023)
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
Visualizing the disordered nuclear transport machinery in situ. Nature (2023)
Journal Article
3 (4), pp. 334 - 345 (2023)
Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science
Journal Article
10, pp. 1 - 12 (2023)
Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology
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
Journal Article
127 (4), pp. 1050 - 1062 (2023)
Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations. The Journal of Physical Chemistry B 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
RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B (2022)
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
Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials (2022)
Journal Article
617, pp. 36 - 41 (2022)
One of the two N-glycans on the human Gb3/CD77 synthase is essential for its activity and allosterically regulates its function. Biochemical and Biophysical Research Communications (Orlando, FL)
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
50 (10), pp. 5726 - 5739 (2022)
Twisting DNA by salt. Nucleic Acids Research (London)
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, 862851 (2022)
Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Frontiers in immunology
Journal Article
13 (19), pp. 5734 - 5740 (2022)
Angle-dependent strength of a single chemical bond by stereographic force spectroscopy. Chemical Science
Journal Article
9, 826505 (2022)
Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Frontiers in Molecular Biosciences
Journal Article
156 (11), 114501 (2022)
Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E. The Journal of Chemical Physics
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
119 (8), e2122030119 (2022)
Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
18 (2), pp. 1202 - 1212 (2022)
Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA. Journal of Chemical Theory and Computation
Journal Article
41 (3), e108443 (2022)
Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal
Journal Article
18 (1), pp. 526 - 537 (2022)
Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. Journal of Chemical Theory and Computation
Journal Article
13 (1), 85 (2022)
Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding. Nature Communications 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
595 (21), pp. 2701 - 2714 (2021)
Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Letters
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
155 (8), 084503 (2021)
Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field. The Journal of Chemical Physics
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
11 (1), 13657 (2021)
A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Scientific Reports
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
154 (17), 171102 (2021)
Extended magnesium and calcium force field parameters for accurate ion–nucleic acid interactions in biomolecular simulations. The Journal of Chemical Physics
Journal Article
17 (4), pp. 2530 - 2540 (2021)
Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties. Journal of Chemical Theory and Computation
Journal Article
9, 680533 (2021)
Editorial: Integrating Timescales From Molecules Up. Frontiers in Chemistry
Journal Article
17 (4), e1008790 (2021)
Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology
Journal Article
8, 636562 (2021)
Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Frontiers in Molecular Biosciences
Journal Article
26 (6), 1664 (2021)
PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules
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
21 (1), 586 (2020)
An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics
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
34 (10), pp. 1063 - 1077 (2020)
Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. Journal of Computer-Aided Molecular Design
Journal Article
119, pp. 939 - 949 (2020)
Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular Dynamics Study. Biophysical Journal
Journal Article
369 (6508), eaaz7714 (2020)
Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science
Journal Article
16 (8), e1007898 (2020)
In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Computational Biology
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
152 (22), 224106 (2020)
Kinetic pathways of water exchange in the first hydration shell of magnesium. 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
36 (21), pp. 5979 - 5989 (2020)
Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics. Langmuir
Journal Article
60 (5), pp. 2413 - 2418 (2020)
Need for Cross-Validation of Single Particle Cryo-EM. Journal of Chemical Information and Modeling
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