MPI für Biophysik
Refine
Year of publication
Document Type
- Article (135)
- Preprint (24)
- Doctoral Thesis (5)
- Bachelor Thesis (1)
- Part of a Book (1)
- Conference Proceeding (1)
- Review (1)
Has Fulltext
- yes (168)
Is part of the Bibliography
- no (168)
Keywords
- Research article (8)
- Cryoelectron microscopy (6)
- Biophysics and structural biology (4)
- X-ray crystallography (4)
- mitochondria (4)
- Bacterial structural biology (3)
- Biochemistry (3)
- Bioenergetics (3)
- Cellular microbiology (3)
- Enzyme mechanisms (3)
- Thermus thermophilus (3)
- structural biology (3)
- subtomogram averaging (3)
- Biophysics (2)
- Cell biology (2)
- Cryo-electron microscopy (2)
- Cryo-em (2)
- Cytochrome Oxidase (2)
- DNA Transformation (2)
- Electrophysiology (2)
- Membrane Proteins (2)
- Membrane Transport (2)
- Mitochondria (2)
- Permeation and transport (2)
- Proteomics (2)
- Secretin (2)
- bioenergetics (2)
- biophysics (2)
- electron cryo-tomography (2)
- electrophysiology (2)
- membrane protein complex (2)
- membrane structure (2)
- membrane transport (2)
- site-directed mutagenesis (2)
- sodium-proton exchange (2)
- structural biology and molecular biophysics (2)
- 3D reconstruction and image processing (1)
- ATP synthase (1)
- Absolute quantification (1)
- Anion Transport System (1)
- Antimicrobial resistance (1)
- Archaea (1)
- Asymmetrie Reconstitution (1)
- Band 3 Protein (1)
- Biocatalysis (1)
- Biophysical Chemistry (1)
- Bos taurus (1)
- Cation Proton Antiporter (1)
- Cation/proton antiport (1)
- Chaperones (1)
- Chemical labeling (1)
- Computation (1)
- Computational Biology (1)
- Computational models (1)
- Cryo-electron Tomography (1)
- Cryoelectron tomography (1)
- Cytochrome c Oxidase (1)
- D. melanogaster (1)
- DNA transporter (1)
- Data Standard (1)
- Dimethyl maleic anhydride (1)
- Dynamin-related-proteins (1)
- EPR spectroscopy (1)
- EcNhaA (1)
- Electron Microscopy (1)
- Erythrocyte Membrane (1)
- Escherichia coli (1)
- FF-ATP synthase dimer (1)
- FXIII deficiency (1)
- Factor XIII (1)
- Helicobacter pylori (1)
- Heme (1)
- Herbicide Resistance (1)
- Hippocampus (1)
- IHMCIF (1)
- Induced pluripotent stem cells (1)
- Integrative Modeling (1)
- Ion transport (1)
- Isotope labeling (1)
- Kinetics (1)
- LILBID-MS (1)
- Label-free (1)
- Ligand-gated ion channel (1)
- Mass spectrometry (1)
- Md simulations (1)
- Membrane Protein (1)
- Membrane Protein Complex (1)
- Membrane and lipid biology (1)
- Membrane fusion (1)
- Membrane protein complex (1)
- Membrane proteins (1)
- Membrane transport (1)
- Metabolic labeling (1)
- Methanogenesis (1)
- Mitochondrial dynamics (1)
- Mitofusin (1)
- MjNhaP1 (1)
- Molecular Physiology of the Cell Membrane (1)
- N5 -methyl-tetrahydromethanopterin: coenzyme M methyltransferase (1)
- NADH:ubiquinone oxidoreductase (1)
- Natural transformation (1)
- Neuron-glia interactions (1)
- Neuroscience (1)
- Neurospora crassa (1)
- NhaA (1)
- Open Access (1)
- Optogenetics (1)
- Oxidoreductases (1)
- PDB-Dev (1)
- PDBx/mmCIF (1)
- PELDOR/DEER spectroscopy (1)
- Photosynthesis (1)
- Photosynthetic Reaction Center (1)
- Pilus (1)
- Potassium transport (1)
- Protein Assembly (1)
- Protein Complexes (1)
- Protein DNA-Interaction (1)
- Protein Purification (1)
- Protein Shape (1)
- Protein Structure (1)
- Protein Structure and Dynamics (1)
- Protein folding (1)
- Protein homeostasis (1)
- Protein turnover (1)
- Proton Transfer Kinetics (1)
- Proton Transport (1)
- Pulsed epr (1)
- RNA dynamics (1)
- RNA structures (1)
- Raman Spectroscopy (1)
- Redox-linked Proton Pump (1)
- Relative quantification (1)
- Respiratory chain (1)
- Rieske domains (1)
- S. Cerevisiae (1)
- SEC-MALS (1)
- Salmonella typhimurium (1)
- Secretins (1)
- Sodium Proton Exchange (1)
- Solid Supported Membrane (1)
- Solid supported membrane (1)
- Solid-state NMR (1)
- Spectroscopy (1)
- Stem-cell differentiation (1)
- Subtomogram averaging (1)
- Supercomplex (1)
- TOM complex (1)
- Terbutryn (1)
- Thermophile (1)
- Three-Dimensional Structure (1)
- Time-resolved Absorption Spectroscopy (1)
- Type IV Pili (1)
- Worldwide Protein Data Bank (1)
- Yarrowia lipolytica (1)
- Yarrowia lipolytica F1Fo-ATP synthase (1)
- active/deactive transition (1)
- ageing (1)
- automation (1)
- bacterial secretion (1)
- beam-induced movement (1)
- biochemistry (1)
- biophysics and structural biology (1)
- cell respiration (1)
- cellular self-organization (1)
- channelrhodopsin (1)
- cholesterol-dependent cytolysin (cdc) (1)
- coarse-grained simulations (1)
- complement system (1)
- complex III2 (1)
- computational modeling (1)
- conformational changes (1)
- conformational heterogeneity (1)
- crista junction (1)
- cristae (1)
- cryo-EM (1)
- cryo-electron microscopy (1)
- cryo-electron tomography (1)
- cryo-tomography (1)
- cryoelectron microscopy (1)
- cryoem (1)
- cryoet (1)
- cytochrome c oxidase (1)
- devitrification (1)
- diffusion model (1)
- digital twin (1)
- electron cryo-microscopy (1)
- electron cryo-microscopy (cryoem) (1)
- electron cryo-tomography (cryoet) (1)
- electron cryotomography (1)
- electron transfer (1)
- endoplasmic reticulum (1)
- enzyme mechanism (1)
- excipients (1)
- fluorescence (1)
- graphene (1)
- guanidine-II riboswitch (1)
- heme-regulated inhibitory kinase (1)
- inner membrane morphology (1)
- iron-sulfur proteins (1)
- light-gated ion channel (1)
- mass spectrometry (1)
- membrane curvature (1)
- membrane pore (1)
- microbial rhodopsin (1)
- microbiology and infectious disease (1)
- mitochondrial inner membrane (1)
- mitochondrial protein import (1)
- molecular dynamics (1)
- molecular simulations (1)
- mouse (1)
- oxysterol-binding protein homology protein (1)
- pH Indicator Dye (1)
- pH Regulation (1)
- peroxide radicals (1)
- phosphatidylinositol 4-phosphate 5-kinase (1)
- phosphatidylserine (1)
- photopharmacology (1)
- plasma membrane (1)
- pleiotropy (1)
- pore-forming toxin (1)
- protein degradation (1)
- protein denaturation (1)
- protein synthesis (1)
- proteostasis (1)
- rat (1)
- redox-linked proton translocation (1)
- respirasomes (1)
- respiratory activity (1)
- respiratory chain supercomplexes (1)
- respiratory complex I (1)
- respiratory complex IV (1)
- ribosomes (1)
- riboswitch (1)
- rotary ATPase mechanism (1)
- secondary active transport (1)
- single-molecule FRET (1)
- single-particle cryo-EM (1)
- site-directed spin labeling (1)
- sterol (1)
- structure determination (1)
- translation (1)
- transport mechanism (1)
- transporter (1)
- type IV pilus (1)
- unsaturated phospholipid (1)
- wwPDB (1)
- x-ray crystallography (1)
- yeast (1)
Institute
- MPI für Biophysik (168)
- Physik (65)
- Biochemie und Chemie (50)
- Biowissenschaften (23)
- Biochemie, Chemie und Pharmazie (15)
- Medizin (15)
- Buchmann Institut für Molekulare Lebenswissenschaften (BMLS) (12)
- Exzellenzcluster Makromolekulare Komplexe (4)
- Frankfurt Institute for Advanced Studies (FIAS) (4)
- MPI für Hirnforschung (4)
Movement of the Rieske domain of the iron–sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
Bei der UV-Bestrahlung (2537 Å) des Zn-Insulins beobachtet man für kleinere Dosen (bis 10 Einstein/Mol) eine direkte Korrelation zwischen der Inaktivierung und der Photoreduktion einer der drei Disulfidbrücken. Mit steigender Dosis wird die Quantenausbeute für die Reduktion der Disulfidbrücken (Bildung von SH-Gruppen) sehr klein, dagegen führen dann andere Prozesse zunehmend zur photochemischen Zerstörung der Disulfidbrücken. Für größere Strahlendosen (über 100 Einstein/Mol) ergibt die Extrapolation, daß für die völlige Inaktivierung des Insulins sämtliche drei Cystinreste zerstört werden müssen. Von den übrigen Aminosäuren wird durch Dosen um 100 Einstein/Mol nur der Tyrosin-Anteil signifikant vermindert. Mit steigender Strahlendosis ändert sich — wahrscheinlich infolge von Konformationsänderungen der Polypeptidketten — die Photosensibilität der Aminosäuren.
The dependence of the Escherichia coli Na+H+ antiporter A (EcNhaA) pH sensor mutant E241C on H+ and Na+ concentrations was tested using a solid supported membrane (SSM) based electrophysiological approach. Proteoliposome preparations with right side out (RSO) oriented carriers were used to investigate the passive downhill uptake mode (physiologically the reverse transport mode) at zero membrane potential. Na+ concentration gradients established with a rapid solution exchange acted as the driving force. When a Na+ concentration gradient was established at symmetrical pH, the transport activity of the E241C EcNhaA variant was similar to that of the wildtype EcNhaA, with no shift of the bell-shaped pH dependence, an increase of the KmNa at acidic pH and a decrease of the KmNa at alkaline pH, supporting the model of a competitive binding of Na+ and H+ to a common binding site.
A new type of Na+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif
(2013)
Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consistently, activity measurements showed Na+ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na+ ionophore monensin. Furthermore, Na+ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na+ coupling is provided by two identical crystal structures of the c11 ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na+ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na+ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.
Author Summary: Essential cellular processes such as biosynthesis, transport, and motility are sustained by the energy released in the hydrolysis of ATP, the universal energy carrier in living cells. Most ATP in the cell is produced by a membrane-bound enzyme, the ATP synthase, through a rotary mechanism that is coupled to the translocation of ions across the membrane. The majority of ATP synthases are energized by transmembrane electrochemical gradients of protons (proton-motive force), but a number of organisms, including some important human pathogens, use gradients of sodium ions instead (sodium-motive force). The ion specificity of ATP synthases is determined by a membrane-embedded sub-complex, the c-ring, which is the smallest known biological rotor. The functional mechanism of the rotor ring and its variations among different organisms are of wide interest, because of this enzyme's impact on metabolism and disease, and because of its potential for nanotechnology applications. Here, we characterize a previously unrecognized type of Na+-driven ATP synthase from the opportunistic human pathogen Fusobacterium nucleatum, which is implicated in periodontal diseases. We analyzed this ATP synthase and its rotor ring through a multi-disciplinary approach, combining cell-growth and biochemical assays, X-ray crystallography and computer-simulation methods. Two crystal structures of the membrane rotor were solved, at low and high pH, revealing an atypical ion-recognition motif mediated by two carboxylate side-chains. This motif is shared by other human pathogens, such as Mycobacterium tuberculosis or Streptococcus pneumonia, whose ATP synthases are targets of novel antibiotic drugs. The implications of this ion-recognition mode on the mechanism of the ATP synthase and the cellular bioenergetics of F. nucleatum were thus examined. Our results provide the basis for future pharmacological efforts against this important pathogen.
Fusion of mitochondrial outer membranes is crucial for proper organelle function and involves large GTPases called mitofusins. The discrete steps that allow mitochondria to attach to one another and merge their outer membranes are unknown. By combining an in vitro mitochondrial fusion assay with electron cryo-tomography (cryo-ET), we visualize the junction between attached mitochondria isolated from Saccharomyces cerevisiae and observe complexes that mediate this attachment. We find that cycles of GTP hydrolysis induce progressive formation of a docking ring structure around extended areas of contact. Further GTP hydrolysis triggers local outer membrane fusion at the periphery of the contact region. These findings unravel key features of mitofusin-dependent fusion of outer membranes and constitute an important advance in our understanding of how mitochondria connect and merge.