Max Planck Institute of Biophysics

Frankfurt am Main, Germany

Max Planck Institute of Biophysics

Frankfurt am Main, Germany

The Max Planck Institute for Biophysics is located in Frankfurt am Main, Germany. It was founded as Kaiser Wilhelm Institute for Biophysics in 1937, and moved into a new building in 2003. It is one of 80 institutes in the Max Planck Society .A prerequisite for the understanding of the fundamental processes of life is the knowledge of the structure of the participating macromolecules. Two of the four departments are devoted to the challenging task of determining the structure of membrane proteins. Under the direction of Hartmut Michel , the Department of Molecular Membrane Biology approaches this problem primarily by x-ray crystallography, whereas the Department of Structural Biology, headed by Werner Kühlbrandt, uses the complementary technique of electron microscopy. The Department of Biophysical Chemistry, directed by Ernst Bamberg, studies the function of these proteins in native or reconstituted membranes by electrophysiological and spectroscopic methods. The fourth department "Molecular Neurogenetics" under the direction of Peter Mombaerts has started its work in 2007. Since 2007, the institute hosts two Max-Planck Research Groups: "Computational Structural Biology", led by Lucy R. Forrest, and "Theoretical Molecular Biophysics", directed by José D. Faraldo-Gómez.Since April 2003, the institute's four departments are housed in the same building, resulting in improved scientific interaction between the research groups. Scientific links to fellow researchers at Frankfurt University have been strengthened further as the institute is now situated next to the University's biology, chemistry and physics laboratories.Together with the Max Planck Institute for Brain Research and the Goethe University of Frankfurt am Main the institute runs the International Max Planck Research School on the Structure and Function of Biological Membranes, a graduate program offering a Ph.D. Wikipedia.

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Khan M.,Max Planck Institute of Biophysics | Vaes E.,Max Planck Institute of Biophysics | Mombaerts P.,Max Planck Institute of Biophysics
Cell | Year: 2011

Each olfactory sensory neuron (OSN) in mouse chooses one of 1,200 odorant receptor (OR) genes for expression. OR genes are chosen for expression by greatly varying numbers of OSNs. The mechanisms that regulate the probability of OR gene choice remain unclear. Here, we have applied the NanoString platform of fluorescent barcodes and digital readout to measure RNA levels of 577 OR genes in a single reaction, with probes designed against coding sequences. In an inbred mouse strain with a targeted deletion in the P element, we find that this element regulates OR gene choice differentially across its cluster of 24 OR genes. Importantly, the fold changes of NanoString counts in ΔP or ΔH mice are in very close agreement with the fold changes of cell counts, determined by in situ hybridization. Thus, the P and H elements regulate the probability of OR gene choice, not OR transcript level per OSN. © 2011 Elsevier Inc.

Kuhlbrandt W.,Max Planck Institute of Biophysics
EMBO Journal | Year: 2016

Sodium channels are central to a host of fundamental cellular processes, including sensory perception, pain, and muscle contraction. In order to understand any of these processes in detail, it is necessary to know the atomic structure of the channel proteins both with and without bound sodium ions. In this issue, Naylor et al (2016) present the structure of a bacterial sodium channel tetramer. The three bound, partially hydrated sodium ions line up neatly in a row inside the selectivity filter, providing us with the first detailed insights into ion conduction in sodium channels, and the mechanisms by which sodium and potassium ions are discriminated. © 2016 EMBO.

Okazaki K.-I.,Max Planck Institute of Biophysics | Hummer G.,Max Planck Institute of Biophysics
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

We combine molecular simulations and mechanical modeling to explore the mechanism of energy conversion in the coupled rotary motors of FoF1-ATP synthase. A torsional viscoelastic model with frictional dissipation quantitatively reproduces the dynamics and energetics seen in atomistic molecular dynamics simulations of torquedriven γ-subunit rotation in the F1-ATPase rotary motor. The torsional elastic coefficients determined from the simulations agree with results from independent single-molecule experiments probing different segments of the γ-subunit, which resolves a long-lasting controversy. At steady rotational speeds of ~1 kHz corresponding to experimental turnover, the calculated frictional dissipation of less than kBT per rotation is consistent with the high thermodynamic efficiency of the fully reversible motor. Without load, the maximum rotational speed during transitions between dwells is reached at ~1 MHz. Energetic constraints dictate a unique pathway For the coupled rotations of the Fo and F1 rotary motors in ATP synthase, and explain the need For the finer stepping of the F1 motor in the mammalian system, as seen in recent experiments. Compensating For incommensurate eightfold and threefold rotational symmetries in Fo and F1, respectively, a significant fraction of the external mechanical work is transiently stored as elastic energy in the γ-subunit. The general framework developed here should be applicable to other molecular machines.

Paulino C.,Max Planck Institute of Biophysics | Kuhlbrandt W.,Max Planck Institute of Biophysics
eLife | Year: 2014

We examined substrate-induced conformational changes in MjNhaP1, an archaeal electroneutral Na+/H+-antiporter resembling the human antiporter NHE1, by electron crystallography of 2D crystals in a range of physiological pH and Na+ conditions. In the absence of sodium, changes in pH had no major effect. By contrast, changes in Na+ concentration caused a marked conformational change that was largely pH-independent. Crystallographically determined, apparent dissociation constants indicated ~10-fold stronger Na+ binding at pH 8 than at pH 4, consistent with substrate competition for a common ion-binding site. Projection difference maps indicated helix movements by about 2 Å in the 6-helix bundle region of MjNhaP1 that is thought to contain the ion translocation site. We propose that these movements convert the antiporter from the proton-bound, outward-open state to the Na+-bound, inward-open state. Oscillation between the two states would result in rapid Na+/H+ antiport. © Paulino and Kühlbrandt.

Kuhlbrandt W.,Max Planck Institute of Biophysics | Davies K.M.,Max Planck Institute of Biophysics
Trends in Biochemical Sciences | Year: 2016

Rotary ATPases are energy-converting nanomachines found in the membranes of all living organisms. The mechanism by which proton translocation through the membrane drives ATP synthesis, or how ATP hydrolysis generates a transmembrane proton gradient, has been unresolved for decades because the structure of a critical subunit in the membrane was unknown. Electron cryomicroscopy (cryoEM) studies of two rotary ATPases have now revealed a hairpin of long, horizontal, membrane-intrinsic α-helices in the a-subunit next to the c-ring rotor. The horizontal helices create a pair of aqueous half-channels in the membrane that provide access to the proton-binding sites in the rotor ring. These recent findings help to explain the highly conserved mechanism of ion translocation by rotary ATPases. Rotary ATPases are ancient nanomachines that couple the translocation of protons across membranes to ATP synthesis or ATP hydrolysis. The mechanism of proton translocation through the membrane by rotary ATPases has been unresolved for decades because the structure of critical subunits was unknown. Recent electron cryomicroscopy (cryoEM) structures of rotary ATPases have revealed a pair of long, horizontal, membrane-intrinsic helices in subunit a next to the c-ring rotor. At the interface between the rotor and subunit a, the horizontal helices create two offset hydrophilic half-channels that provide access to the proton-binding sites in the rotor. On the basis of the new cryoEM structures, realistic models of how proton translocation drives rotation and ATP synthesis can now be formulated and tested. © 2015 Elsevier Ltd.

Wohlert D.,Max Planck Institute of Biophysics | Kuhlbrandt W.,Max Planck Institute of Biophysics | Yildiz O.,Max Planck Institute of Biophysics
eLife | Year: 2014

Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters.

Daum B.,Max Planck Institute of Biophysics | Kuhlbrandt W.,Max Planck Institute of Biophysics
Journal of Experimental Botany | Year: 2011

For more than half a century, electron microscopy has been a main tool for investigating the complex ultrastructure and organization of chloroplast thylakoid membranes, but, even today, the three-dimensional relationship between stroma and grana thylakoids, and the arrangement of the membrane protein complexes within them are not fully understood. Electron cryo-tomography (cryo-ET) is a powerful new technique for visualizing cellular structures, especially membranes, in three dimensions. By this technique, large membrane protein complexes, such as the photosystem II supercomplex or the chloroplast ATP synthase, can be visualized directly in the thylakoid membrane at molecular (4-5nm) resolution. This short review compares recent advances by cryo-ET of plant thylakoid membranes with earlier results obtained by conventional electron microscopy. © The Author 2010.

Marinelli F.,Max Planck Institute of Biophysics
Biophysical Journal | Year: 2013

In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a broad range of conformations is explored, including nearly native ones, initiating the simulation from a completely unfolded conformation. Finally, several folding/unfolding trajectories give a systematic description of the Trp-cage folding pathways, leading to a unified view for the folding mechanisms of this protein. The proposed mechanism is consistent with NMR chemical shift data at increasing temperature and recent experimental observations pointing to a pivotal role of secondary structure elements in directing the folding process toward the native state. © 2013 Biophysical Society.

Preiss L.,Max Planck Institute of Biophysics
PLoS biology | Year: 2010

We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 A, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle.

Allegretti M.,Max Planck Institute of Biophysics | Klusch N.,Max Planck Institute of Biophysics | Mills D.J.,Max Planck Institute of Biophysics | Vonck J.,Max Planck Institute of Biophysics | And 2 more authors.
Nature | Year: 2015

ATP, the universal energy currency of cells, is produced by F-type ATP synthases, which are ancient, membrane-bound nanomachines. F-type ATP synthases use the energy of a transmembrane electrochemical gradient to generate ATP by rotary catalysis. Protons moving across the membrane drive a rotor ring composed of 8-15 c-subunits1. A central stalk transmits the rotation of the c-ring to the catalytic F1 head, where a series of conformational changes results in ATP synthesis2. A key unresolved question in this fundamental process is how protons pass through the membrane to drive ATP production. Mitochondrial ATP synthases form V-shaped homodimers in cristae membranes3. Here we report the structure of a native and active mitochondrial ATP synthase dimer, determined by single-particle electron cryomicroscopy at 6.2 Å resolution. Our structure shows four long, horizontal membrane-intrinsic α-helices in the a-subunit, arranged in two hairpins at an angle of approximately 70° relative to the c-ring helices. It has been proposed that a strictly conserved membrane-embedded arginine in the a-subunit couples proton translocation to c-ring rotation4. A fit of the conserved carboxy-terminal a-subunit sequence places the conserved arginine next to a proton-binding c-subunit glutamate. The map shows a slanting solvent-accessible channel that extends from the mitochondrial matrix to the conserved arginine. Another hydrophilic cavity on the lumenal membrane surface defines a direct route for the protons to an essential histidine-glutamate pair5. Our results provide unique new insights into the structure and function of rotary ATP synthases and explain how ATP production is coupled to proton translocation. ©2015 Macmillan Publishers Limited. All rights reserved.

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