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Nanoelectronics : a molecular view
\"This is a reference book for graduate students and researchers in the areas of nanomaterials, nanoelectronics, solid state physics and solid state devices. Segments of this book are also useful as textbook for a course in nanoelectronics\"-- Provided by publisher.
Book
Structural basis of mitochondrial membrane bending by the I-II-III 2 -IV 2 supercomplex
Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane
. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III
-IV
supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
Journal Article
Atomistic simulation of quantum transport in nanoelectronic devices
\"Computational nanoelectronics is an emerging multi-disciplinary field covering condensed matter physics, applied mathematics, computer science, and electronic engineering. In recent decades, a few state-of-the-art software packages have been developed to carry out first-principle atomistic device simulations. Nevertheless those packages are either black boxes (commercial codes) or accessible only to very limited users (private research codes). The purpose of this book is to open one of the commercial black boxes, and to demonstrate the complete procedure from theoretical derivation, to numerical implementation, all the way to device simulation. Meanwhile the affiliated source code constitutes an open platform for new researchers. This is the first book of its kind. We hope the book will make a modest contribution to the field of computational nanoelectronics\"-- Provided by publisher.
Book
New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II
A project to systematically investigate respiratory supercomplexes in plant mitochondria was initiated. Mitochondrial fractions from Arabidopsis, potato (Solanum tuberosum), bean (Phaseolus vulgaris), and barley (Hordeum vulgare) were carefully treated with various concentrations of the nonionic detergents dodecylmaltoside, Triton X-100, or digitonin, and proteins were subsequently separated by (a) Blue-native polyacrylamide gel electrophoresis (PAGE), (b) two-dimensional Blue-native/sodium dodecyl sulfate-PAGE, and (c) two-dimensional Blue-native/Blue-native PAGE. Three high molecular mass complexes of 1,100, 1,500, and 3,000 kD are visible on one-dimensional Blue native gels, which were identified by separations on second gel dimensions and protein analyses by mass spectrometry. The 1,100-kD complex represents dimeric ATP synthase and is only stable under very low concentrations of detergents. In contrast, the 1,500-kD complex is stable at medium and even high concentrations of detergents and includes the complexes I and $\\text{III}_{2}$. Depending on the investigated organism, 50% to 90% of complex I forms part of this supercomplex if solubilized with digitonin. The 3,000-kD complex, which also includes the complexes I and III, is of low abundance and most likely has a $\\text{III}_{4}\\text{I}_{2}$ structure. The complexes IV, II, and the alternative oxidase were not part of supercomplexes under all conditions applied. Digitonin proved to be the ideal detergent for supercomplex stabilization and also allows optimal visualization of the complexes II and IV on Blue-native gels. Complex II unexpectedly was found to be composed of seven subunits, and complex IV is present in two different forms on the Blue-native gels, the larger of which comprises additional subunits including a 32-kD protein resembling COX VIb from other organisms. We speculate that supercomplex formation between the complexes I and III limits access of alternative oxidase to its substrate ubiquinol and possibly regulates alternative respiration. The data of this investigation are available at http://www.gartenbau.uni-hannover.de/genetik/braun/AMPP.
Journal Article
Supercomplex Assembly Determines Electron Flux in the Mitochondrial Electron Transport Chain
The textbook description of mitochondrial respiratory complexes (RCs) views them as free-moving entities linked by the mobile carriers coenzyme Q (CoQ) and cytochrome c (cyt c). This model (known as the fluid model) is challenged by the proposal that all RCs except complex II can associate in supercomplexes (SCs). The proposed SCs are the respirasome (complexes I, III, and IV), complexes I and III, and complexes III and IV. The role of SCs is unclear, and their existence is debated. By genetic modulation of interactions between complexes I and III and III and IV, we show that these associations define dedicated CoQ and cyt c pools and that SC assembly is dynamic and organizes electron flux to optimize the use of available substrates.
Journal Article
The architecture of respiratory supercomplexes
Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII
2
CIV (the respirasome)—a major ‘tight’ form and a minor ‘loose’ form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII
2
at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.
Respirasomes are supercomplexes of mitochondrial electron transport chain complexes that are responsible for cellular respiration and energy production; cryo-electron microscopy structures of mammalian (sheep) respirasomes are presented.
Inside the mammalian respirasome supercomplex
Mitochondrial electron transport chain complexes are responsible for cellular respiration and energy production. They are organized in supercomplexes called respirasomes. Two studies in this issue of
Nature
report cryo-electron microscopy structures of the supercomplex consisting of complex I, the dimer of complex III and complex IV at resolutions ranging from 5.4 Å to 7.8 Å. Maojun Yang and colleagues study the respirasome isolated from porcine heart, whereas Leonid Sazanov and colleagues obtain it from ovine heart. The structures provide insights into the organization of subunits within complexes and the interactions between the complexes.
Journal Article
Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography
The respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. Here we report the 3D reconstruction of the bovine heart respirasome, composed of dimeric complex III and single copies of complex I and IV, at about 2.2-nm resolution, determined by cryoelectron tomography and subvolume averaging. Fitting of X-ray structures of single complexes I, III2, and IV with high fidelity allows interpretation of the model at the level of secondary structures and shows how the individual complexes interact within the respirasome. Surprisingly, the distance between cytochrome c binding sites of complexes III2 and IV is about 10 nm. Modeling indicates a loose interaction between the three complexes and provides evidence that lipids are gluing them at the interfaces.
Journal Article
Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1
The respiratory chain in the inner mitochondrial membrane contains three large multi‐enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19‐Å 3D map of the 1.7‐MDa amphipol‐solubilized supercomplex I
1
III
2
IV
1
from bovine heart obtained by single‐particle electron cryo‐microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X‐ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol‐binding sites of complexes I and III, and of 10–11 nm between the cytochrome
c
binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.
The respiratory chain complexes of the mitochondrial inner membrane are organized as three higher‐order multi‐enzyme complexes. This study puts forward the first cryo‐EM map for one of these supercomplexes and provides insight into possible pathways for efficient electron transfer.
Journal Article
The potential of respiration inhibition as a new approach to combat human fungal pathogens
The respiratory chain has been proposed as an attractive target for the development of new therapies to tackle human fungal pathogens. This arises from the presence of fungal-specific electron transport chain components and links between respiration and the control of virulence traits in several pathogenic species. However, as the physiological roles of mitochondria remain largely undetermined with respect to pathogenesis, its value as a potential new drug target remains to be determined. The use of respiration inhibitors as fungicides is well developed but has been hampered by the emergence of rapid resistance to current inhibitors. In addition, recent data suggest that adaptation of the human fungal pathogen, Candida albicans, to respiration inhibitors can enhance virulence traits such as yeast-to-hypha transition and cell wall organisation. We conclude that although respiration holds promise as a target for the development of new therapies to treat human fungal infections, we require a more detailed understanding of the role that mitochondria play in stress adaption and virulence.
Journal Article
A giant molecular proton pump: structure and mechanism of respiratory complex I
Key Points
The electron transport chain (ETC) is crucial for life, as it is essential for cellular ATP production.
Most ETC enzymes are large multi-subunit protein assemblies. Of these, complex I is the largest and most elaborate, and such complexity has made it difficult to elucidate the details of its function.
The bacterial complex I represents the minimal version of the enzyme and has 14 conserved subunits that are necessary and essential for function. The subunits are shared between the peripheral arm (where electron transfer takes place) and the membrane arm (which carries out proton translocation).
The mitochondrial enzyme shares this structure and has acquired supernumerary subunits.
Novel insights have recently been obtained on the evolution of antiporter-like subunits of complex I, which are part of the membrane arm, from the Mrp family of antiporters.
The mechanism of complex I is unique in that it must couple the spatially separated electron transfer and proton translocation pathways.
The mechanism of coupling between electron transfer and proton translocation probably involves long-range conformational changes driven mainly by quinone redox reactions.
The mitochondrial respiratory chain comprises large multi-subunit protein complexes that generate ATP. The crystal structure of the entire bacterial complex I was recently solved, providing novel insights into its core architecture, as well as the electron transfer and proton translocation pathways and the coupling between them.
The mitochondrial respiratory chain, also known as the electron transport chain (ETC), is crucial to life, and energy production in the form of ATP is the main mitochondrial function. Three proton-translocating enzymes of the ETC, namely complexes I, III and IV, generate proton motive force, which in turn drives ATP synthase (complex V). The atomic structures and basic mechanisms of most respiratory complexes have previously been established, with the exception of complex I, the largest complex in the ETC. Recently, the crystal structure of the entire complex I was solved using a bacterial enzyme. The structure provided novel insights into the core architecture of the complex, the electron transfer and proton translocation pathways, as well as the mechanism that couples these two processes.
Journal Article