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Efremov R.G.,Medical Research Council Mitochondrial Biology Unit | Efremov R.G.,Max Planck Institute of Molecular Physiology | Sazanov L.A.,Medical Research Council Mitochondrial Biology Unit
Biochimica et Biophysica Acta - Bioenergetics | Year: 2012

Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes. © 2012 Elsevier B.V. All rights reserved.


Divakaruni A.S.,Medical Research Council Mitochondrial Biology Unit
Physiology (Bethesda, Md.) | Year: 2011

Mitochondria couple respiration to ATP synthesis through an electrochemical proton gradient. Proton leak across the inner membrane allows adjustment of the coupling efficiency. The aim of this review is threefold: 1) introduce the unfamiliar reader to proton leak and its physiological significance, 2) review the role and regulation of uncoupling proteins, and 3) outline the prospects of proton leak as an avenue to treat obesity, diabetes, and age-related disease.


Requejo R.,Medical Research Council Mitochondrial Biology Unit
Methods in enzymology | Year: 2010

Protein thiols are an important component of mammalian intramitochondrial antioxidant defenses owing to their selective interaction with reactive oxygen and nitrogen species (ROS and RNS). Reversible modifications of protein thiols resulting from these interactions are also an important aspect of redox signal transduction. Therefore, to assess how mitochondria respond to oxidative stress and act as nodes in redox signaling pathways, it is important to measure general changes to protein thiol redox states and also to identify the specific mitochondrial thiol proteins involved. Here we outline some of the approaches that can be used to accomplish these goals and thereby infer the multiple roles of mammalian mitochondrial protein thiols in antioxidant defense and redox signaling. Copyright (c) 2010 Elsevier Inc. All rights reserved.


Murphy M.P.,Medical Research Council Mitochondrial Biology Unit
Free Radical Biology and Medicine | Year: 2014

Although oxidative damage contributes to many pathologies the use of naturally occurring, small-molecule antioxidants as therapies for these disorders has not been successful. Here I discuss some of the reasons this may be so. Paramount among these are the difficulties in delivering enough of the antioxidant to the intracellular location required to decrease pathological oxidative damage and the challenge of assessing whether the intervention has actually decreased oxidative damage in the patient to a therapeutically useful extent. To develop effective antioxidant therapies the best strategy may be to create new chemical entities designed to detoxify a defined reactive oxygen species-dependent process that underlies a particular pathology, in the same way a conventional drug is designed to modulate a biochemical process, rather than applying antioxidants in an unfocused manner. In developing new antioxidants it will be useful to utilize endogenous processes to activate and recycle the molecules in parallel with the targeting of compounds to cells and organelles in ways that are not limited by the constraints that impair the distribution of endogenous antioxidants. In short, I suggest that the future development of antioxidant therapies should be viewed as an arm of drug development, utilizing focused approaches similar to those of medicinal chemistry and pharmacology, rather than as a branch of nutrition. © 2013 Elsevier Inc.


Murphy M.P.,Medical Research Council Mitochondrial Biology Unit
Science Signaling | Year: 2012

Mitochondria have various essential functions in metabolism and in determining cell fate during apoptosis. In addition, mitochondria are also important nodes in a number of signaling pathways. For example, mitochondria can modulate signals transmitted by second messengers such as calcium. Because mitochondria are also major sources of reactive oxygen species (ROS), they can contribute to redox signaling - for example, by the production of ROS such as hydrogen peroxide that can reversibly modify cysteine residues and thus the activity of target proteins. Mitochondrial ROS production is thought to play a role in hypoxia signaling by stabilizing the oxygen-sensitive transcription factor hypoxia-inducible factor-1α. New evidence has extended the mechanism of mitochondrial redox signaling in cellular responses to hypoxia in interesting and unexpected ways. Hypoxia altered the microtubule-dependent transport of mitochondria so that the organelles accumulated in the perinuclear region, where they increased the intranuclear concentration of ROS. The increased ROS in turn enhanced the expression of hypoxia-sensitive genes such as VEGF (vascular endothelial growth factor) not by reversibly oxidizing a protein, but by oxidizing DNA sequences in the hypoxia response element of the VEGF promoter. This paper and other recent work suggest a new twist on mitochondrial signaling: that the redistribution of mitochondria within the cell can be a component of regulatory pathways.


Smith A.C.,Medical Research Council Mitochondrial Biology Unit | Blackshaw J.A.,Medical Research Council Mitochondrial Biology Unit | Robinson A.J.,Medical Research Council Mitochondrial Biology Unit
Nucleic Acids Research | Year: 2012

MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/) is a data warehouse for the storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed. The latest release of MitoMiner stores proteomics data sets from 46 studies covering 11 different species from eumetazoa, viridiplantae, fungi and protista. MitoMiner is implemented by using the open source InterMine data warehouse system, which provides a user interface allowing users to upload data for analysis, personal accounts to store queries and results and enables queries of any data in the data model. MitoMiner also provides lists of proteins for use in analyses, including the new MitoMiner mitochondrial proteome reference sets that specify proteins with substantial experimental evidence for mitochondrial localization. As further mitochondrial proteomics data sets from normal and diseased tissue are published, MitoMiner can be used to characterize the variability of the mitochondrial proteome between tissues and investigate how changes in the proteome may contribute to mitochondrial dysfunction and mitochondrial-associated diseases such as cancer, neurodegenerative diseases, obesity, diabetes, heart failure and the ageing process. © The Author(s) 2011. Published by Oxford University Press.


Youle R.J.,U.S. National Institutes of Health | Narendra D.P.,U.S. National Institutes of Health | Narendra D.P.,Medical Research Council Mitochondrial Biology Unit
Nature Reviews Molecular Cell Biology | Year: 2011

Autophagy not only recycles intracellular components to compensate for nutrient deprivation but also selectively eliminates organelles to regulate their number and maintain quality control. Mitophagy, the specific autophagic elimination of mitochondria, has been identified in yeast, mediated by autophagy-related 32 (Atg32), and in mammals during red blood cell differentiation, mediated by NIP3-like protein X (NIX; also known as BNIP3L). Moreover, mitophagy is regulated in many metazoan cell types by parkin and PTEN-induced putative kinase protein 1 (PINK1), and mutations in the genes encoding these proteins have been linked to forms of Parkinson's disease. © 2011 Macmillan Publishers Limited. All rights reserved.


Hirst J.,Medical Research Council Mitochondrial Biology Unit
Annual Review of Biochemistry | Year: 2013

Complex I (NADH:ubiquinone oxidoreductase) is crucial for respiration in many aerobic organisms. In mitochondria, it oxidizes NADH from the tricarboxylic acid cycle and β-oxidation, reduces ubiquinone, and transports protons across the inner membrane, contributing to the proton-motive force. It is also a major contributor to cellular production of reactive oxygen species. The redox reaction of complex I is catalyzed in the hydrophilic domain; it comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer along a chain of iron-sulfur clusters, and ubiquinone reduction. Redox-coupled proton translocation in the membrane domain requires long-range energy transfer through the protein complex, and the molecular mechanisms that couple the redox and proton-transfer half-reactions are currently unknown. This review evaluates extant data on the mechanisms of energy transduction and superoxide production by complex I, discusses contemporary mechanistic models, and explores how mechanistic studies may contribute to understanding the roles of complex I dysfunctions in human diseases. © 2013 by Annual Reviews. All rights reserved.


Hirst J.,Medical Research Council Mitochondrial Biology Unit
Biochemical Journal | Year: 2010

Complex I (NADH:quinone oxidoreductase) is crucial to respiration in many aerobic organisms. In mitochondria, it oxidizes NADH (to regenerate NAD+ for the tricarboxylic acid cycle and fatty-acid oxidation), reduces ubiquinone (the electrons are ultimately used to reduce oxygen to water) and transports protons across the mitochondrial innermembrane (to produce and sustain the protonmotive force that supports ATP synthesis and transport processes). Complex I is also a major contributor to reactive oxygen species production in the cell. Understanding the mechanisms of energy transduction and reactive oxygen species production by complex I is not only a significant intellectual challenge, but also a prerequisite for understanding the roles of complex I in disease, and for the development of effective therapies. One approach to defining a complicated reaction mechanism is to break it down into manageable parts that can be tackled individually, before being recombined and integrated to produce the complete picture. Thus energy transduction by complex I comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer from the flavin to bound quinone along a chain of iron-sulfur clusters, quinone reduction and proton translocation. More simply, molecular oxygen is reduced by the flavin, to form the reactive oxygen species superoxide and hydrogen peroxide. The present review summarizes and evaluates experimental data that pertain to the reaction mechanisms of complex I, and describes and discusses contemporary mechanistic hypotheses, proposals and models. © The Authors Journal compilation.


Chinnery P.F.,University of Cambridge | Chinnery P.F.,Medical Research Council Mitochondrial Biology Unit
EMBO Molecular Medicine | Year: 2015

Ten years ago, there was an emerging view that the molecular basis for adult mitochondrial disorders was largely known and that the clinical phenotypes had been well described. Nothing could have been further from the truth. The establishment of large cohorts of patients has revealed new aspects of the clinical presentation that were not previously appreciated. Over time, this approach is starting to provide an accurate understanding of the natural history of mitochondrial disease in adults. Advances in molecular diagnostics, underpinned by next generation sequencing technology, have identified novel molecular mechanisms. Recently described mitochondrial disease phenotypes have disparate causes, and yet share common mechanistic themes. In particular, disorders of mtDNA maintenance have emerged as a major cause of mitochondrial disease in adults. Progressive mtDNA depletion and the accumulation of mtDNA mutations explain some of the clinical features, but the genetic and cellular processes responsible for the mtDNA abnormalities are not entirely clear in each instance. Unfortunately, apart from a few specific examples, treatments for adult mitochondrial disease have not been forthcoming. However, the establishment of international consortia, and the first multinational randomised controlled trial, have paved the way for major progress in the near future, underpinned by growing interest from the pharmaceutical industry. Adult mitochondrial medicine is, therefore, in its infancy, and the challenge is to harness the new understanding of its molecular and cellular basis to develop treatments of real benefit to patients. A state-of-the art, comprehensive overview on adult mitochondrial disorders including discussion of current directions for therapy and patient priorities for treatment. A must-read for basic and clinical researchers alike. © 2015 EMBO.

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