A Structural Perspective on Respiratory Complex I: Structure and Function of NADH:ubiquinone oxidoreductase

280 Pages·2012·3.982 MB·English

by  Rouslan G. Efremov, Leonid Sazanov (auth.), Leonid Sazanov (eds.)

A Structural Perspective on Respiratory Complex I

Leonid Sazanov
Editor
A Structural Perspective
on Respiratory Complex I
Structure and Function of
NADH:ubiquinone oxidoreductase
Editor
Leonid Sazanov
Medical Research Council Mitochondrial Biology Unit
Wellcome Trust/MRC Building, Hills Road
Cambridge CB2 0XY, UK
ISBN 978-94-007-4137-9 ISBN 978-94-007-4138-6 (eBook)
DOI 10.1007/978-94-007-4138-6
Springer Dordrecht Heidelberg New York London
Library of Congress Control Number: 2012938257
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Foreword
Complex I (NADH:ubiquinone oxidoreductase) is the fi rst enzyme of the respira-
tory chain in mitochondria and bacteria. It is one of the largest and most elaborate
membrane protein assemblies known. It plays a central role in cellular energy pro-
duction, providing about 40% of the proton fl ux required for ATP synthesis. Complex
I dysfunction has been implicated in many human neurodegenerative diseases and
mutations in its subunits are the most common human genetic disorders known.
Complex I is also a major source of reactive oxygen species in mitochondria, which
may lead to Parkinson’s disease and could be involved in aging. The enzyme transfers
two electrons from NADH to quinone, coupling this process to the translocation of
four protons across the membrane out of the mitochondrial matrix, by a mechanism
as yet not fully established. Mitochondrial complex I consists of 45 different subunits,
whilst the prokaryotic enzyme is simpler, consisting of 14 “core” subunits with a
total mass of about 550 kDa. The mitochondrial and bacterial enzymes contain
equivalent redox components ( fl avin and 8–9 Fe-S clusters) and have a similar,
rather unusual, L-shaped structure. The hydrophobic arm is embedded in the mem-
brane and the hydrophilic peripheral arm protrudes into the mitochondrial matrix or
the bacterial cytoplasm. The “core” subunits exhibit a high degree of sequence
conservation, which suggests that the complex I mechanism is likely to be the same
throughout all species. Hence, the bacterial enzyme is used as a ‘minimal’ model of
human complex I in order to understand its structure and mechanism. Recent years
have been marked by spectacular progress in the structural characterization of complex
I, which now fi nally allows us to begin to understand the mechanics of this large
molecular machine, making this book very timely.
Until about 5–6 years ago structural information on complex I was absent, and so
understanding of it was very limited, especially compared to other enzymes of the
respiratory chain. Complex I used to be known as a notorious “monster” enzyme,
the “black box” of bioenergetics. In 40 or so years since its discovery it was esta-
blished that complex I most likely pumps four protons per two electrons transferred
from NADH to quinone. Electron transfer was known to occur via fl avin mononu-
cleotide (FMN) and series of at least 6 iron-sulfur (Fe-S) clusters, which were
detected by electron paramagnetic resonance (EPR). Not all the clusters were
v
vi Foreword
observed experimentally, since the presence of 8–9 Fe-S clusters was predicted on
the basis of sequence analysis. The sequence of events during electron transfer was
unknown and the mechanism of proton translocation was even more enigmatic. Two
possible mechanisms of coupling between electron transfer and proton translocation
have been vigorously discussed: direct (redox-driven, akin to the Q-cycle) and indirect
(conformation-driven). However, in the absence of structural information, they were
mostly speculative.
All started to change in 2005–2006, when we solved the fi rst crystal structure of
the hydrophilic domain of complex I, using the enzyme from T hermus thermophilus.
It established the electron transfer pathway from NADH, through fl avin mononu-
cleotide (FMN) and seven conserved Fe-S clusters, to the quinone-binding site at
the interface with the membrane domain. In 2010–2011 we have solved the struc-
ture of the membrane domain of E. coli complex I and determined the architecture
of the entire T . thermophilus enzyme at lower resolution. Thus, the atomic structure
of only one “core” subunit, Nqo8/NuoH (T hermus/E. coli nomenclature), found at
the interface of the two main domains, remains unknown. Additionally, low-resolution
X-ray analysis of the mitochondrial enzyme from Y arrowia lypolityca was published
in 2010, indicating a similar arrangement of the “core” subunits, surrounded by
many supernumerary subunits. The membrane-spanning part of the enzyme lacks
covalently bound prosthetic groups, but our structures show how proton translocation
through the three largest hydrophobic subunits of complex I, homologous to each
other and to the antiporter family, may be driven by a long a -helix, akin to the cou-
pling rod in a steam engine. This and other features of the structure strongly suggest
that electron transfer in the peripheral arm is coupled to proton translocation in the
membrane arm purely by long-range conformational changes. Mutations causing
human diseases are found near key residues involved in proton transfer, explaining
their effects on activity.
Not all the details of the mechanism are clear yet, but we are now operating on a
completely different level of knowledge than just a few years ago. This led to the
idea of summarizing in book form current knowledge of complex I, taking into
account structural information. No books on complex I have been published previ-
ously, and the last special issue of a journal devoted to complex I was published in
2001, when it was still known as a “black box”. Therefore, it is hoped that this book
will provide the reader with a timely and comprehensive review of current state-
of-the-art research on complex I.
In Chap. 1 , current knowledge of the structure of complex I is reviewed, starting
from the peripheral domain, followed by a detailed description of the new structure of
the membrane domain, and ending with implications for the mechanism. In Chap. 2 ,
the binding of substrates, the role of individual Fe-S clusters (in particular those away
from the main pathway) and the mechanism of proton translocation are discussed on
the basis of data from site-directed mutagenesis, EPR and FTIR spectroscopy, as
well as other studies. In Chap. 3 , current knowledge of the characteristics and roles
of each Fe-S cluster in complex I is overviewed. Chapter 4 provides a review of
many speci fi c inhibitors of complex I, the use of which has been very informative in
characterisation of the quinone-binding site and the terminal electron transfer step.
Foreword vii
In Chap. 5 , some of the earliest studies on complex I, in particular EPR spectroscopy
leading to the fi rst identi fi cation of Fe-S clusters, are summarised.
Complex I has an intricate evolutionary history, originating from the uni fi cation
of hydrogenase and transporter modules. In Chap. 6 , the evolutionary relationship
with [Ni-Fe]-hydrogenases is analysed and mechanistic implications are derived
from comparisons of known crystal structures. In Chap. 7 , the emphasis is on the
relationship with the Mrp antiporter family and it is proposed that antiporter-like
subunits in modern complex I may have different functions.
Mutations in complex I subunits, both mitochondrially- and nuclear-encoded,
lead to a range of human diseases. Many of these mutations have been reproduced
in bacterial systems for mechanistic studies. Chapter 8 provides a review of site-
directed mutagenesis studies that helped in identifying residues essential for
structural integrity, cofactor ligation, substrate binding, electron transfer and proton
translocation. In Chap. 9 , a comprehensive overview of the cellular consequences of
pathological mtDNA-encoded mutations in complex I subunits is provided.
Mitochondrial complex I contains, in addition to the “core” subunits, up to 31
“supernumerary” subunits, with poorly understood roles. Chapter 1 0 describes an
intricate process of assembly of the complex in several stages, involving distinct func-
tionally and evolutionarily conserved modules, and requiring a number of chaperones.
In Chap. 11 , the similarities and peculiarities of the subunit composition of mitochon-
drial complex I in plants and the complex I analogue in chloroplasts are described.
In the respiratory chain of mitochondria complex I appears not to exist on its own,
but as part of even larger assemblies, or “supercomplexes”. These involve complexes
I, III and IV, as described in Chap. 1 1 , and may promote substrate channelling.
Thus, combined, the chapters cover a wide range of topics which should provide
the reader with an up-to-date review of research on complex I in these exiting times,
when the molecular basis for its mechanism is fi nally starting to become clear.
Leonid Sazanov
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust/MRC Building, Hills Road
Cambridge, UK

Contents
Part I Structure and Mechanism of Complex I
1 Structure of Complex I ........................................................................... 3
Rouslan G. Efremov and Leonid Sazanov
2 On the Mechanism of the Respiratory Complex I ............................... 23
Thorsten Friedrich, Petra Hellwig, and Oliver Einsle
3 Iron–Sulfur Clusters in Complex I ........................................................ 61
Eiko Nakamaru-Ogiso
4 Current Topics of the Inhibitors of Mitochondrial Complex I ........... 81
Hideto Miyoshi
5 My Fifty Years Association with Complex I Study .............................. 99
Tomoko Ohnishi
Part II Evolution of Complex I
6 The Evolutionary Relationship Between
Complex I and [NiFe]-Hydrogenase ...................................................... 109
Anne Volbeda and Juan C. Fontecilla-Camps
7 Recruitment of the Antiporter Module – A Key
Event in Complex I Evolution ................................................................ 123
Vamsi Krishna Moparthi and Cecilia Hägerhäll
Part III Mutations in Complex I Subunits and Medical Implications
8 Characterization of Bacterial Complex I
(NDH-1) by a Genetic Engineering Approach ...................................... 147
Takao Yagi, Jesus Torres-Bacete, Prem Kumar Sinha,
Norma Castro-Guerrero, and Akemi Matsuno-Yagi
ix
x Contents
9 Cellular Consequences of mtDNA-Encoded Mutations
in NADH:Ubiquinone Oxidoreductase .................................................. 171
Mina Pellegrini, Jan A.M. Smeitink, Peter H.G.M. Willems,
and Werner J.H. Koopman
Part IV Subunit Composition and Assembly
of Mitochondrial Complex I
10 The Assembly of Human Complex I...................................................... 193
Jessica Nouws, Maria Antonietta Calvaruso, and Leo Nijtmans
11 Complexes I in the Green Lineage ......................................................... 219
Claire Remacle, Patrice Hamel, Véronique Larosa,
Nitya Subrahmanian, and Pierre Cardol
Part V Supercomplexes in Mitochondria
12 Supramolecular Organization of the Respiratory Chain .................... 247
Janet Vonck
A Structural Perspective on Complex I ........................................................ 279
Index ................................................................................................................. 281