Editing Respiratory complex I (section)

==Mechanism==

=== Overall mechanism ===
All redox reactions take place in the hydrophilic domain of complex I. NADH initially binds to complex I, and transfers two electrons to the [[flavin mononucleotide]] (FMN) prosthetic group of the enzyme, creating FMNH<sub>2</sub>. The electron acceptor – the isoalloxazine ring – of FMN is identical to that of [[Flavin adenine dinucleotide|FAD]]. The electrons are then transferred through the FMN via a series of [[Iron–sulfur protein|iron-sulfur (Fe-S) clusters]],<ref name=":0" /> and finally to [[coenzyme Q10]] (ubiquinone). This electron flow changes the redox state of the protein, inducing conformational changes of the protein which alters the p''K'' values of ionizable side chain, and causes four hydrogen ions to be pumped out of the mitochondrial matrix.<ref name="BioChem">{{cite book | title = Principles of Biochemistry, 3rd Edition | chapter = Chapter 18, Mitochondrial ATP synthesis | vauthors = Voet DJ, Voet GJ, Pratt CW | publisher = Wiley | year = 2008 | isbn = 978-0-470-23396-2 | page = 608 }}</ref> [[Ubiquinone]] (CoQ) accepts two electrons to be reduced to [[ubiquinol]] (CoQH<sub>2</sub>).<ref name="Berg"/>

=== Electron transfer mechanism ===
The proposed pathway for electron transport prior to ubiquinone reduction is as follows: NADH – FMN – N3 – N1b – N4 – N5 – N6a – N6b – N2 – Q, where Nx is a labelling convention for iron sulfur clusters.<ref name=":0">{{cite journal | vauthors = Sazanov LA | title = A giant molecular proton pump: structure and mechanism of respiratory complex I | journal = Nature Reviews. Molecular Cell Biology | volume = 16 | issue = 6 | pages = 375–88 | date = June 2015 | pmid = 25991374 | doi = 10.1038/nrm3997 | s2cid = 31633494 }}</ref> The high reduction potential of the N2 cluster and the relative proximity of the other clusters in the chain enable efficient electron transfer over long distance in the protein (with transfer rates from NADH to N2 iron-sulfur cluster of about 100 μs).<ref>{{cite journal | vauthors = Ohnishi T | title = Iron-sulfur clusters/semiquinones in complex I | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1364 | issue = 2 | pages = 186–206 | date = May 1998 | pmid = 9593887 | doi = 10.1016/s0005-2728(98)00027-9 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Bridges HR, Bill E, Hirst J | title = Mössbauer spectroscopy on respiratory complex I: the iron-sulfur cluster ensemble in the NADH-reduced enzyme is partially oxidized | journal = Biochemistry | volume = 51 | issue = 1 | pages = 149–58 | date = January 2012 | pmid = 22122402 | pmc = 3254188 | doi = 10.1021/bi201644x }}</ref>

The equilibrium dynamics of Complex I are primarily driven by the quinone redox cycle. In conditions of high proton motive force (and accordingly, a ubiquinol-concentrated pool), the enzyme runs in the reverse direction. Ubiquinol is oxidized to ubiquinone, and the resulting released protons reduce the proton motive force.<ref name="Efremov 1785–1795">{{cite journal | vauthors = Efremov RG, [[Leonid Sazanov|Sazanov LA]] | title = The coupling mechanism of respiratory complex I - a structural and evolutionary perspective | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1817 | issue = 10 | pages = 1785–95 | date = October 2012 | pmid = 22386882 | doi = 10.1016/j.bbabio.2012.02.015 | doi-access = free }}</ref>

=== Proton translocation mechanism ===
The coupling of proton translocation and electron transport in Complex I is currently proposed as being indirect (long range conformational changes) as opposed to direct (redox intermediates in the hydrogen pumps as in [[heme]] groups of Complexes [[Coenzyme Q – cytochrome c reductase|III]] and [[Cytochrome c oxidase|IV]]).<ref name=":0" /> The architecture of the hydrophobic region of complex I shows multiple proton transporters that are mechanically interlinked. The three central components believed to contribute to this long-range conformational change event are the pH-coupled N2 iron-sulfur cluster, the quinone reduction, and the transmembrane helix subunits of the membrane arm. Transduction of conformational changes to drive the transmembrane transporters linked by a 'connecting rod' during the reduction of ubiquinone can account for two or three of the four protons pumped per NADH oxidized. The remaining proton must be pumped by direct coupling at the ubiquinone-binding site. It is proposed that direct and indirect coupling mechanisms account for the pumping of the four protons.<ref>{{cite journal | vauthors = Treberg JR, Quinlan CL, Brand MD | title = Evidence for two sites of superoxide production by mitochondrial NADH-ubiquinone oxidoreductase (complex I) | journal = The Journal of Biological Chemistry | volume = 286 | issue = 31 | pages = 27103–10 | date = August 2011 | pmid = 21659507 | pmc = 3149303 | doi = 10.1074/jbc.M111.252502 | doi-access = free }}</ref>

The N2 cluster's proximity to a nearby cysteine residue results in a conformational change upon reduction in the nearby helices, leading to small but important changes in the overall protein conformation.<ref>{{cite journal | vauthors = Berrisford JM, [[Leonid Sazanov|Sazanov LA]] | title = Structural basis for the mechanism of respiratory complex I | journal = The Journal of Biological Chemistry | volume = 284 | issue = 43 | pages = 29773–83 | date = October 2009 | pmid = 19635800 | pmc = 2785608 | doi = 10.1074/jbc.m109.032144 | doi-access = free }}</ref> Further [[electron paramagnetic resonance]] studies of the electron transfer have demonstrated that most of the energy that is released during the subsequent CoQ reduction is on the final [[ubiquinol]] formation step from [[semiquinone]], providing evidence for the "single stroke" H<sup>+</sup> translocation mechanism (i.e. all four protons move across the membrane at the same time).<ref name="Efremov 1785–1795" /><ref>{{cite journal | vauthors = Baranova EA, Morgan DJ, [[Leonid Sazanov|Sazanov LA]] | title = Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I | journal = Journal of Structural Biology | volume = 159 | issue = 2 | pages = 238–42 | date = August 2007 | pmid = 17360196 | doi = 10.1016/j.jsb.2007.01.009 }}</ref> Alternative theories suggest a "two stroke mechanism" where each reduction step ([[semiquinone]] and [[ubiquinol]]) results in a stroke of two protons entering the intermembrane space.<ref>{{cite journal | vauthors = Brandt U | title = A two-state stabilization-change mechanism for proton-pumping complex I | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1807 | issue = 10 | pages = 1364–9 | date = October 2011 | pmid = 21565159 | doi = 10.1016/j.bbabio.2011.04.006 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Zickermann V, Wirth C, Nasiri H, Siegmund K, Schwalbe H, Hunte C, Brandt U | title = Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I | journal = Science | volume = 347 | issue = 6217 | pages = 44–9 | date = January 2015 | pmid = 25554780 | doi = 10.1126/science.1259859 | s2cid = 23582849 | url = http://publikationen.ub.uni-frankfurt.de/files/44770/Zickermann_et_al_Zweitveroeffentlichung.pdf }}</ref>

The resulting [[ubiquinol]] localized to the membrane domain interacts with negatively charged residues in the membrane arm, stabilizing conformational changes.<ref name=":0" /> An [[antiporter]] mechanism (Na<sup>+</sup>/H<sup>+</sup> swap) has been proposed using evidence of conserved Asp residues in the membrane arm.<ref>{{cite journal | vauthors = Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, Michel H | title = Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH | journal = Nature | volume = 435 | issue = 7046 | pages = 1197–202 | date = June 2005 | pmid = 15988517 | doi = 10.1038/nature03692 | bibcode = 2005Natur.435.1197H | s2cid = 4372674 }}</ref> The presence of Lys, Glu, and His residues enable for proton gating (a protonation followed by deprotonation event across the membrane) driven by the pK<sub>a</sub> of the residues.<ref name=":0" />