to the membrane arm to drive proton pumping.
It postulates that complex I switches between
the E state, in which ubiquinone can be reduced
by cluster N2, and the P state, in which it is moved
away from its electron donor. This description is
reminiscent of the A and D state conformations
discussed above. A displacement of the acidic
loop TMH5–6ND1 at the start of the chain of
titratable residues reaching through the membrane arm seems ideally suited to transmit an
“electrostatic pulse” ( 37). We therefore hypothesize that an orchestrated movement of the three
loops associated with the A/D transition could
also reflect the critical energy-converting steps
during catalytic turnover (Fig. 6). Such a mechanism would imply that the E state corresponds
essentially to the A form, whereas the P state
would resemble the D form, with the notable
exception that the D form cannot revert rapidly
and spontaneously to the E/A state, because this
is prevented by a yet unidentified structural
feature not present in the bacterial enzyme.
Because the A/D transition is observed only with
eukaryotic enzymes, it is tempting to speculate
that stabilization of the D state may involve
nearby accessory subunits such as NUEM, which
has been shown to take part in the associated
conformational changes ( 38).
Notably, this series of events could be triggered not only by stabilization of ubisemiquinone,
but also of the ubiquinol anion resulting from
the second reduction step ( 36). Although so far
experimental evidence for such a second pump
stroke is missing, partitioning of the free energy
change by making use of both electron transfer
steps to ubiquinone seems to make thermodynamic and mechanistic sense, given that complex I
can operate in reverse as a proton gradient–driven
The described mechanistic principle—
charge-induced conformational changes that result
in secondary electrostatic polarization of charged
residues—may also be important to drive the individual proton-pumping sites of complex I. Defined localized conformational changes should
ensure controlled vectorial charge translocation,
whereas energy transfer between the sites could
occur by electrostatic coupling. Indeed, recent
large-scale molecular dynamics simulations suggested that long-range energy transmission in
complex I is executed through charge-induced
protonation changes of key residues ( 39).
REFERENCES AND NOTES
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3. W. J. Koopman, P. H. Willems, J. A. Smeitink, N. Engl.
J. Med. 366, 1132–1141 (2012).
4. M. E. Breuer et al., Neurobiol. Dis. 51, 27–34 (2013).
5. S. Dröse, U. Brandt, Adv. Exp. Med. Biol. 748, 145–169
6. R. Betarbet et al., Nat. Neurosci. 3, 1301–1306
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48 2 JANUARY 2015 • VOL 347 ISSUE 6217 sciencemag.org SCIENCE
Fig. 6. Hypothetical two-state stabilization change mechanism. Electrons are transferred (red arrow)
via a chain of iron-sulfur clusters from NADH to ubiquinone (Q). Within three antiporter-like subunits
(violet frame) and the other ND subunits, a pattern of titratable residues defines a central axis in the
membrane connected to the IMS and matrix side by putative proton translocation pathways (dark
blue). Loop TMH5–6ND1 (red), loop b1-b249-kDa (green), and the tip of loop TMH1–2ND3 (yellow) line the
ubiquinone exchange cavity. During turnover, these loops perform a coordinated rearrangement
resulting in a shift of the ubiquinone binding site and movement of the cluster of negative charges in
loop TMH5–6ND1, which may trigger an electrostatic pulse toward the membrane arm. Stabilization of
the anionic species in the site leads to transition from E state (left) to P state (right), driving a stroke of
proton pumping. The idling enzyme can convert reversibly from the active A form into the deactive D
form with a structure similar to the P state.
Fig. 5. Binding site of the ubiquinone analogous inhibitor DQA. (A) Constitutions of DQA and
bromo-substituted derivatives QA-1 and QA-2. (B) Stereo view of inhibitor binding pocket (colors as
in Fig. 1). Single peaks in the bromine anomalous Fourier electron density maps are shown (purple,
QA-1, 3.8s; red, QA-2, 4s; superimposition of electron density maps from two separate experiments
on structure). Orange, quinazoline ring modeled into the site.