Biological complexity: Driving the production of ATP energy (Introduction)

by David Turell , Thursday, October 29, 2020, 20:52 (1264 days ago) @ David Turell

Mammalian respiratory complex I is a huge enzyme whose structure in now more understood:

https://science.sciencemag.org/content/370/6516/eabc4209?utm_campaign=toc_sci-mag_2020-...

"Secrets of a proton pumping machine:
Mitochondrial complex I serves as a primary entry point for electrons from the tricarboxylic acid cycle into the mitochondrial electron transport chain. This massive, membrane-embedded protein complex must couple quinone reduction to conformational changes across more than 150 angstroms within four separate proton pumps. Kampjut et al. determined five structures of complex I in states along the catalytic cycle, a deactive conformation, and one with the inhibitor rotenone bound. The resolution of some structures was sufficient to see water molecules and to trace putative paths for proton transfer within the proton-pumping membrane domain. The structures add valuable details that provide a basis for generating mechanistic hypotheses for this crucial complex.

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"We showed that opening and closing movements of the peripheral and membrane arms of complex I are critical for catalysis. Opening and closing is accompanied by coordinated conformational changes at the junction between the two arms, around the quinone binding cavity. These changes involve five conserved protein loops and are initiated by the reduction of quinone, the resulting negative charge in its cavity, and decylubiquinone (DQ) movement between the deep and the shallow binding sites. The bulky inhibitor rotenone also binds at these two sites and, unexpectedly, also within ND4—one of the three antiporter-like subunits. The deactive state is defined by a notable relocation of the entire ND6 transmembrane (TM) helix 4, arresting the enzyme in the open conformation.

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"A key role in this process is played by electrostatic interactions between the conserved charged residues, forming the highly hydrated “central axis” of the membrane arm. The distribution of the observed water molecules also suggests that links to the matrix and intermembrane space (IMS) sides in the distal subunit ND5 are much more hydrated than in other antiporters, and we propose the possibility that all four protons per cycle are ejected into the IMS via this subunit, rather than one per each antiporter (dashed arrows in the figure).

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"Abstract
Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo–electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions."

Comment: Read the entire site and the complexity of their findings will make your eyes roll. Mine did. Remember this sx a giant enzyme which could not have developed by chance.