Cardiolipin modulates the activity of membrane-bound respiratory enzymes that catalyze biological energy transduction. The respiratory complex I functions as the primary redox-driven proton pump in ...mitochondrial and bacterial respiratory chains, and its activity is strongly enhanced by cardiolipin. However, despite recent advances in the structural biology of complex I, cardiolipin-specific interaction mechanisms currently remain unknown. On the basis of millisecond molecular simulations, we suggest that cardiolipin binds to proton-pumping subunits of complex I and induces global conformational changes that modulate the accessibility of the quinone substrate to the enzyme. Our findings provide key information on the coupling between complex I dynamics and activity and suggest how biological membranes modulate the structure and activity of proteins.
Abstract Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these ...energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III 2 IV 2 obligate supercomplex from Mycobacterium smegmatis , a close relative of M. tuberculosis , the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
β‐Crustacyanin (β‐CR) is a pigment protein responsible for the blue color of lobsters. We show using correlated ab initio calculations how the protein environment tunes the chromophores of β‐CR ...through electrostatic and steric effects.
True blue: The pigment protein β‐crustacyanin, which is responsible for the blue color of lobsters, tunes the color of its two bound astaxanthin chromophores through electrostatic polarization and steric planarization.
Photosystem II (PSII), the water/plastoquinone photo-oxidoreductase, plays a key energy input role in the biosphere. Q∙−A, the reduced semiquinone form of the nonexchangeable quinone, is often ...considered capable of a side reaction with O2, forming superoxide, but this reaction has not yet been demonstrated experimentally. Here, using chlorophyll fluorescence in plant PSII membranes, we show that O2 does oxidize Q∙−A at physiological O2 concentrations with a t1/2 of 10 s. Superoxide is formed stoichiometrically, and the reaction kinetics are controlled by the accessibility of O2 to a binding site near Q∙−A, with an apparent dissociation constant of 70 ± 20 µM. Unexpectedly, Q∙−A could only reduce O2 when bicarbonate was absent from its binding site on the nonheme iron (Fe2+) and the addition of bicarbonate or formate blocked the O2-dependant decay of Q∙−A. These results, together with molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations, indicate that electron transfer from Q∙−A to O2 occurs when the O2 is bound to the empty bicarbonate site on Fe2+. A protective role for bicarbonate in PSII was recently reported, involving long-lived Q∙−A triggering bicarbonate dissociation from Fe2+ Brinkert et al., Proc. Natl. Acad. Sci. U.S.A. 113, 12144–12149 (2016). The present findings extend this mechanism by showing that bicarbonate release allows O2 to bind to Fe2+ and to oxidize Q∙−A. This could be beneficial by oxidizing Q∙−A and by producing superoxide, a chemical signal for the overreduced state of the electron transfer chain.
Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome
oxidase (C
O) functions as a terminal electron ...acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O
reduction into proton pumping. Here we show that C
O creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme
, leads to dissociation of an arginine (Arg438)-heme
D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V Å
along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.
The recently discovered Fe
/α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans stereoselectively catalyzes a multistep synthesis of quinolone alkaloids, natural products with ...significant biomedical applications. To probe molecular mechanisms of this elusive catalytic process, we combine here multi-scale quantum and classical molecular simulations with X-ray crystallography, and in vitro biochemical activity studies. We discover that methylation of the substrate is essential for the activity of AsqJ, establishing molecular strain that fine-tunes π-stacking interactions within the active site. To rationally engineer AsqJ for modified substrates, we amplify dispersive interactions within the active site. We demonstrate that the engineered enzyme has a drastically enhanced catalytic activity for non-methylated surrogates, confirming our computational data and resolved high-resolution X-ray structures at 1.55 Å resolution. Our combined findings provide crucial mechanistic understanding of the function of AsqJ and showcase how combination of computational and experimental data enables to rationally engineer enzymes.
The light-harvesting chlorophyll (Chl) molecules of photosynthetic systems form the basis for light-driven energy conversion. In biological environments, the Chl chromophores occur in two distinct ...diastereotopic configurations, where the α and β configurations have a magnesium-ligating histidine residue and a 17-propionic acid moiety on the opposite side or on the same side of the Chl ring, respectively. Although β-ligated Chl dimers occupy conserved positions around the reaction center of photosystem I (PSI), the functional relevance of the α/β configuration of the ligation is poorly understood. We employ here correlated ab initio calculations using the algebraic-diagrammatic construction through second order (ADC(2)) and the approximate second-order coupled cluster (CC2) methods in combination with the reduced virtual space (RVS) approach in studies of the intrinsic excited-state properties of α-ligated and β-ligated Chl dimers of PSI. Our ab initio calculations suggest that the absorption of the α-ligated reaction-center Chl dimer of PSI is redshifted by 0.13-0.14 eV in comparison to the β-ligated dimers due to combined excitonic coupling and strain effects. We also show that time-dependent density functional theory (TDDFT) calculations using range-separated density functionals underestimate the absorption shift between the α- and β-ligated dimers. Our findings may provide a molecular starting point for understanding the energy flow in natural photosynthetic systems, as well as a blueprint for developing new molecules that convert sunlight into other forms of energy.
NDH-1 is a gigantic redox-driven proton pump linked with respiration and cyclic electron flow in cyanobacterial cells. Based on experimentally resolved X-ray and cryo-EM structures of the respiratory ...complex I, we derive here molecular models of two isoforms of the cyanobacterial NDH-1 complex involved in redox-driven proton pumping (NDH-1L) and CO2-fixation (NDH-1MS). Our models show distinct structural and dynamic similarities to the core architecture of the bacterial and mammalian respiratory complex I. We identify putative plastoquinone-binding sites that are coupled by an electrostatic wire to the proton pumping elements in the membrane domain of the enzyme. Molecular simulations suggest that the NDH-1L isoform undergoes large-scale hydration changes that support proton-pumping within antiporter-like subunits, whereas the terminal subunit of the NDH-1MS isoform lacks such structural motifs. Our work provides a putative molecular blueprint for the complex I-analogue in the photosynthetic energy transduction machinery and demonstrates that general mechanistic features of the long-range proton-pumping machinery are evolutionary conserved in the complex I-superfamily.
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•Molecular models of the cyanobacterial NDH-1 complex were computationally derived•NDH-1 shows distinct structural and dynamical similarities to respiratory complex I•Plastoquinone binding sites electrostatically interact with proton pumping elements•Plastoquinol dynamics couple with conformational changes in the membrane domain•Four proton channels were identified in the antiporter-like subunits in NDH-1L
Heat shock protein 90 (Hsp90) is a dimeric molecular chaperone that undergoes large conformational changes during its functional cycle. It has been established that conformational switch points exist ...in the N-terminal (Hsp90-N) and C-terminal (Hsp90-C) domains of Hsp90, however information for switch points in the large middle-domain (Hsp90-M) is scarce. Here we report on a tryptophan residue in Hsp90-M as a new type of switch point. Our study shows that this conserved tryptophan senses the interaction of Hsp90 with a stringent client protein and transfers this information via a cation-π interaction with a neighboring lysine. Mutations at this position hamper the communication between domains and the ability of a client protein to affect the Hsp90 cycle. The residue thus allows Hsp90 to transmit information on the binding of a client from Hsp90-M to Hsp90-N which is important for progression of the conformational cycle and the efficient processing of client proteins.
Synthetic lipid membranes have served as important models for cellular membranes. However, these static membranes do not recapitulate the dynamic nature of the biological membranes which are ...frequently remodeled to support cellular function. An ideal membrane model would thus also display dynamic exchange of lipids. In this work, we achieve such a system by coupling the self‐assembly of peptides into membranes with a chemical reaction cycle. The reaction cycle activates and deactivates the peptides for self‐assembly at the expense of a chemical fuel. The resulting membranes are dynamically remodeled, and, over their 40 min lifetime, they emerge, grow, and are torn apart before they eventually decay.
Keep it moving: The self‐assembly of peptides into vesicles is coupled to a dynamic chemical reaction cycle. These vesicles emerge in response to fuel, and continuously remodel and decay when all fuel is depleted.
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