Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force

Abstract

Adenosine triphosphate (ATP) synthases populate the inner membranes of mitochondria, where they produce the majority of the ATP required by the cell. From yeast to vertebrates, cryoelectron tomograms of these membranes have consistently revealed a very precise organization of these enzymes. Rather than being scattered throughout the membrane, the ATP synthases form dimers, and these dimers are organized into rows that extend for hundreds of nanometers. The rows are only observed in the membrane invaginations known as cristae, specifically along their sharply curved edges. Although the presence of these macromolecular structures has been irrefutably linked to the proper development of cristae morphology, it has been unclear what drives the formation of the rows and why they are specifically localized in the cristae. In this study, we present a quantitative molecular-simulation analysis that strongly suggests that the dimers of ATP synthases organize into rows spontaneously, driven by a long-range attractive force that arises from the relief of the overall elastic strain of the membrane. The strain is caused by the V-like shape of the dimers, unique among membrane protein complexes, which induces a strong deformation in the surrounding membrane. The process of row formation is therefore not a result of direct protein-protein interactions or a specific lipid composition of the membrane. We further hypothesize that, once assembled, the ATP synthase dimer rows prime the inner mitochondrial membrane to develop folds and invaginations by causing macroscopic membrane ridges that ultimately become the edges of cristae. In this way, mitochondrial ATP synthases would contribute to the generation of a morphology that maximizes the surface area of the inner membrane, and thus ATP production. Finally, we outline key experiments that would be required to verify or refute this hypothesis.

Figure 1.

Organization of mitochondrial ATP synthase dimers and their membrane-bending properties. (A) Tomographic slice through an intact mitochondrion of Podospora anserina; yellow arrowheads mark the location of the ATP synthase dimers. (B) Three-dimensional reconstruction of the data in A; yellow spheres indicate the catalytic domains in the ATP synthase dimers against the cristae membrane (cyan). (C) Curvature perturbation caused by an isolated ATP synthase dimer along the direction parallel to the dimer long axis, from CG molecular dynamics simulations. (D) Same as C, along the direction perpendicular to the dimer. (E) Same as D, for a row of four ATP synthase dimers, arranged side by side as observed in mitochondrial cristae. Note that the membrane is flat between adjacent dimers along the direction of the row. In the perpendicular direction, the membrane profile is nearly identical to that in C. A and B are adapted from Davies et al. (2011), and C and D are adapted from Davies et al. (2012).

Figure 2.

Molecular-simulation system comprising two ATP synthase dimers in a model lipid bilayer. (A and B) Views of the system along the perpendicular to the membrane and along the membrane plane, respectively. The calculation is based on a CG representation of all molecular components (Materials and methods). The ATP synthase dimers are shown in yellow in a surface representation. Lipid molecules are represented with spheres, with the head groups (choline and phosphate) in purple and the acyl chains in gray. The solvent is omitted for clarity. The number of particles in the system is ∼6 million. (C) Magnified view of an ATP synthase dimer seen along the membrane plane. The structure is based on earlier cryo-EM studies. In the dimer, the monomers are approximately at a right angle.

Figure 3.

Energetics of association of two ATP synthase dimers driven by the membrane. (A) Deformation of the membrane induced by two ATP synthase dimers for different values of the dimer-to-dimer distance. The deformation is quantified by the position-dependent curvature of the membrane (Materials and methods) along the two directions defining the membrane plane. (B) Potential of mean force as a function of the distance between the two dimers, calculated using umbrella-sampling molecular dynamics simulations, totaling 15 μs (Materials and methods). The sampling error is indicated with a gray band along the free-energy profile. (C) Distribution of dimer-to-dimer distances deduced from analysis of published cryo-EM tomograms of fragmented mitochondrial cristae. Inset figure adapted from Davies et al. (2012).

Figure 4.

Bending modulus of the model phospholipid membrane used in the simulations. The plot shows the relationship between the wavelength of the each of the undulatory modes of the membrane, 1/q, and the amplitude of these undulations, u. The slope of the linear fit (red line) is s = 1.8 × 10⁻⁷ Å⁻². The corresponding value of k_c is k_B T (s A)⁻¹ = 1.2 × 10⁻¹⁹ J, where A is the area of the membrane (Materials and methods). This value is in good agreement with that determined experimentally, namely, ∼10⁻¹⁹ J (Marsh, 2006).

Figure 5.

Proposed mechanism of cristae formation induced by the ATP synthase dimers. (A) ATP synthases (yellow) fold and assemble as monomers in the membrane. (B) As the ATP synthase monomers dimerize, they cause a long-range deformation in the membrane that extends up to 40 nm away from the complex. (C) As the dimers encounter each other, the energy gained from reduced membrane curvature drives the dimers to self-assemble into rows. (D) The dimer rows form a macroscopic membrane ridge that primes the inner membrane to fold and as its surface area increases during mitochondrial development; the membrane invaginates exactly at the location of the dimer rows, and cristae are generated. Inner membrane, light blue; outer membrane, gray.