Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes

The biological significance of protein supercomplexes have remained contentious, particularly how they tune the shuttling of charge-carrier redox proteins across cell membranes during biological energy conversion. We employ multiscale modeling and single particle cryo-electron microscopy (cryo-EM) to determine the mechanisms of diffusive electron transfer in mitochondrial supercomplexes, composed of respiratory complexes III and IV (CIII and CIV). Using a combination of bioinformatic and entropy maximization tools, we model an ensemble of structures representing the conformational space of CIII’s disordered QCR6 ‘hinge’ within the yeast CIII ₂ CIV ₂ supercomplex. Molecular and Brownian Dynamics simulations of the entire supercomplex reveal a mechanism for electrostatic coupling between these negatively charged hinge conformations, and binding and directional diffusion of the redox proteins on the mitochondrial membrane, which is simulated over the millisecond timescale. Anionic lipids reinforce this conformationally-coupled recognition of the supercomplex by retaining a pool of the redox proteins in the vicinity of the membrane when the hinges are of a critical length. Cryo-EM models reveal a large-scale rearrangement of the ΔQCR6 supercomplex, which retains a surprisingly robust electrostatic environment for recognition of the redox protein, despite compromise in the supercomplex’s negative charge, still enabling a surface-mediated electron transfer in this CIII ₂ CIV ₂ variant. Altogether, the evolutionary need of confining electron carriers on the surface of bioenergetic membranes is found to give rise to a refolding-guided diffusion model of the redox proteins, which improves the energy conversion efficiency within the supercomplex by nearly 30%.