Conformational dynamics of ND2 antiporter-like subunit in intact and truncated complex I

Respiratory complex I is a large redox-driven proton pump and contributes to the proton motive force required for ATP generation in mitochondria and bacteria. It has been extensively studied with structural and biochemical approaches leading to enhanced understanding of its three- dimensional architecture. Despite significant progress in deciphering its catalytic function, the redox-coupled proton pumping mechanism remains unclear and extensively debated. The three membrane-bound antiporter-like subunits ND2, ND4 and ND5 are responsible for pumping protons from the negatively charged side (N-side) of the membrane to the positively charged side (P-side). Emerging evidence supports the role of ND5 subunit in releasing pumped protons to the P-side of the membrane, but the question whether ND2 and ND4 also contribute to proton release remains unanswered. Here, we performed atomistic molecular dynamics (MD) simulations of an intact and a truncated model of complex I in which ND5 and ND4 subunits are removed in-silico. The simulation data reveals a previously unobserved conformational change in the P-side region of ND2 subunit that occurs much more easily in a truncated model of complex I, as also estimated based on free energy calculations. The conformational change, in part triggered by the artificial exposure of ND2 subunit to lipid bilayer, results in a local hydration of the region, similar to what has been observed in recent cryo-EM structure of plant CI:CIII2 supercomplex. We discuss the functional relevance of observed conformational transitions and identify residues that can be manipulated with biochemical approaches to shed light on proton pumping by complex I.