Biology subjects

Endres, E.

Publications and source records attributed to Endres, E..

2 recordsLinked to original sources

bioRxiv2026

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.

biophysics↗

bioRxiv2026

Molecular and Energetic Basis of Histidine Switch Dynamics in Respiratory Complex I

The respiratory complex I in mitochondria and bacteria drives the two-electron reduction of quinone to pump protons across the membrane. The molecular basis of this catalytic reaction remains enigmatic despite significant progress in structural characterization of the complex. A highly conserved histidine residue in the distal antiporter-like subunit of its membrane domain has been shown to undergo conformational changes in molecular simulations and cryo-EM structures. However, the function of histidine switch dynamics, and energetics of its conformational transitions remain unclear. Here, by applying enhanced sampling simulations, we evaluate the energetics of the histidine switch dynamics and demonstrate that it is coupled to the charge state of lysine residues ca. 10 [A] apart, which cause hydrogen bond restructuring and stabilize histidine in specific conformations. Hybrid QM/MM metadynamics simulations show that the histidine participates in gated proton transfer and may function as a proton confurcation device in complex I and related proteins. Importance of workProton pumping by the mitochondrial respiratory chain enzymes needs to be highly directional so that the ATP production occurs as efficiently as possible during high energy demands. With the protons being hard to detect by most methods of structural biology, computer simulation approaches as applied in this work offer critical information on how molecular gates within respiratory complexes can function and help elucidate the challenging questions in the field of mitochondrial bioenergetics.

biophysics↗