Quantum transport in mitochondrial complex I is governed by a conserved structural bottleneck

Electron transport in mitochondrial complex I is mediated by a chain of redox centers, yet how electrons traverse this network beyond the canonical pathway remains unclear. While prior models treat transport as a sequential process, they do not resolve whether alternative pathways contribute to functional electron flow. Here, we formulate electron transport as a continuous-time quantum walk on a structure-derived redox network and systematically map pathway-level electron flux inferred from quantum-walk dynamics across species. We identify a conserved structural bottleneck at the N5 N6a interface that suppresses direct electron transfer. Strikingly, quantum-walk flux analysis indicates that this bottleneck does not simply limit transport, but can redistribute electron flux into residue-mediated alternative pathways. Across species, these alternative routes support substantial flux and, in several cases, are comparable to or can exceed the canonical direct pathway, indicating a conserved mechanism of pathway-level flux redistribution. This behavior arises from geometric constraints encoded in protein structure and persists under environmental decoherence, demonstrating that architecture governs not only transport efficiency but also the organization of electron flow within the network. Together, our findings suggest a network-level organization of electron transport in complex I, in which a structurally encoded bottleneck reshapes flux through alternative pathways, consistent with a structurally encoded link between protein geometry and quantum transport behavior. We note that the bottleneck-dominated and flux-redistribution observations are not in tension: suppression of the direct N5 N6a step is precisely what redirects amplitude into the parallel residue-mediated routes.