A nested shell structure coordinates enzyme communication in pyruvate oxidation

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Abstract The pyruvate dehydrogenase complex (PDHc) 1 links glycolysis to the Krebs cycle by catalyzing the oxidative decarboxylation of pyruvate to acetyl-CoA and CO₂, a process essential for life 2,3 . PDHc is formed by structural proteins (E3-binding protein, E3BP) 4–7 , enzymatic subunits (E1, E2, E3) 4,6 , and mobile lipoyl domains (LDs), the latter shuttling intermediates across active sites 6,8 . Although numerous details regarding pyruvate oxidation steps have been elucidated 9 , the precise organization of the entire PDHc remains unknown due to its large size and dynamic heterogeneity. Here, we employ in silico , in vitro , and in situ methods to propose a multi-scale model of PDHc that includes approximately one million atoms and to visualize multiple conformational states. This model reveals a ∼40-50 nm nested shell structure, formed by flexible linkers that spatially coordinate the E1 and E3 enzyme complexes around the E2-E3BP core scaffold. This structure acts as a molecular sieve, selectively guiding lipoyl arms while maintaining enzyme positioning with sub-nm precision. During catalysis, the nested shell structure expands and adopts a mechanically reinforced state comparable in magnitude to viral assemblies 10 . Our findings provide structural context for the textbook “link reaction” 11 , building on decades of biochemical knowledge, are transferable to functional aspects of other α-ketoacid dehydrogenase complexes, and, ultimately, expand our understanding of primary metabolism as a whole. Abstract Figure

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