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bioRxiv · 10.1101/2025.06.23.661104

AlphaFold 3-enabled in silico exploration of PGAM1 interactions in cancer

Clarke, J. J.·Colcombe, J. L.·Rigden, D. J.
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Abstract

Cancer cell metabolism is commonly reprogrammed to favour glycolysis over oxidative phosphorylation, even under aerobic conditions, a phenomenon known as the Warburg effect. A key enzyme implicated in this shift is phosphoglycerate mutase 1 (PGAM1), which catalyses the conversion of 3-phosphoglycerate to 2-phosphoglycerate. The human enzyme is dependent on cofactor 2,3-bisphosphoglycerate which can phosphorylate and thereby activate the enzyme at histidine 11 (H11). A recently characterised moonlighting activity of pyruvate kinase M2 (PKM2), in its monomeric or dimeric forms, leads to phosphoenolpyruvate (PEP)-dependent phosphorylation of PGAM1 at the same position. Crucially, this phosphorylation is dependent on prior tyrosine 119 (Y119) phosphorylation of PGAM1 by Src kinase, itself activated by oncogenic growth factors. Using AlphaFold 3 (AF3), this study models the conformational changes induced by PGAM1 Y119 phosphorylation and investigates the molecular basis for its role in facilitating PEP-dependent phosphorylation at H11. Structural comparisons suggest that Y119 phosphorylation induces rearrangement of the C-terminal tail of PGAM1, opening the catalytic site around H11 to enable binding of phosphoenolpyruvate (PEP). Use of molecular docking (Webina, SwissDock, and DiffDock) found that AF3 generated models of PGAM1 with Y119 phosphorylation showed enhanced binding of PEP in comparison to non-phosphorylated PGAM1. However, extensive protein-protein docking (ClusPro, AF3 multimer generation) failed to identify configurations of PGAM1 and PKM2 where catalytic sites were proximal. Overall, this study supports a model in which phosphorylation of PGAM1 at Y119 enables access to the active site for PEP, thus enhancing its enzymatic activation. These findings underscore the critical role of post-translational modifications in modulating protein function and exemplify the utility of AF3 in predicting PTM-induced structural changes relevant to cancer metabolism.

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Clarke, J. J., Colcombe, J. L., Rigden, D. J.. 2025-06-24. AlphaFold 3-enabled in silico exploration of PGAM1 interactions in cancer. https://doi.org/10.1101/2025.06.23.661104

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