Ageing alters cysteine oxidation-regulated redox signalling in skeletal muscle: Integrative omics and AI-based structural predictions.

Abstract

Ageing is associated with loss of skeletal muscle mass and strength (sarcopenia) and disrupted redox homeostasis. Redox signalling is essential for muscle adaptation, yet the mechanisms by which ageing disrupts cysteine-based regulation are poorly defined. The drivers of site-specific reactivity and signalling specificity in aged muscle remain unknown. Here, we interrogated the OxiMouse dataset to map age-related cysteine oxidation in skeletal muscle and, using AI, simulate oxidative modifications at key cysteine residues to predict structural and functional consequences for specific proteins. Ageing was found to remodel the redox landscape through selective oxidation of discrete cysteine residues, in a site-specific manner, even within the same protein. These findings support that ageing drives pathway-targeted modulation of protein function rather than a uniform, global oxidative shift. Moreover, age-related cysteine oxidation is not randomly distributed but appears to target interconnected protein networks involved in mitochondrial metabolic pathways, muscle function and proteostasis, indicating a coordinated remodelling in redox signalling as a hallmark of skeletal muscle ageing. To connect proteomic signatures to mechanisms, AlphaFold3 was used to simulate progressive cysteine oxidation and predict structural outcomes. Protein docking simulations were then performed using HADDOCK. This approach was applied to prioritise functionally important cysteines identified in the dataset. These results suggest that skeletal muscle ageing drives selective rewiring of physiologically relevant cysteine-based redox signalling networks. By integrating redox proteomics with AI-based structural simulation, this study provides a framework to prioritise key oxidation-sensitive cysteines, including within the 26S proteasome, as potential mechanistic nodes and intervention targets for sarcopenia.