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The self-perpetuation of atrial fibrillation (AF) is associated with atrial remodeling, including the degradation of the myofibril structure (myolysis). Myolysis is related to AF-induced activation of cysteine proteases and underlies loss of contractile function. In this study, we investigated which proteases are involved in the degradation of myofibrillar proteins during AF and whether their inhibition leads to preservation of contractile function after AF. In tachypaced HL-1 cardiomyocytes and atrial tissue from AF and control patients, degradation of myofibrillar proteins troponin (cTn) T, I, C, human cTnT and actin was investigated by Western blotting, and contractile function was analyzed by cell-shortening measurements. The role of major proteases was determined by applying specific inhibitors. Tachypacing of HL-1 cardiomyocytes induced a gradual and significant degradation of cTns but not actin, and caused contractile dysfunction. Both were prevented by inhibition of calpain but not by inhibition of caspases or the proteasome. In patients with persistent AF, a significant degradation of cTnT, cTnI and cTnC was found compared to sinus rhythm or paroxysmal AF, which correlated significantly with both calpain activity and the amount of myolysis. Additionally, by utilizing tachypaced human cTnT-transfected HL-1 cardiomyocytes, we directly showed that the degradation of human cTnT was mediated by calpain and not by caspases or proteasome. Our results suggest that calpain inhibition may therefore represent a key target in combating AF-related structural and functional remodeling.