The cardiac-specific N-terminus of cardiac troponin I (cTnI) is known to modulate the activity of troponin upon phosphorylation with protein kinase A (PKA) by decreasing its Ca(2+) affinity and increasing the relaxation rate of the thin filament. The molecular details of this modulation have not been elaborated to date. We have established that the N-terminus and the switch region of cTnI bind to cNTnC [the N-domain of cardiac troponin C (cTnC)] simultaneously and that the PKA signal is transferred via the cTnI N-terminus modulating the cNTnC affinity toward cTnI(147-163) but not toward Ca(2+). The K(d) of cNTnC for cTnI(147-163) was found to be 600 microM in the presence of cTnI(1-29) and 370 microM in the presence of cTn1(1-29)PP, which can explain the difference in muscle relaxation rates upon the phosphorylation with PKA in experiments with cardiac fibers. In the light of newly found mutations in cNTnC that are associated with cardiomyopathies, the important role played by the cTnI N-terminus in the development of heart disorders emerges. The mutants studied, L29Q (the N-domain of cTnC containing mutation L29Q) and E59D/D75Y (the N-domain of cTnC containing mutation E59D/D75Y), demonstrated unchanged Ca(2+) affinity per se and in complex with the cTnI N-terminus (cTnI(1-29) and cTnI(1-29)PP). The affinity of L29Q and E59D/D75Y toward cTnI(147-163) was significantly perturbed, both alone and in complex with cTnI(1-29) and cTnI(1-29)PP, which is likely to be responsible for the development of malfunctions.