Previously, we utilized N-15 transverse relaxation rates to demonstrate significant mobility in the linker region and conformational exchange in the regulatory domain of Ca2+-saturated cardiac troponin C bound to the isolated N-domain of cardiac troponin I (Gaponenko, V,, Abusamhadneh, E., Abbott, M. B., Finley, N., Gasmi-Seabrook, G., Solaro, R.J., Rance, RI., and Rosevear, P.R. (1999) J. Biol. Chem. 274, 16681-16684). Here we show a large decrease in cardiac troponin C linker flexbility, corresponding to residues 85-93, when bound to intact cardiac troponin I. The addition of 2 M urea to the intact cardiac troponin I-troponin C complex significantly increased linker flexibility, Conformational changes in the regulatory domain of cardiac troponin C were monitored in complexes with troponin I-(1-211), troponin I-(33-211), troponin I-(1-80) and bisphosphorylated troponin I-(1-80), The cardiac specific N terminus, residues 1-32, and the C-domain, residues 81-211, of troponin I are both capable of inducing conformational changes in the troponin C regulatory domain. Phosphorylation of the cardiac specific N terminus reversed its effects on the regulatory domain. These studies provide the first evidence that the cardiac specific N terminus can modulate the function of troponin C by altering the conformational equilibrium of the regulatory domain.