Figure 4. Ca²⁺-free state structure of the cardiac troponin complex.

The cTn structure after 9.5²⁺-free state is depicted using CCP4MG version 2.7.3. (a) The cTn complex is positioned such as to see the dynamics of the cTnI-Md. The cTnI-Md is seen to have positioned itself close to the cTnC helix A. The cTnI-Rr held within the cTnC N-domain hydrophobic pocket has its secondary structure perturbed due to the closing of the hydrophobic pocket. (b) Depicts the cTnC N-domain wherein the loss of regulatory Ca²⁺ led to structural rearrangement of the helices B, C and D. The helices B and C are almost parallel to each other. (c) View of the N-terminal extension of cTnI above the cTn core domain complex. In this view the collapsed conformation of the cTnC N-domain hydrophobic pocket is well seen. It may be compared against the conformation of the open cTnC N-domain hydrophobic pocket in Fig. 5c. (d) The averaged structure of the cardiac troponin complex in the Ca²⁺ free state from 2 ns to 9.5 ns. The first two nanoseconds were given for the system to equilibrate. (e) The secondary structure of the troponin C in the presence of FRET distance restraints are calculated from 2 ns till 11.1 ns. The cTnC N-domain helices N (residues 4–11), A (residues 14–28), B (residues 38–47), C (residues 54–61) and D (residues 74–85) experienced considerable secondary structure evolution, but in contrast, the cTnC C-domain helices E (residues 94–104), F (residues 117–123), G (residues 130–140), and H (residues 150–157) are comparatively stable. Perturbation in the structure of helix D pulls and releases the D/E linker which in turn unfolds and refolds helix E. This fluctuations cause the D/E linker to alternate between flexible and rigid conformations that effectively helps release and retract the cTnI-Ir towards and away from actin in the absence and presence of Ca²⁺. The residue numbers associated with the helices of cTnC which are given within brackets were derived from the crystal structure 1J1E.pdb.