Table 4. Comparison of measured FRET distances against model and crystal structure.

cTnI	cTnI	FRET distance [54]		MD model		crystal structure (PDB ID:1J1E)
		Mg (Å)	Ca (Å)	Mg (Å) 9.5 ns	Ca (Å) 11.1 ns	Mg (Å)	Ca (Å)
L129	S151	26.8(5.0)	32.5(4.6)	24.64	30.08	—	38.87

In the table above the distances from our model are compared against previously measured FRET distances [13], [54]. Also the distances in the Ca²⁺-saturated state crystal structure are provided for comparison [10]. The Mg refers to the Ca²⁺-free state and Ca refers to the Ca²⁺-saturated state. The FRET distances in the table were not incorporated in the simulations and hence serve as a check to see if the model generated is valid. In the FRET analysis, due to the ambiguity in the value of the dipole–dipole orientation factor between energy donor molecules and energy acceptor molecules and due to the dimensions of the probes attached by linkers to the side chains of the amino acid residues, the measured distance will have an uncertainty of ±10% [53]. Although the length of probe linkers is ∼10 Å, the linker is not unidirectional but folds randomly (during folding and rotation the probe and can acquire length of ∼7 Å).

Based on these above factors there is good correlation between the measured FRET distances and the model. The value within the bracket pertains to the half-widths.