The classification of mutants based on secondary structure (helix, strand, turn and coil) and solvent accessibility (buried, partially buried, partially exposed and exposed) distinguished the stabilizing/destabilizing mutants at an average accuracy of 81% and 80%, respectively for ΔΔG and ΔΔGH2O.
For solvent accessibility: buried or exposed to solvent, as predicted by ACCpro [36].
It can be clearly seen from Figure 5(a) that the number of two types of solvent accessibility (buried and exposed) was equal.
We considered residues with less than 25% relative solvent accessibility as buried.
Stabilization of the ARD fold by nucleotides may also affect the accessibility of buried cysteine residues.
Three-state predictions (secondary structure elements helix, strand, other and solvent accessibility states buried, intermediate, exposed) were handled similarly.
Collapse of some structural constraints is also supported by the accessibility of buried Cys residues in helix I, s5A, and helix F regions to PEGylation even at low GdmCl concentrations.
However, those models used a 2- or 3-state definition of solvent accessibility (e.g., buried, half-buried, and exposed), which limits its applicability.
Table 1 gives detailed results for each label of solvent accessibility prediction, say buried, intermediate, and exposed.
To gain further insights into the effect of ATP binding on ARD stability, we used single-cysteine mutants, allowing us to specifically address the accessibility of a buried cysteine.
Secondary structural properties, that is, "helix," "strand," and "others," and the solvent accessibility, that is, "buried" and "exposed," of an amino acid were calculated by the predicting software of protein structure and structural feature [ 29], resulting in a 5-dimensional encoding vector consisting of 0 or 1.
