Estimating affinities of calcium ions to proteins

Figures & data

Figure 1 Correlation of Fold-X predictions and experiment. The straight line is a least-square fit between experimentally determined Ca²⁺-protein affinities (ΔG_exp) and affinities predicted with Fold-X (ΔG_pred). Pearson correlation coefficient is r = 0.67. Data.⁸

Figure 2 Correlation of AutoDock vina predictions and experiment. The dashed straight line is the least-square fit between experimentally determined Ca²⁺-protein affinities (ΔG_exp) and affinities predicted with AutoDock vina (ΔG_pred). Pearson correlation coefficient is r = 0.71. If the outlier in the lower-left is dropped, r decreases to 0.63 (solid line). Experimental affinities.⁸

Table 1 Spearman rank correlation ρ of four models with experimental affinities ΔG_exp and residuals e

Modela	ρ(ΔGexp, Model)b	ρ(eΔGexp, SAS1.4, Model)c	ρ(eΔGexp, SAS0.5, Model)d
SAS1.4	−0.52 (2 · 10^−4)
SAS0.5	−0.52 (2 · 10^−4)
ΔGFoldX	0.66 (2 · 10^−6)	0.52 (4 · 10^−4)	0.39 (0.01)
ΔGvina	0.64 (3 · 10^−6)	0.50 (4 · 10^−4)	0.34 (0.02)

a Notes: four linear least squares fit models with input variables SAS with probe radius 1.4 Å, SAS with probe radius of 0.5 Å (see Eq. (1)$\mathrm{\Delta }{G}_{exp}\approx -0.63·SA{S}_{0.5}+11.95$(1) ), affinities computed with Fold-X, affinities computed with AutoDock vina;

b Spearman rank correlation ρ of experimental affinities ΔG_exp with predictions of fitted models;

c ρ of residuals of model based on fit with SAS^1.4 with Fold-X and AutoDock vina, respectively;

d ρ of residuals of model based on fit with SAS^0.5 with Fold-X and AutoDock vina. Numbers in parentheses are p-values for the null-hypothesis that ρ = 0.

Figure 3 Correlation of SAS (probe radius 0.5 Å) and experiment. The straight line is the least-squares fit between experimentally determined Ca²⁺-protein affinities (ΔG_exp) and the solvent accessible surfaces (SAS) of the Ca²⁺-ions. Spearman rank correlation coefficient ρ is −0.53 (P = 2 · 10⁻⁴ for null-hypothesis ρ = 0). Experimental affinities.⁸

BogutaGStepkowskiDBierzyńskiATheoretical estimation of the calcium-binding constants for proteins from the troponin c superfamily based on a secondary structure prediction method. ii. applicationsJ Theor Biol198813563733256717

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