(a and b) Correlation between experimental ln(kcat/Km) and electrostatic potential differences for TPI and (c and d) prediction of kcat/Km for TPI for the substrate glyceraldehyde-3-phosphate. Correlations (a and b) are for differences in ln(kcat/Km) and electrostatic potential differences of each TPI protein pair, after excluding TPI1_GIALA and TPIS_RABIT. The straight lines correspond to the best linear fit and are given by y = 1.59*x (a) and y = 0.95*x (b). Predictions (c and d) were made for 10 TPIs based on experimental measurements for the two TPIs (from V. marinus (TPIS_VIBMA) and P. falciparum (TPIS_PLAFA), see Table 2) at the minimum and maximum points on the y = x line, respectively. These 2 cases were selected to derive the correlation factor α in equation (1). Then this factor was used to compute the kinetic parameter in the other cases – there are 2 predictions for each case and their deviation defines the error bars. Two outliers (with errors greater than 1.5 RMS deviation from y = x) are labeled, see text. Correlations and predictions for (a) and (c) were done using Modeller protein structural models, whereas SwissModel models were used for the correlations and predictions presented in (b) and (d).
Gabdoulline et al. BMC Bioinformatics 2007 8:373 doi:10.1186/1471-2105-8-373