Figure 4.

(a) Correlation between experimental ln(kcat /Km) for superoxide and electrostatic potential differences for SOD from different organisms or under different conditions, and (b) experimental and calculated pH dependence of the rate constant for association of superoxide with bovine SOD. (a) The reference point (0,0) marked by a cross is for bovine SOD at pH 7.7 and 20 mM ionic strength with corresponding experimental rate constant of 3.8 109M-1s-1 [26]. The other 2 crosses are for human and Photobacterium leiognathi SODs with experimental rate constants of 2.5 and 8.5 109M-1s-1, respectively, at pH7 and 20 mM ionic strength [55]. Open circles : bovine SOD at pH 7.7 under ionic strength values of 20, 40, 90, 160 and 250 mM [26]. Connected filled circles: bovine SOD at 20 mM ionic strength and pH values ranging from 7.7 to 12.3 [26]. All points can be approximated by a linear relation y = 0.45*x (R-coefficient 0.97). The ionic strength dependence alone can be fit with y = 0.3*x (R-coefficient 0.99). On panel (b), experimental rates [26] are shown as filled circles. The pH dependence of the rates is calculated by assigning 2 different values of the dielectric constant of the protein interior (ε), 4 and 78, when computing residue pKa values (see Methods section). The value of 78 was used for pKa calculations for all titratable residues and was expected to give better agreement with experiment [28].

Gabdoulline et al. BMC Bioinformatics 2007 8:373   doi:10.1186/1471-2105-8-373
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