B. Carrasco et al., Novel size-independent modeling of the dilute solution conformation of theimmunoglobulin IgG Fab ' domain using SOLPRO and ELLIPS, BIOPHYS J, 77(6), 1999, pp. 2902-2910
The proliferation of hydrodynamic modeling strategies to represent the shap
e of quasirigid macromolecules in solution has been hampered by ambiguities
caused by size. Universal shape parameters, independent of size, developed
originally for ellipsoid modeling, are now available for modeling using th
e bead-shell approximation via the algorithm SOLPRO. This paper validates s
uch a "size-independent" bead-shell approach by comparison with the exact h
ydrodynamics of 1) an ellipsoid of revolution and 2) a general triaxial ell
ipsoid (semiaxial ratios a/b, b/c) based on a fit using the routine ELLIPSE
(Taylor et al., 1983. J. Mo Graph. 1:30-38) to the chimeric (human/mouse)
IgG Fab' B72.3; a similar fit is obtained for other Fabs. Size-independent
application of the bead-shell approximation yields errors of only similar t
o 1% in frictional ratio based shape functions and similar to 3% in the rad
ius of gyration. With the viscosity increment, errors have been reduced to
similar to 3%, representing a significant improvement on earlier procedures
. Combination of the Perrin frictional ratio function with the experimental
ly measured sedimentation coefficient: for the same Fab' from B72.3 yields
an estimate for the molecular hydration of the Fab' fragment of similar to(
0.43 +/- 0.07) g/g. This value is compared to values obtained in a similar
way for deoxyhemoglobin (0.44) and ribonuclease (0.27). The application of
SOLPRO to the shape analysis of more complex macromolecules is indicated, a
nd we encourage such sire-independent strategies. The utility of modern sed
imentation data,, analysis software such as SVEDBERG, DCDT, LAMM, and MSTAR
is also clearly demonstrated.