Novel size-independent modeling of the dilute solution conformation of theimmunoglobulin IgG Fab ' domain using SOLPRO and ELLIPS

Citation
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
Citations number
52
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
BIOPHYSICAL JOURNAL
ISSN journal
0006-3495 → ACNP
Volume
77
Issue
6
Year of publication
1999
Pages
2902 - 2910
Database
ISI
SICI code
0006-3495(199912)77:6<2902:NSMOTD>2.0.ZU;2-3
Abstract
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.