Novel Size-Independent Modeling of the Dilute Solution Conformation of the Immunoglobulin IgG Fab′ Domain Using SOLPRO and ELLIPS

• Published in: Biophysical journal Vol. 77; no. 6; pp. 2902 - 2910
• Main Authors: Carrasco, Beatriz, de la Torre, Jose Garcia, Byron, Olwyn, King, David, Walters, Chris, Jones, Susan, Harding, Stephen E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-12-1999
• Subjects: Algorithms; Animals; Biophysical Phenomena; Biophysics; Hemoglobins - chemistry; Humans; Immunoglobulin Fab Fragments - chemistry; Macromolecular Substances; Mice; Models, Molecular; Molecular Weight; Particle Size; Protein Conformation; Ribonucleases - chemistry
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/S0006-3495(99)77123-7

The proliferation of hydrodynamic modeling strategies to represent the shape 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 the bead-shell approximation via the algorithm SOLPRO. This paper validates such a “size-independent” bead-shell approach by comparison with the exact hydrodynamics of 1) an ellipsoid of revolution and 2) a general triaxial ellipsoid (semiaxial ratios a/b, b/c) based on a fit using the routine ELLIPSE (Taylor et al., 1983.
J. Mol. 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 ∼1% in frictional ratio based shape functions and ∼3% in the radius of gyration. With the viscosity increment, errors have been reduced to ∼3%, representing a significant improvement on earlier procedures. Combination of the Perrin frictional ratio function with the experimentally measured sedimentation coefficient for the same Fab′ from B72.3 yields an estimate for the molecular hydration of the Fab′ fragment of ∼(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, and we encourage such size-independent strategies. The utility of modern sedimentation data analysis software such as SVEDBERG, DCDT, LAMM, and MSTAR is also clearly demonstrated.