title: Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS.
abstract: 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 (. 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 approximately 1% in frictional ratio based shape functions and approximately 3% in the radius of gyration. With the viscosity increment, errors have been reduced to approximately 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 approximately (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.
authors.affiliation: Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.
authors.forename: B
authors.initials: B
authors.lastname: Carrasco
authors.forename: J G
authors.initials: JG
authors.lastname: de la Torre
authors.forename: O
authors.initials: O
authors.lastname: Byron
authors.forename: D
authors.initials: D
authors.lastname: King
authors.forename: C
authors.initials: C
authors.lastname: Walters
authors.forename: S
authors.initials: S
authors.lastname: Jones
authors.forename: S E
authors.initials: SE
authors.lastname: Harding
mesh_terms: D000465:Algorithms; D000818:Animals; D055592:Biophysical Phenomena; D001703:Biophysics; D006454:Hemoglobins / Q000737:chemistry; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry*; D046911:Macromolecular Substances; D051379:Mice; D008958:Models, Molecular; D008970:Molecular Weight; D010316:Particle Size; D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry
chemical_list: D006454:Hemoglobins; D007140:Immunoglobulin Fab Fragments; D046911:Macromolecular Substances; C100003:deoxyhemoglobin; D012260:Ribonucleases