5. Studying Antibody Conformations by Ultracentrifugation and Hydrodynamic Modeling
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Intact immunologically active antibodies are too large for high-resolution structural analysis by nuclear magnetic resonance
(NMR) spectroscopy. The flexibility between the Fab and Fc domains at the hinge region also makes structure determination
by X-ray crystallography generally difficult, except for a limited number of cases (antibodies that possess short hinge regions,
hinge-deleted mutants, or those stabilized by complexation with antigen). Hydrody-namic methods—such as measurement of the
translational frictional ratio by ultracentrifugation or dynamic light scattering—have no such limitations. However, two caveats
exist. First, the structures obtained are only low-resolution models. Second, hydrodynamic parameters, such as the frictional
ratio, are often at least as sensitive to the volume of the particle as to conformation. This is tricky, since this volume
includes a significant contribution from any solvent associated with the antibody; and this “solvation” or “hydration” is
a complex dynamic process. Nonetheless, if the hydration problem can be adequately dealt with, useful information about domain
orientation can be obtained, and in particular how orientations differ between different antibody classes and subclasses,
and between wild-type and mutant or engineered structures. This information may ultimately assist with strategies for antibody
engineering, particularly if we can understand which sequences are responsible for “compact” as opposed to open structures.
Affiliation(s): (2) National Centre for Macromolecular Dynamics, University of Nottingham, School of Biosciences, Loughborough, UK
(3) National Centre for Macromolecular Dynamics, School of Biosciences, University of Nottingham, UK
(4) Departamento de Química Física, Facultad de Química, Universidad de Murcia, Murcia, Spain
(3) National Centre for Macromolecular Dynamics, School of Biosciences, University of Nottingham, UK
(4) Departamento de Química Física, Facultad de Química, Universidad de Murcia, Murcia, Spain
Book Title: Antibody Engineering: Methods and Protocols
Series: Methods in Molecular Biology | Volume: 248 | Pub. Date: Dec-05-2003 | Page Range: 93-113 | DOI: 10.1385/1-59259-666-5:93
Subject: Biochemistry
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