Hydrodynamic modeling: the solution conformation of macromolecules and their complexes

Byron, O. (2008) Hydrodynamic modeling: the solution conformation of macromolecules and their complexes. In: Correia, J. J. and Detrich, III, H. W. (eds.) Biophysical Tools for Biologists, Volume One: In Vitro Techniques. Series: Methods in cell biology (84). Academic Press: Amsterdam ; London, pp. 327-373. ISBN 9780123725202 (doi: 10.1016/S0091-679X(07)84012-X)

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Abstract

Hydrodynamic bead modeling (HBM) is the representation of a macromolecule by an assembly of spheres (or beads) for which measurable hydrodynamic (and related) parameters are then computed in order to understand better the macromolecular solution conformation. An example‐based account is given of the main stages in HBM of rigid macromolecules, namely: model construction, model visualization, accounting for hydration, and hydrodynamic calculations. Different types of models are appropriate for different macromolecules, according to their composition, to what is known about the molecule or according to the types of experimental data that the model should reproduce. Accordingly, the construction of models based on atomic coordinates as well as much lower resolution data (e.g., electron microscopy images) is described. Similarly, several programs for hydrodynamic calculations are summarized, some generating the most basic set of solution parameters (e.g., sedimentation and translational diffusion coefficients, intrinsic viscosity, radius of gyration, and Stokes radius) while others extend to data determined by nuclear magnetic resonance, fluorescence anisotropy, and electric birefringence methods. An insight into the topic of hydrodynamic hydration is given, together with some practical suggestions for its satisfactory treatment in the modeling context. All programs reviewed are freely available.

Item Type:Book Sections
Status:Published
Glasgow Author(s) Enlighten ID:Byron, Professor Olwyn
Authors: Byron, O.
College/School:College of Medical Veterinary and Life Sciences > School of Life Sciences
Publisher:Academic Press
ISBN:9780123725202
Published Online:26 October 2007
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