Zipper, Peter and Durchschlag, Helmut (2013) Hydrodynamic multibead modeling: problems, pitfalls and solutions. 3. Comparison of new approaches for improved predictions of translational properties. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42 (7). pp. 559-573. ISSN 0175-7571,
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Modeling simple and complex biopolymers in solution requires the shapes of these molecules to be approximated by bead modeling procedures, primarily for the prediction of hydrodynamic and scattering quantities. Though several bead modeling strategies (strict, shell and filling models) and a variety of computer programs (preferably the HYDRO suite by the Garcia de la Torre group) are available, several subtle questions remain to be answered, in particular concerning the appropriate volume correction for intrinsic viscosity computations. In this context, various versions of the HYDRO programs and different types of volume corrections, as well as the novel, alternative program ZENO of the Mansfield group, were applied to a plethora of thoroughly designed multibead models of spherical, ellipsoidal, cylindrical and prismatic shapes. A critical comparison of the results obtained reveals a variety of new aspects, useful for many future applications. Among these, application of our recently suggested "reduced volume correction" (RVC) together with specially adapted HYDRO versions and use of ZENO turned out to be highly effective, in particular when aiming at filling model strategies and using high bead numbers, a domain not fully supported by the recent HYDRO++ versions. By our approaches, the values of translational properties (diffusion coefficients, D, and intrinsic viscosities, [eta]) of all multibead models applied were anticipated correctly.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | MACROMOLECULAR BEAD MODELS; INTRINSIC-VISCOSITY; ROTATIONAL DIFFUSION; BIOLOGICAL MACROMOLECULES; PROTEINS; NANOPARTICLES; PARAMETERS; COMPLEXES; Multibead models; Novel approaches; Translational diffusion coefficient; Intrinsic viscosity; Parameter predictions; Hydrodynamics |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 07 Apr 2020 09:29 |
| Last Modified: | 07 Apr 2020 09:29 |
| URI: | https://pred.uni-regensburg.de/id/eprint/16469 |
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