Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 1. Ellipsoid models

• Published in: European biophysics journal Vol. 39; no. 3; pp. 437 - 447
• Main Authors: Zipper, Peter, Durchschlag, Helmut
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01-02-2010; Springer-Verlag; Springer Nature B.V
• Subjects: Biochemistry; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Computers; Diffusion; Fluid mechanics; Life Sciences; Macromolecular Substances - chemistry; Membrane Biology; Models, Chemical; Molecules; Nanotechnology; Neurobiology; Original Paper; Software; Viscosity; Volume; Water - chemistry; Modeling problems; Hydrodynamics; Multibead models; Parameter predictions; Volume corrections
• ISSN: 0175-7571; 1432-1017
• DOI: 10.1007/s00249-009-0424-2

The shape of macromolecules can be approximated by filling models, if both hydrodynamic and scattering properties should be predicted. Modeling of complex biological macromolecules, such as oligomeric proteins, or of molecule details calls for usage of many beads to preserve the original features. However, the calculation of precise values for structural and hydrodynamic parameters has to consider many problems and pitfalls. Among these, the huge number of beads required for modeling details and the choice of appropriate volume corrections for the calculation of intrinsic viscosities are pestering problems to date. As a first step to tackle these problems, various tests with multibead models (ellipsoids of different axial ratios) were performed. The agreement of the predicted molecular properties with those derived from whole-body approaches can be used as evaluation criteria. Modification of previously available versions of García de la Torre's program HYDRO allows hydrodynamic modeling of macromolecules composed of a maximum of about 11,000 beads. Moreover, application of our recently suggested “reduced volume correction” enables a fast and efficient anticipation of intrinsic viscosities. Correct parameter predictions were obtained for all models analyzed. The data obtained were compared to the results of calculations based on HYDRO programs available to the public. The calculations revealed some unexpected results and allowed founded conclusions of general importance for precise calculations on multibead models (e.g., the requirement of calculations in the double-precision mode).