GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules

Biophysical Journal
Pawel J ZukPiotr Szymczak

Abstract

Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.

Citations

Dec 8, 2020·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Radost Waszkiewicz, Maciej Lisicki
Dec 27, 2019·Journal of Molecular Biology·J García de la Torre, J G Hernández Cifre

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