GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.
Biophys J
; 115(5): 782-800, 2018 09 04.
Article
em En
| MEDLINE
| ID: mdl-30144937
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Substâncias Macromoleculares
/
Hidrodinâmica
/
Microesferas
Idioma:
En
Revista:
Biophys J
Ano de publicação:
2018
Tipo de documento:
Article