Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect

Mukherjee, Arnab and Bagchi, Biman (2004) Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect. [Preprint]

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Abstract

Rotational friction on proteins and macromolecules is known to derive contributions from at least two distinct sources –hydrodynamic (due to viscosity) and dielectric friction (due to polar interactions). In the existing theoretical approaches, the effect of the latter is taken into account in an ad hoc manner, by increasing the size of the protein with the addition of a hydration layer. Here we calculate the rotational dielectric friction on a protein ($\zeta_{DF}$) by using a generalized arbitrary charge distribution model (where the charges are obtained from quantum chemical calculation) and the hydrodynamic friction with stick boundary condition, ($\zeta_{hyd}^{stick}$) by using the sophisticated theoretical technique known as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp. Biol. Med. 12, 75 (1982)]. The calculation of hydrodynamic friction is done with only the dry volume of the protein (no hydration layer). We find that the total friction obtained by summing up $\zeta_{DF}$ and $\zeta_{hyd}^{stick}$ gives reasonable agreement With the experimental results, i.e., $\zeta_{exp} \approx \zeta_{DF} + \zeta_{hyd}^{stick}$.

Item Type:	Preprint
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	03 May 2006
Last Modified:	19 Sep 2010 04:25
URI:	http://eprints.iisc.ac.in/id/eprint/6291

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