English

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

Biological Physics 2015-06-26 v1 Computational Physics

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 {\it 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 (ζDF\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, (ζhydstick\zeta_{hyd}^{stick}) by using the sophisticated theoretical technique known as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp. Biol. Med. {\bf 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 ζDF\zeta_{DF} and ζhydstick\zeta_{hyd}^{stick} gives reasonable agreement with the experimental results, i.e., ζexpζDF+ζhydstick\zeta_{exp} \approx \zeta_{DF} + \zeta_{hyd}^{stick}.

Keywords

Cite

@article{arxiv.physics/0408071,
  title  = {Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect},
  author = {Arnab Mukherjee and Biman Bagchi},
  journal= {arXiv preprint arXiv:physics/0408071},
  year   = {2015}
}