The Impact of Bending and Twisting Rigidity of DNA on Protein Induced Looping Dynamics

Abstract

Nano-sized fullerene aggregates can enter cells and alter their functions, but the mechanisms of cell damage is unclear. In our previous work [1] we used coarsegrained molecular dynamics simulations to characterize the thermodynamics and kinetics of permeation of fullerene clusters through a model membrane. We also showed that high fullerene concentrations induce changes in the structural and elastic properties of the lipid bilayer, but these are not sufficient to cause a direct mechanical damage to the membrane. Now we explore the effect of fullerene on model membranes including an ion channel protein, Kv1.2, using computer simulations with both a coarse-grained and an atomistic representation. We also investigate the effects of a naturally abundant organic compound, gallic acid, on fullerene-membrane interactions. Recent work [2] has shown that gallic acid-coated fullerenes cause cell contraction. We use computer simulations to describe possible mechanisms of cell damage.[1] Wong-ekkabut et al., Nature Nanotech (2008), 3, 363. [2] Salonen et al., Small, in press.