Paper Citing NAMD - Abstract
Naddaf, Lamis; Sayyed-Ahmad, Abdallah
Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 564:12-19, DEC 15 2014
The dimerization rate of the bacterial cell division protein FtsZ is strongly affected by the intracellular crowding. Yet the complexity of the intracellular environment makes it difficult to investigate via all-atom molecular dynamics or other detailed theoretical methods. We study the crowding effect on FtsZ dimerization which is the first step of an oligomerization process that results in more elaborate supramolecular structures. In particular, we consider the effect of intracellular crowding on the reaction rates, and their dependence on the different concentrations of crowding agents. We achieved this goal by using Brownian dynamics (BD) simulation techniques and a modified post-processing approach in which we decompose the rate constant in crowded media as a product of the rate constant in the dilute solution times a factor that incorporates the crowding effect. The latter factor accounts for the diffusion reduction and crowder induced energy. In addition we include the crowding effects on water viscosity in the BD simulations of crowded media. We finally show that biomolecular crowding has a considerable effect on the FtsZ dimerization by increasing the dimerization rate constant from 2.6 x 10(7) M-1 s(-1) in the absence of crowders to 1.0 x 10(8) M-1 s(-1) at crowding level of 0.30. (C) 2014 Elsevier Inc. All rights reserved.
