Paper Citing NAMD - Abstract
Poyry, Sanja; Cramariuc, Oana; Postila, Pekka A.; Kaszuba, Karol; Sarewicz, Marcin; Osyczka, Artur; Vattulainen, Ilpo; Rog, Tomasz
Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc(1) complex
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1827:769-778, JUN 2013
The reaction mechanism of the cytochrome (cyt) bc(1) complex relies on proton and electron transfer to/from the substrate quinone/quinol, which in turn generate a proton gradient across the mitochondrial membrane. Cardiolipin (CL) have been suggested to play an important role in cyt bc(1) function by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics simulations that are applied to the entire cyt bc(1) dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complex's catalytic Q(i)-sites. This observation is in full agreement with crystallographic studies of the complex, and supports the view that CLs are key players in the proton uptake. The simulation results also allow us to present a refined picture for the dimer arrangement in the cyt bc(1) complex, the novelty of our work being the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics of cyt bc(1) with lipids, complementing previous experimental findings. (c) 2013 Elsevier B.V. All rights reserved.
