Molecular dynamics simulations of creatine kinase and adenine nucleotide translocase in mitochondrial membrane patch.

Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies.

Molecular dynamics modeling of proton transport in nafion and hyflon nanostructures.

Classical molecular dynamics modeling studies at 363 K are reported of the local atomic-level and macroscopic nanostructures of two well-known perfluorosulfonic acid proton exchange polymer membrane materials: Nafion and Hyflon. The influence of the different side-chain lengths in the two polymers on local structure is relatively small: Hyflon exhibits slightly greater sulfonate-group clustering, while Nafion has more isolated side chains with a higher degree of hydration around the SO(3)(-) side-chain ends. This results in shorter mean residence times for water molecules around the end groups in Nafion. Hyflon also displays a lower degree of phase separation than Nafion. The velocities of the water molecules and hydronium ions are seen to increase steadily from the polymer backbone/water interface toward the center of the water channels. Because of its shorter side chains, the number of hydronium ions is approximately 50% higher at the center of the water channels in Hyflon, and their velocities are approximately 10% higher. The water and H(3)O(+) diffusion coefficients are therefore higher in the shorter side-chain Hyflon system: 6.5 x 10(-6) cm(2)/s and 25.2 x 10(-6) cm(2)/s, respectively; the corresponding values for Nafion are 6.1 x 10(-6) cm(2)/s and 21.3 x 10(-6) cm(2)/s, respectively. These calculated values compare well with experiment: 4 x 10(-6) cm(2)/s for vehicular H(3)O(+) diffusion.

Molecular dynamics studies of the Nafion, Dow and Aciplex fuel-cell polymer membrane systems.

The Nafion, Dow and Aciplex systems--where the prime differences lies in the side-chain length--have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO(3) end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H(3)O(+)/H(2)O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility.