Additional File 1 - Molecular Dynamics and Molecular Modeling
For molecular dynamics (MD) and molecular mechanics (MM), an appropriate force field is required that` can adequately describe the potential energy surface for proteins. In this study we used GROMOS-42B1 (initial force field) and GROMACS ffgmx (final force field) (1), for all energy minimization and MD simulations of the transmembrane and loop regions of the human ND6 protein and its mutations. To account to some extent for the membrane environment, appropriate values of distance-dependent dielectric constants, 1-4 non-bonded interactions scaling factors and non-bonded cut-offs were chosen. The steepest descent method followed by conjugate gradient minimization algorithm was used until the rms energy gradient was below 10.0 kJ/mol.nm. The N-terminus was capped with an acetamido group and the C-terminus with a carboxamido group.
For initial MD simulations, we fixed backbones of the helices in the proteins, and the simulations were restricted to the loop regions and to the side chains of the amino acids in TMHs. Their non-covalent interactions were evaluated as well. No explicit water molecules were added. The potential types were assigned by using the automatic assignment module of the GROMACS molecular simulation package (2). The main MD simulation protocol included an initial step of minimization by using the conjugate gradient algorithm, a 100 ps MD run with positional restraints followed by a 500 ps MD run without restraints. Thus, the overall MD simulation with duration of 600 ps was performed for the total protein. Weak coupling of the protein to a solvent bath of constant temperature (300 K) and constant pressure (1 bar) was maintained with a coupling time of 1.0 ps. The simulation was carried out at a temperature of 300° K. An integration step of 1.00 ps was used throughout all simulations. From the conformations of the production time the 20 lowest energies were selected and an energy minimization of the complete ensemble was performed by using the conjugated gradient method.
The interactive modeling, display of initial data analysis, and generation of files, was achieved with the molecular modeling package Swiss-PdbViewer (3). The probable interactions and structural analysis of key residues involved in the maintenance of the 3D-structure of the human ND6 protein and its mutations were quantitatively identified from analysis of the 3D structure of proteins by the GROMACS molecular simulation package.
References
1. Guex, N. and Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18: 2714-2723, 1997.
2. Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Computer
Physics Communications, 91: 43-56, 1995.
3. Lindahl, E., Hess, B., and van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling,
7: 306-317, 2001.