We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation.
- Authors
WOLF, MAARTEN G.; HOEFLING, MARTIN; APONTE-SANTAMARÍA, CAMILO; GRUBMÜLLER, HELMUT; GROENHOF, GERRIT
- Abstract
To efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal membrane perturbation we present a computational tool, called g_membed, which is part of the Gromacs suite of programs. The input consists of an equilibrated membrane system, either flat or curved, and a protein structure in the right position and orientation with respect to the lipid bilayer. g_membed first decreases the width of the protein in the xy-plane and removes all molecules (generally lipids and waters) that overlap with the narrowed protein. Then the protein is grown back to its full size in a short molecular dynamics simulation (typically 1000 steps), thereby pushing the lipids away to optimally accommodate the protein in the membrane. After embedding the protein in the membrane, both the lipid properties and the hydration layer are still close to equilibrium. Thus, only a short equilibration run (less then 1 ns in the cases tested) is required to re-equilibrate the membrane. Its simplicity makes g_membed very practical for use in scripting and high-throughput molecular dynamics simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
- Subjects
PROTEIN analysis; BIOLOGICAL membranes; MOLECULAR dynamics; SIMULATION methods &; models; LIPIDS
- Publication
Journal of Computational Chemistry, 2010, Vol 31, Issue 11, p2169
- ISSN
0192-8651
- Publication type
Article
- DOI
10.1002/jcc.21507