Premium
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
Author(s) -
Wolf Maarten G.,
Hoefling Martin,
AponteSantamaría Camilo,
Grubmüller Helmut,
Groenhof Gerrit
Publication year - 2010
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21507
Subject(s) - membrane , lipid bilayer , bilayer , molecular dynamics , membrane protein , chemistry , crystallography , chemical physics , biophysics , computational chemistry , biochemistry , biology
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