Membrane proteins

Methods for setting up membrane protein simulations

Published methods:

g_membed

Slowly growing a shrunken peptide into a bilayer. See g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:10.1002/jcc.21507

Tielemann's "shrinking an exploded bilayer"

Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). Setting up and running molecular dynamics simulations of membrane proteins. Kandt C, Ash WL, Tieleman DP. Methods 41 (2007), 475-88. doi:10.1016/j.ymeth.2006.08.006

TaraGrid

an update on the Faraldo-Goméz/Smith "make hole" approach (?); Automated Protein-Insertion into Membranes for Molecular Dynamics Simulation Set-Up Using Taragrid, René Staritzbichler, Lucy R. Forrest and José Faraldo-Gómez. Biophysics 2010 abstract 10.1016/j.bpj.2009.12.2105

Griffin

Biophysics 2010 abstract Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin, René Staritzbichler, Lucy R. Forresta and José D. Faraldo-Gómez doi:10.1016/j.bpj.2009.12.3070

gromacs make_hole

Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary mdrun_make_hole. Setting up and optimization of membrane protein simulations. Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '31 (2002), 217-227. doi:10.1007/s00249-002-0207-5

CHARMM style (Woolf & Roux)

build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at membrane builder. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Woolf TB, Roux B. Proc Natl Acad Sci U S A. 91 (1994), 11631-5 and Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer, T. Woolf and B. Roux, Proteins 24 (1996) 92-114 doi:10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q

CHARMM-GUI Membrane-builder

automated web procedure (generate input files, run locally. Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations, S. Jo, T. Kim, and W. Im PLoS ONE 2 (2007) e880 . 10.1371/journal.pone.0000880.