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| − | == Methods for setting up membrane protein simulations ==
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| − | Published methods:
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| − | ; [http://wwwuser.gwdg.de/~ggroenh/membed.html 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:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507]
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| − | ; 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:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006]
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| − | ; 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 [http://dx.doi.org/10.1016/j.bpj.2009.12.2105 10.1016/j.bpj.2009.12.2105]
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| − | ; 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:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070]
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| − | ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz 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:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5]
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| − | ; 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 [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html 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:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q]
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| − | ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane 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 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880].
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| − | [[Category:MembraneInsertion]]
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| | [[Category:Lipids]] | | [[Category:Lipids]] |
| | [[Category:Protocols]] | | [[Category:Protocols]] |
| − | [[Category:Gromacs]] | + | |
| − | [[Category:CHARMM]] | + | == Setting up membrane protein simulations == |
| | + | # decide on the [[Protein/Membrane system size|size of the protein/membrane system]] |
| | + | # obtain parameters (for lipids see, for instance, [http://lipidbook.bioch.ox.ac.uk Lipidbook]) |
| | + | # choose a [[transmembrane protein insertion methods|transmembrane protein insertion method]] |
| | + | # run simulation |
