Transmembrane protein insertion methods: Difference between revisions
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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] | ; [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] | ||
; 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] | ; 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] | ||
; | ; GRIFFIN: Calculates realistic lipid conformations even for large TM protein systems with complex topology starting from a pre-equilibrated bilayer. The implicit force field of GRIFFIN guides buried bilayer atoms towards the surface of the protein, while water or lipid atoms outside of the protein volume experience the interaction forces of the protein. Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using GRIFFIN'', René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] | ||
; gromacs make_hole: The predecessor of GRIFFIN (part of Gromacs 3.1). 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] | |||
; gromacs make_hole: | |||
; 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] | ; 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] | ||
; 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]. | ; 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]. | ||
Latest revision as of 15:32, 12 October 2010
Published methods for setting up membrane protein simulations; please add more.
- 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
- GRIFFIN
- Calculates realistic lipid conformations even for large TM protein systems with complex topology starting from a pre-equilibrated bilayer. The implicit force field of GRIFFIN guides buried bilayer atoms towards the surface of the protein, while water or lipid atoms outside of the protein volume experience the interaction forces of the protein. Biophysics 2010 abstract Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using GRIFFIN, René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:10.1016/j.bpj.2009.12.3070
- gromacs make_hole
- The predecessor of GRIFFIN (part of Gromacs 3.1). 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.
