Membrane Simulations in GROMACS Lipid bilayers and membrane proteins Justin A. Lemkul September 13, 2013 jalemkul@outerbanks.umaryland.edu
Objectives Learn the fundamentals of Self-consistent force fields Membrane and membrane protein simulations Perform common analysis routines for lipids
Background References Theory Kandt, C.L., Ash, W.L., and Tieleman, D.P. (2007) Methods 41: 475-488. http://lipidbook.bioch.ox.ac.uk/ Relevant to today s example Kandasamy, S.K. and Larson, R.G. (2006) Biophys. J. 90: 2326. Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput. Chem. 30: 1952.
References Theory Biomolecular force fields often built in stages Proteins, nucleic acids, lipids, other stuff Important to use self-consistent parameters Nowadays most force fields include support for all major macromolecule types
References Theory Lipid parameters (NOT exhaustive!) CHARMM36 Klauda, J.B. et al. (2010) J. Phys. Chem. B 114: 7830. Pastor, R.W. and MacKerell Jr., A.D. (2011) J. Phys. Chem. Lett. 2: 1526. OPLS-AA Ulmschneider, J.P. and Ulmschneider, M.B. (2009) J. Chem. Theory Comput. 5: 1803. GROMOS96 Kukol, A. (2009) J. Chem. Theory Comput. 5: 615. AMBER Siu, S.W.I. et al. (2008) J. Chem. Phys. 128: 125103.
Tutorial files provided membrane_tutorial/conf Sample configurations /data Sample data /gromos53a6_lipid.ff Force field /mdp parameters /scripts Accessory scripts /top Topologies /tpr input files Protocol online http://www.bevanlab.biochem.vt.edu/pages/personal/justin/gmx-tutorials/membrane_protein/index.html
Challenge #1: selecting a force field Challenge #2: building the starting configuration InflateGRO Kandt, C.L. et al. (2007) Methods 41: 475. Schmidt, T.H. and Kandt, C.L. (2012) J. Chem. Inf. Model. 52: 2657. g_membed Wolf, M.G. et al. (2010) J. Comput. Chem. 31: 2169.
Placing a protein: editconf center Protein COM coincident with membrane COM Protein COM above membrane COM
Placing a protein: editconf center editconf center x/2 y/2 z/2 box x y z Protein COM coincident with membrane COM Protein COM above membrane COM
Placing a protein: editconf center editconf center x/2 y/2 z/2 box x y z g_traj n p8.ndx ox nox noy z com editconf center x/2 y/2 z* -box x y z Protein COM coincident with membrane COM Protein COM above membrane COM
Topology generation: different approaches With CHARMM, simply use pdb2gmx Check contents of lipid.rtp With others, introduce lipid-specific terms lipid.itp (Berger parameters) Approach used here to combine Berger lipids with GROMOS96 More complicated procedure for combining allatom proteins with united-atom lipids http://www.pomeslab.com/files/lipidcombinationrules.pdf
ffnonbonded.itp [ defaults ] [ atomtypes ] [ nonbond_params] [ pairtypes ] lipid.itp [ defaults ] [ atomtypes ] [ nonbond_params] Lipid-Lipid terms Lipid-GROMOS terms [ pairtypes ] ffbonded.itp [ bondtypes ] [ angletypes ] [ dihedraltypes ] [ dihedraltypes ]
Membrane-specific run settings comm_grps tc_grps ref_t for tens or hundreds of ns
Notes on cutoffs Berger: plain 1.0-nm cutoffs GROMOS96: 0.9/1.4-nm twin-range Here we use 1.2-nm (single-range) APL and membrane properties unaffected Peptide secondary structure
Analysis techniques to be covered Lateral diffusion/diffusion constant Membrane thickness Deuterium order parameters Area per lipid
Index groups Lateral diffusion: P8 atoms Membrane thickness: P8 atoms in each leaflet Deuterium order parameters: each acyl C atom
All P8 atoms Use make_ndx or g_select In make_ndx: a P8 In g_select: name P8; Top and bottom leaflet P8 atoms Use g_select (file p8_selection.dat) top_p8 = name P8 and (z > 3.2); bot_p8 = name P8 and (z < 3.2); top_p8; bot_p8; About middle of box
Acyl chain C atoms use make_ndx sn-1 and sn-2 chains separately a C34 a C36 a C37 a C50 a C15 a C17 a C18 a C31
Lateral diffusion echo 0 g_msd s md.tpr f traj.xtc n all_p8.ndx lateral z o msd_p8.xvg May have to deal with PBC separately for each leaflet Membrane thickness echo 0 1 g_dist s md.tpr f traj.xtc n top_bot_p8.ndx Only z-distance important (x/y should be 0) May not tell the whole story
Deuterium order parameters g_order s md.tpr f traj.xtc n sn1.ndx od deuter_sn1.xvg d z g_order s md.tpr f traj.xtc n sn2.ndx od deuter_sn2.xvg d z Important to consider equilibration time, usually need b Unsaturated lipids require unsat option separately for double bond atoms C n-1 C n =C n+1 C n+2
Area per lipid Trivial for pure membranes (Box-X * Box-Y)/(# of lipids per leaflet) Use g_energy to extract Box-X and Box-Y g_energy f ener.edr o box.xvg perl scripts/area.pl box.xvg 64
Area per lipid (and membrane thickness) Complicated problem if a protein is embedded Shameless self-promotion: GridMAT-MD http://www.bevanlab.biochem.vt.edu/gridmat-md/ Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput. Chem. 30: 1952.