Brief instruction for PMF analysis of self-association of TM helical peptides.

 

This instruction illustrates how we analyzed the PMF profile of interaction between two TM peptides, using as an example 'CG-WALP19-oc' (the set #19b of our 2014 paper "Potential of mean force analysis of the self-association of leucine-rich transmembrane -helices: difference between atomistic and coarse-grained simulations" by M. Nishizawa and K. Nishizawa (2014)  J Chem Phys ). 

 

1. Please get a computer that runs Gromacs 4.x ready.

Download the zip file or its content (eight files): .gro, .top, .itp, .itp (Martini-v2.1), .itp (Martini-sol), .ndx, pre.mdp and run.mdp (named cg_w22.mdp) files.  ( When you publish your results obtained using the Martini itp files above, please cite the Martini paper(s) by Marrink and coworkers. )

 

2.  First, initial coordinates (gro files) that have various inter-helical distances have to be prepared.  Do 'grompp' using the pre.mdp file and the above listed gro, top, itp files.  Then, do 'mdrun' the obtained tpr file, which is a steered dynamics run that gradually brings the helices closer to each other ( from 2.2 nm to 0.4 nm). 

 

3.  Do trjconv against the .trr file obtained in 2.  For this trjconv, we suggest to use " -sep  -skip 10".   This generates a series of gro files with inter-helical distances of 2.1nm, 2.0 nm, 1.9nm,.. and so on.  Please rename the .gro files, including the number reflecting inter-helical distance in the name, like , such as, walp19_21.gro,  walp19_20.gro,  walp19_19.gro,... etc.    For each of these gro files. do the following 4 and 5.

 

4.  To make .tpr file, do grompp  (e.g.,  grompp  -f  cg_22w.mdp  -c  walp19_21(and so on).gro  -n  *.ndx  -p  *.top   -o  walp19_21(and so on).tpr ).  Of course, the 'pull_init1' value in the run.mdp file has to be altered in advance appropriately; this restrains the inter-helical distance (in nm) by the umbrella harmonic potential. 

 

5.  Run the tpr.  (  e.g.,   mdrun  -deffnm  walp19_21(and so on).tpr    -px  pullx_walp19_21(and so on).xvg  -pf  pullf_walp19_21(and so on).xvg    ) .  If the peptide has popped out the octane slab, repeat the 4 and 5 with another set of the initial velocities.

 

6.  Create a file named  ' tpr-files_walp19.dat ',  which is a list file of walp19_21(and so on).tpr.  Also, create pullf-files_walp19.dat, which is a list file of pullf_walp19_21(and so on).xvg .  To do so, enter one file name per line

just like,

walp19_21.tpr

walp19_20.tpr

walp19_19.tpr

....

.

 Then do  g_wham.  (e.g.,   g_wham  -it  tpr-files_walp19.dat  -if  pullf-files_walp19.dat  -o  profile.xvg  -hist  hist.xvg -unit  kJ  -b  500000  -temp  323  -min  0.5  -max  2.3  )

 

Actually, by modifying the step 3, we generated and used 23 windows (inter-helical distances) in total: 0.6, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1.0,1.05, 1.1, 1.15, 1.2, 1.25, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2 nm. 

For this set, we obtained a PMF curve with a depth of  ~ 28.5 kJ/mol.