[gmx-users] g_sas values for peptide in water and in DPC micelle

[Justin A. Lemkul]

sa wrote:
> Dear all,
> 
> 
> Firstly, I wish you a happy new year filled with joy, health and lots of 
> finding !!
> 
> 
> Now my question:
> 
> 
> I have simulated one peptide (25 AA length + N- and C- caps) in two 
> environment: one in bulk water TIP3P water (A) and one with a DPC 
> micelle in water (B). My peptide keep in the two simulations a very 
> similar secondary structure (alpha helix). The peptide in the system B, 
> during the last 50 ns of the simulation time, is located in the 
> micelle/water interface in the little crevice formed by the DPC 
> hydrophobic chain and remains in the same place.
> 
> I would like to compute the accessible surface area with respect to 
> solvent for some residues of the peptide and especially for the single 
> TRP  of the peptide (TRP553) and compare with the SA obtained for the 
> same peptide in water.  By examining several configurations of the 
> peptide in the B system at the end of the simulation (~150 ns) with 
> pymol, I found that TRP553 residue is mainly in contact with the DPC 
> micelle hydrophobic core and is not fully exposed to the solvent. So i 
> expect that the average SA value for TRP553 (and for the others 
> residues) in system B will be smaller than the values obtained for the 
> same residues in the system A.
> 
> 
> 
> I used the following command for the two systems
> 
> 
> g_sas_mpi -f *.xtc -s md_0_24.tpr -b 99500 -e 100000 -dt 10 -or 
> mTM10-TIP3_per_residu_TRP553_SAS.xvg -oa 
> mTM10-TIP3_per_atom_TRP553_SAS.xvg -n System_TRP553.ndx
> 
> 
> I choose the option 2 (Protein-H) in the menu. It is the correct 
> combination for g_sas ?
> 
> 
> The output of g_sas (gmx 4.5.3) are shown below for the two systems. 
> Average values are computed for A and B from the last  500 ps (extracted 
> every 10 frames -> 50 values)
> 
> 
> ---- System A
> 
> 
> @ s0 legend "Average (nm\S2\N)"
> @ s1 legend "Standard deviation (nm\S2\N)"
>        545    0.723556  0.0709648
>        546    0.851864  0.0780804
>        547    0.782327  0.0548426
>        548     0.97012  0.0836672
>        549    0.339449  0.0611941
>        550    0.839293  0.0795415
>        551     1.34999   0.104301
>        552    0.708079  0.0693484
>        553     1.95306   0.135732
>        554     1.02126  0.0899936
>        555     0.32233  0.0755605
>        556    0.643128  0.0645317
>        557    0.842983  0.0683777
>        558     1.37868   0.107237
>        559    0.972423   0.108448
>        560    0.875918  0.0707144
>        561     0.56353  0.0494754
>        562    0.979795  0.0875196
>        563      0.6764  0.0599796
>        564    0.792996  0.0830322
>        565     1.29532   0.123898
>        566    0.493239  0.0679436
>        567    0.991596  0.0743836
>        568     1.71456   0.121319
>        569    0.943561  0.0747361
>        570     1.12007  0.0511916
>        571    0.572433  0.0343254
> 
> ---- System B
> 
> 
> @ s0 legend "Average (nm\S2\N)"
> @ s1 legend "Standard deviation (nm\S2\N)"
>        545    0.721979  0.0582663
>        546    0.905305  0.0508979
>        547    0.785995   0.053198
>        548    0.944034  0.0688671
>        549    0.394531  0.0606229
>        550    0.803279  0.0667054
>        551     1.38402   0.083296
>        552    0.920283    0.06624
>        553       1.824   0.127784
>        554    0.688272  0.0821362
>        555     0.50046  0.0694137
>        556    0.870991  0.0733946
>        557    0.765114  0.0651865
>        558     1.27511   0.116357
>        559     1.14207  0.0791716
>        560    0.950344  0.0677436
>        561    0.564978   0.052539
>        562    0.983167  0.0857281
>        563    0.670499  0.0607886
>        564    0.814746  0.0638795
>        565     1.16659  0.0778935
>        566    0.551229  0.0534253
>        567     1.02231  0.0561598
>        568     1.69817   0.115372
>        569    0.878103  0.0621447
>        570    0.982666  0.0652861
>        571    0.742895  0.0373423
> 
> 
> As you can see, it is not the case since the SA values are not 
> significantly different between the two systems, i don t understand why. 
> Did i use use the good combination for g_sas ?
> 

No.  If you have a DPC micelle, it needs to be part of the calculation group, as 
well.  The output group can then be whatever you want it to be.  But if you 
don't consider the micelle, g_sas will happily calculate SASA as if your peptide 
were simply in water.  Your results seem to agree.

g_sas -h:

..."The calculation group should always consists of all the non-solvent atoms in 
the system"...

-Justin

> 
> Thank you in advance for your help/advices.
> 
> 
> Stephane
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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