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I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer.

The domain of the protein looks like this:

enter image description here

Thus I'd like to have the transmembrane part of the protein to be buried in lipid membrane, and the extracellular part of it to be placed outside membrane.

I was following the Gromacs Membrane Protein Tutorial.

However the protein orientation I get is not as I expected:

enter image description here

Notice that the whole protein is buried in the lipid and in tilted position instead of perpendicular with respect to the lipid bilayer. How can I properly orient the protein in the membrane?

G.V.

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  • $\begingroup$ Did you get the tilted position AFTER running the simulation? $\endgroup$
    – Camps
    Commented Sep 26, 2022 at 20:19
  • $\begingroup$ @Camps no, I haven't run the MD gmx mdrun -deffnm md_0_1. $\endgroup$ Commented Sep 27, 2022 at 0:15

2 Answers 2

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In the Step One: Prepare the Topology, second paragraph, you can find the following information:

The peptide was prepared in-house using the xLeap module of AmberTools, using ideal backbone geometry of an α-helix (φ = -60°, ψ = -40°). The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation about the y axis. Note that in GROMACS-3.3.x, the -princ option oriented the long axis of the structure (in this case, the helix axis) along the z-axis by default, but this option has changed as of GROMACS-4.0.4, which orients the long axis along the x-axis. If you want to skip the construction of this peptide, the properly oriented structure can be found here.

I think that before setting up your system, you can prepare (rotate) your protein and use it in the orientation you want.

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    $\begingroup$ Beautiful! I had bookmarked this question out of keen interest! My background as an undergrad was largely in biology, and now I wish I could answer questions like these! Maybe we need to do more computational biochemistry papers :) $\endgroup$ Commented Sep 26, 2022 at 20:28
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I used VMD to re-orient the protein in combination with editconf rotation:

gmx editconf -f myprotein_processed.gro -rotate 0 90 0 -o myprotein_newbox.gro -c -box 6.41840 6.44350 6.59650

It worked.

The final result I got is this:

enter image description here

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