SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 26)

2 PLACING KCSA IN A MEMBRANE 26

Notice the use of the transaxis function. This is one of a few functions

which generate transformation matrices of the type we took from the orig-

inal PDB ﬁle. In this case, the matrix rotates about the z-axis by −25

degrees.

5 Now we simply combine the two temporary ﬁles into one set of PSF and

PDB ﬁles:

mol delete all

package require psfgen

resetpsf

readpsf popc.psf

coordpdb popc TEMP.pdb

readpsf ../01-BUILD/kcsa solv.psf

coordpdb kcsa TEMP.pdb

writepsf kcsa popc raw.psf

writepdb kcsa popc raw.pdb

file delete kcsa TEMP.pdb

file delete popc TEMP.pdb

6 Load the ﬁles kcsa popc raw.psf and kcsa popc raw.pdb in VMD. If

something went wrong, you may want to regenerate the ﬁles by using the

script memprot-align.tcl.

7 Before we move on, let’s use one of VMD’s many coloring methods to

make sure our protein is lined up with the membrane in a natural way.

To do this, set up the following representations:

Selection Drawing Method Coloring Method

protein VDW ResType

resname POPC and name P1 VDW Name

The residues of the protein are now colored based on their hydrophobicity

and acidity. We see that the headgroup phosphates (labeled P1 for POPC

membranes) are aligned well with the tyrosine residues, colored green on

the upper corners of the KcsA, as well as the arginine residues on the

lower corners (Fig. 7 B). The white residues between the headgroups are

hydrophobic, meaning we have a good alignment with the membrane. In

some cases, it might be necessary to align protein and membrane manually.

Next, we will take out the lipids overlapping the KcsA.

2.3 Combination of Membrane and Protein

Now we need to make room for the KcsA in the membrane layer, so that the

protein doesn’t overlap any lipid molecules. As in the s ec tion above on using

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SanDisk Membrain Software Bedienungsanleitung Seite 26