SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 25)

2 PLACING KCSA IN A MEMBRANE 25

Figure 7: Embedding Kcs A in a membrane patch. (A) POPC membrane patch.

(B) KcsA protein and location of membrane headgroups.

2.2 Alignment of Membrane and Protein

Now that we have a suitable membrane patch and a partially solvated protein,

the next step is to align them with one another properly.

1 Open the Tk Console window. Be sure your popc.psf/pdb ﬁles are loaded

as the top molecule and set the current directory to memtut-files/02-MEMBRANE.

2 Create a selection for the membrane and load the set of ﬁles for KcsA with

the following commands:

set popc [atomselect top all]

set kcsamol [mol new ../01-BUILD/kcsa solv.psf]

mol addfile ../01-BUILD/kcsa solv.pdb

set kcsa [atomselect $kcsamol all]

3 We will ﬁrst align the membrane with its center of mass:

$popc moveby [vecinvert [measure center $popc weight mass]]

$popc writepdb popc TEMP.pdb

4 For the channel, we will use the center of mass of the main center vestibule,

i.e. residues 97–106. This choice should be tailored to the speciﬁc mem-

brane protein being simulated. We will also rotate the channel about the

z-axis, to align the roughly square top end with the x- and y-axes:

set vest [atomselect $kcsamol "protein and resid 97 to 106"]

$kcsa moveby [vecinvert [measure center $vest weight mass]]

display resetview

$kcsa move [transaxis z -25]

$kcsa writepdb kcsa TEMP.pdb

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SanDisk Membrain Software Bedienungsanleitung Seite 25