SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 13)

1 BUILDING A STRUCTURAL MODEL OF KCSA 13

step using VMD and psfgen. The ﬁrst ﬁve steps are included in the script

prepfiles.tcl.

1 Be sure that KCSA-ALL.pdb is loaded in VMD as the top molecule. Then,

select the Extensions → Tk Console menu item in the VMD Main window.

2 Psfgen requires not covalently linked segments to b e in separate PDB ﬁles.

Save each KcsA segment by typing in the Tk Console window:

cd "< your home directory >/mem-tutorial-files/01-BUILD/"

foreach S { A B C D } {

set seg [atomselect top "segname $S and chain C and protein"]

$seg writepdb seg$S.pdb

$seg delete

}

Check that the ﬁles segA.pdb, segB.pdb, segC.pdb, segD.pdb, were prop-

erly generated by looking at them with a text editor.

Each of the ﬁles you saved contains a single segment (monomer) of the KcsA

membrane protein.

3 Now you will save a segment containing potassium ions by typing in the

Tk Console window:

set pot [atomselect top "name K and resid 3001 3003 3005 3006"]

$pot set name POT

$pot set resname POT

$pot writepdb pot.pdb

Note that we have selected four out of seven possible potassium ions. We choose

a conﬁguration of ions that is actually feasible, with two ions in the selectivity

ﬁlter and two in the intracellular and extracellular vestibules of the protein. We

will use the rest of the ions to place water molecules in the selectivity ﬁlter.

Ions in the selectivity ﬁlter of KcsA. The selectivity ﬁlter of potas-

sium channels is occupied by two or three ions under physiological

conditions. There are ﬁve binding sites for K

ions, and a typical

state correspond to sites 1 and 3 occupied by potassium, while a

water molecule at site 2 separates both ions (this state is denoted

as [1,3]). Transient states with 3 ions in the selectivity ﬁlter, e.g.,

[0,2,4], occur between states [1,3] and [2,4].

4 Select the remaining potassium ions and transform them into water molecules

by typing in the Tk Console window:

1 2 ... 8 9 10 11 12 13 14 15 16 17 18 ... 42 43

Keine Kommentare

SanDisk Membrain Software Bedienungsanleitung Seite 13