SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 24)

2 PLACING KCSA IN A MEMBRANE 24

2 Placing KcsA in a Membrane

In this second unit, you will learn how to take your solvated KcsA channel and

place it in a membrane. Then you will solvate and ionize the entire system.

2.1 Building a Membrane Patch

The ﬁrst step is to prepare a complete membrane. This is usually done by

replicating a pre-equilibrated patch of membrane and water, then trimming it

if necessary. The VMD Membrane Builder plugin automates this process. The

steps in this section and the following one (Alignment of Membrane and Pro-

tein) are also covered in the script memprot-align.tcl.

NOTE: If you skipped the previous section, you should either use the ﬁles

kcsa solv.psf and kcsa solv.pdb from the example output, or replace every

instance of these ﬁles with kcsav.psf and kcsav.pdb in the following instruc-

tions.

1 Navigate to the directory mem-tutorial-files/02-MEMBRANE, op e n VMD,

and select the Extensions → Modeling → Membrane Builder menu item in

the VMD Main window.

2 In the Membrane window, select the POPC Lipid and change the Mem-

brane X Length and the Membrane Y Length to 80. Set the Output Preﬁx to

< your home directory >/mem-tutorial-files/02-MEMBRANE/popc. Click

the Generate Membrane button.

A patch of POPC membrane should appear in the VMD OpenGL display, along

with the two corresponding ﬁles in your 02-MEMBRANE directory.

3 Set up the following representations:

Selection Drawing Method Coloring Method

resname POPC Lines SegName

water Lines Name

Notice how diﬀerent patches of membranes have been combined and how

lipid head-groups are solvated (Fig. 7 A).

More membranes. In some cases certain types of lipids play key

roles in the function of membrane proteins. Therefore, membrane

proteins should be placed i n their native-like environment, namely, in

hydrated bilayers made of diﬀerent combinations of lipids as found

in in vivo conditions. VMD provides POPC and POPE membranes,

but the CHARMM force-ﬁeld supports several other types of lipids.

Remember to set up the temperature of your simulation above the

melting temperature of lipids used in your system.

1 2 ... 19 20 21 22 23 24 25 26 27 28 29 ... 42 43

Sem comentários

SanDisk Membrain Software Manual do Utilizador Página 24