1 BUILDING A STRUCTURAL MODEL OF KCSA 14
set npot [atomselect top "name K and resid 3002 3004 3007"]
$npot set name OH2
$npot set resname TIP3
$npot writepdb filtwat.pdb
It is always desirable to keep as much information from the crystal structure
as possible. In this exercise we will not include in our model antibodies or
lipid fragments resolved in the crystal, but we will keep crystallographic water
molecules located nearby the channel and in protein cavities.
5 Select and save water molecules around the KcsA channel by typing in
the Tk Console window:
foreach S {A B C D} {
set wat [atomselect top "segname $S and
resname HOH and within 10 of (chain C and protein)"]
$wat writepdb crystwat$S.pdb
$wat delete
}
In case anything failed during the above steps, use the script prepfiles.tcl
to create again the corresponding files.
Water Molecules. Water m olecules located in internal cavities of
proteins often play a functionally relevant role. While these water
molecules might already be present in the crystal structure being
used, you may want to use specific software to determine if addi-
tional water molecules can be placed around or inside your protein.
The program DOWSER has been specifically designed to place wa-
ter molecules in internal cavities, and keeps or discards them based
on energetics. In addition t o adding water molecules, it can also
evaluate crystallographic waters such as those seen in 1K4C.pdb
ab ove.
Now you should have separate PDB files for each protein segment, for ions,
and for selected crystallographic water molecules. However, before generating
PSF and PDB files for the KcsA tetramer, we also need to check whether disul-
fide bonds between cysteine residues exist and what the protonation states of
charged residues and histidines are.
6 In VMD, which should be displaying the KCSA-ALL.pdb molecule, create
the following additional graphical representations:
7 By looking at the above representations in the VMD OpenGL display
you should be able to identify one cysteine residue per monomer (Cys90).
(30 Seiten)
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