SanDisk Membrain Software Instrukcja Użytkownika Pobierz pdf (Strona 12)

1 BUILDING A STRUCTURAL MODEL OF KCSA 12

Figure 3: Top and side views of the KcsA tetramer with an antibo dy complex

(1K4C.pdb).

In VMD, you should be able to see the full, tetrameric, KcsA channel along

with water, ions, lipid fragments, and large antibody complexes used to crys-

tallize it (Fig 3).

Homework. Create a VMD script that automates the construc-

tion of multimeric structures. The script should be able to read

the transformation matrices described in REMARK 350 from a raw

PDB ﬁle and output the multimeric form of the protein in a sin-

gle pdb ﬁle. Solution: check the mono2poly script available at

http://www.ks.uiuc.edu/Research/vmd/script library/scripts/

Aligning the protein to the z-axis. The KcsA channel structure

studied here has its principal axis along the channel aligned with

the z-axis. This conﬁguration is very convenient for embedding the

protein in a membrane and also facilitates the use of several analysis

tools. However, membrane proteins obtained from the Protein Data

Bank are often not aligned along the z-axis. For those cases, VMD

provides the orient plugin, which permits alignment of principal

axes of a molecule to x,y,z, directions. The plugin can be found at:

http://www.ks.uiuc.edu/Research/vmd/script library/scripts/orient/

You may also want to check the “Orientations of Proteins in Mem-

branes” database at http://opm.phar.umich.edu/

1.4 Generating PSF and PDB Files for KcsA

Now that you have built the whole structure for KcsA and its antibody com-

plex, you will generate PSF and PDB ﬁles for just the channel protein, crys-

tallographic water molecules, and ions. You will generate these ﬁles step by

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SanDisk Membrain Software Instrukcja Użytkownika Strona 12