The following two tutorials show how to use Memoir to model transmembrane proteins with multiple chains. The free PyMOL visualisation software is required for this tutorial. All the sequence and structure files used and all the Memoir generated models are available for download.
1. Modelling a multi-chain ion channel
In the first example we are going to model a homo-oligomer, ion-channel target (PDB: 2WLJ). The full channel is a tetramer made from four copies of the following sequence:
>2WLJ:A|PDBID|CHAIN|SEQUENCE MTGGMKPPARKPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARP GSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLM MRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFL VLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQHHHHHH
To model this protein we are going to use PDB structure
as a template. This structure has a single chain which is rotated to
produce a tetramer in the biological unit. In this example we will construct
the biological unit from the crystal asymmetric unit. This is possible because
PyMOL is able to interpret the CRYST1, ORIGXn, and SCALEn records present
3SYO PDB file.
- Load the
3SYO.pdbin PyMOL. You can either do this via the menu to load the structure file you downloaded from the PDB or by entering
3SYOin the menu option. When you first load this, the protein will be first displayed as lines. For a less cluttered cartoon representation click on and on . The and menus are found on the right hand side in the below screenshot. The result should look similar to the following image.
- In the case of this protein, the biological unit may be
reconstructed from the crystal asymmetric unit by issuing the following
symexp sym,3SYO,(3SYO),1at the
PyMOL>prompt at the bottom of your PyMOL window. Note that each symmetric unit is now a separate PyMOL object (i.e.
- Save each chain as a separate molecule through the
At the end of this exercise you should have four PDB files:
- We now have the inputs we need to run Memoir. Open four instances of Memoir (in different browser tabs).
Copy and paste the sequence above in the sequence text box of each browser tab.
Then load each of the four PDB files you just created in each different
instance of Memoir. The chain should be set to 'A' for all the Memoir runs.
A single run should look like the screenshot below. Click on the "Model"
button for each Memoir instance. This step will take about 30 minutes to finish.
- When you get the results page, download each "High Accuracy Model"
and save each file separately. Load the four models in PyMOL (convert
to "cartoon" representation as described in Step 1). Note
that using Memoir you can only model the transmembrane region.
- Save everything as one model using the following PyMOL command at the
save memoir_2wlj_complete_final.pdb, all
2. Modelling a large cytochrome complex
In the second example we are going to model a large cytochrome complex (PDB: 1L0L). This complex has 11 chains, but we cannot model all of them because they do not all match the template we selected. Also, Memoir does not model non-transmembrane parts such as chain I in this particular example. The three chains we want to model are C, D, and E. The three sequences in FASTA format are given below:
>1L0L:C|PDBID|CHAIN|SEQUENCE MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTHICRDVNYGWIIR YMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLLTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNL VEWIWGGFSVDKATLTRFFAFHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILILALIPLLHTSKQRSMMFRPL SQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLLILVLMPTAGTIENKLLKW
>1L0L:D|PDBID|CHAIN|SEQUENCE SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDEAKALAEEVEVQDGPNEDGEM FMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGM APPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP K
>1L0L:E|PDBID|CHAIN|SEQUENCE SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSD IPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPC HGSHYDASGRIRKGPAPLNLEVPSYEFTSDDMVIVG
Each of the three chains we wish to model is present in two copies in the biological unit. As a template we are going to use PDB structure 2FYN. We will require 6 Memoir runs to model our target chains — one for each copy of each chain:
- Launch Memoir in six different browser tabs. In the first two tabs copy and paste sequence
1L0L:Cgiven above as the target we want to model. Then enter
2FYNin the PDB code text box and enter chains A and D in the two different tabs (this should be the only difference between the two tabs). In the second two tabs copy and paste sequence for
1L0L:Dgiven above as the target we want to model, enter
2FYNin the PDB code text box and enter chains B and E in the two different text boxes in the two tabs. Then repeat this for the last two Memoir tabs, i.e. copy and paste sequence for
1L0L:Egiven above as the target we want to model, enter
2FYNin the PDB code text box and enter chains C and F in the two different tabs. Press the "Model" button in each of the six tabs. An example of how one of these Memoir instances should look is shown below.
- When you get the six results pages, download each "High Accuracy Model"
and save each file separately. Load the six models in PyMOL (convert
to "cartoon" representation as described in the previous example).
Note that using Memoir you can only model the transmembrane region.
- Save everything as one model using the following PyMOL command:
save memoir_1l0l_complete_final.pdb, all
The above two examples show how to model multiple chain transmembrane proteins using Memoir.