Dear Tony, Tongqing, Tim,
Adding some alanine spacer is good for a simple reason - during
sequence docking ARP/wARP checks the distance between the ends of the
fragments.
Imagine you have two chains, 10 residues each. If you concatenate them
together, terminal residues belonging to different chains will have
consequtive numbers, 10 and 11:
11111111112222222222
Also imagine ARP/wARP built all residues in both fragments and is
about to sequence-dock them. Fortunately (or not) it removes termini,
so that you have:
-11111111--22222222-
Now, if the distance between residue 9 (the last in the first chain)
and 12 (the first in the second chain) is longer than about
3.8*(12-9)=11.4 A (the actual formula is a bit more complex), one of
the fragments will not be sequence docked and its side chains will be
chopped to glycines. Placing a few alaninines (5 to 10) in between the
chains will certainly help.
On the other hand, one should not add too many alanines overall.
ARP/wARP pretends to be clever and tries to figure out the NCS-order
automatically. If you added far too many alanines, you may confuse
ARP/wARP in thinking that your structure is, say, a trimer rather than
a tetramer.
There could be of course better ways of sequence-docking for
heteromers, but the above is the current status in 'ARP/wARP Classic'
protein model building.
With best regards,
Victor
Quoting "Tim Gruene" <[email protected]>:
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Dear Tony, dear Tongqing,
the way I understand the working mechanism of arp/warp works I do not
see the point introducing the polyALA spacer into the sequence. Just
concatenate all sequences into one file as though it was one molecule.
Cheers,
Tim
On 04/19/12 08:51, Antony Oliver wrote:
In the absence of a likely, more sensible, answer - I think the
trick is/was to simply put everything in one pir file, but "link"
each sequence with a run of 20 or so alanines i.e. sequence A
followed by AAAA ... AAAA sequence B AAAA .... AAAA .... AAAA
sequence C.
There may well be a more elegant solution - but I'm fairly sure
this worked previously for us.
With regards,
Tony.
On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]"
<[email protected]> wrote:
Dear All,
I am trying to use Arp/wArp to build an antibody-antigen complex
with 1.65 A data, there are three chains (heavy, light chains of
antibody and the antigen) in the complex, my question is how to
put the sequences in the *.pir file so that it still identifies
different chains. It looks like Arp/wArp only accepts *.pir file
with one sequence id.
Thanks,
Tongqing
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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