Thanks Victor - for giving a rational and detailed explanation. I obviously got carried away with the number of alanines to intersperse!
With regards,
Tony.
On 19 Apr 2012, at 16:52, "Victor Lamzin" <[log in to unmask]> wrote:
> 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" <[log in to unmask]>:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> 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]"
>>> <[log in to unmask]> 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
>>
>> GPG Key ID = A46BEE1A
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr
>> 3cDlEfHVVWxASrw9qxMTwMY=
>> =sFT8
>> -----END PGP SIGNATURE-----
>>
|