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" <vic...@embl-hamburg.de> 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" <t...@shelx.uni-ac.gwdg.de>: > >> -----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]" >>> <tz...@mail.nih.gov> 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----- >>
