Hi,Just to get this out of the way, I am not an expert on GPCR and have never attempted to model them. Still, I suggest you look at my arguments below.
At 09:03 AM 2/2/2006, you wrote:
Hi Guillaume, I'm a little confuse about your explanation...the gap is real or not?Hi Helena, and thank you for answering my unclear question.Probably you will need to write to those who modelled the structures before to ask about this gap. i think is really unusual that someone could published structures that have wrong alignments...This is right, i should probably have started here.I was very surprised by these data, and i've checked every possible confusion, but there's no doubt i'm working on the same structure and sequences. For me, the gap in the helix is really obvious, although it seems to have been ignored in previous papers.here's the 'reference' alignment of the helix sequence found in the literatture :> PLNYILLNLAVADLFMVFGGFTTTLYTSLH > VNNYFLLSLACADLIIGTFSMNLYTTYLLM ** ** ** *** . * and here's the one I use : > PLNYILLNLAVADLFMVFGGFTTTLYTSLH-- > VNNYFLLSLACADL--IIGTFSMNLYTTYLLM ** ** ** *** : * *: ***:
As a general argument, just because an alignment has more true matches does not mean that it is correct. There are penalties associated with those two gaps you introduced that offset the gain from exact residue matching. Not knowing exactly which sequence you are modeling, I submitted P11229 (ACM1_HUMAN) to the SUPERFAMILY server and the alignment come back with no gaps in that region. Take a look at:
http://www.supfam.org/SUPERFAMILY/cgi-bin/gene.cgi?genome=up;seqid=P11229and follow the "Align" link. Obviously, the same can be done for any protein for which you know the SwissProt number by simply inserting it at the end of the link above. Not to get into prolonged argument here, I'll just say that I would trust SUPERFAMILY-based alignment over any human-derived alignment unless there is a very good reason to believe that the server alignment is wrong. And breaking a long helix to make few extra positive matches usually doesn't qualify as a good reason, especially because it forces you to make a compensatory two-residue gap later in the model. But don't take my word for it, try modeling the protein with and without those gaps and see which model evaluates better.
Hope this helps, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: | ==========================================================================