Dear Xavier, Great point and reminder! Thanks, Debanu
> On Feb 1, 2017, at 6:44 AM, Boaz Shaanan <bshaa...@bgu.ac.il> wrote: > > Hi, > One possible (formal, I should say) way around this would be to use one of > the homology modeling servers (my favourite recently is phyre2 but go for any > server you prefer) and feed it with the sequence of the protein in your > structure as if you're trying to get its structure in the''apo'' form (a > wrong term, as was pointed out on the bb recently). I'm quite certain that > with the degree of conservation you mentioned it'll superpose extremely well > on the other ''apo'' structure. This should satisfy the referee I would think > (it's not me though). > Cheers, > Boaz > > > -------- Original message -------- > From: Guillermo Montoya <guillermo.mont...@cpr.ku.dk> > Date: 01/02/2017 07:40 (GMT+02:00) > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] comparison of different protein states > > > Dear all, > > first of all sorry for this off-topic question. I am requesting your help to > find some papers to convince one referee about the comparison > of two different protein states. > > In our manuscript we show the crystal structure of an > enzyme. This structure represents the enzyme after catalysis in complex with > the product. > In the discussion we have superimposed the enzyme in the apo conformation > and the enzyme after catalysis in complex with the product > and we have commented the conformational changes observed > between these 2 states to propose a model. > > The point of the referee is that this comparison is not valid because the > enzymes that we used in the comparison belong to different species. > They are not the same protein. > > However, and this is stated by us in the figs and the manuscript, these two > proteins are > 40% identical and 60% conserved, the polypeptide length is the same, and > the key amino acids and the domain structure are fully conserved. They are > obviously orthologs. > > I´d really appreciate if you can send me some literature/information > to support our approach > > Thanks a lot for your input > > > best > > > > > Guillermo Montoya, Prof., Dr. > Research Director, Protein Structure and Function Programme > Novo Nordisk Foundation Center for Protein Research > Faculty of Health and Medical Sciences, University of Copenhagen, > Blegdamsvej 3A, DK-2200 Copenhagen, Denmark > web: www.cpr.ku.dk > > > >
