Re: [ccp4bb] comparison of different protein states

[Boaz Shaanan]

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