Hi,
This is not a single-step procedure and as far as I know there are several ways to do this - but I would recommend first to build a model of the domain(s) you're interested in. That is, if you can do that. Based on the model you should be able to derermine the first (last) amino acids which 'do not make sense' in the context of the domain. Give a 1-2 aa 'safety margin' and use that. Pay attention to 'special' residues such as GPAS as well as to the predicted solvent exposure, flexibility score, etc. If you don't have a decent model then you may be able to use multiple alignments to deduce the boundaries. Typically (but not always) the domain-bound residues are conserved whereas linkers are not as conserved. However, this is not as good of a predictor as a homologous structure. In a desperate case you may have to resort to 'chopping' the ends up into 3 or 5-residue pieces and trying each subset individually. It's always a good idea to find an experienced molecular biologist and/or protein engineer and discuss the problem with them directly because there is a lot of personal knowledge and intuition involved in these kinds of predictions. I would be glad to take a look at your sequence confidentially. Cheers, Artem _____ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jayashankar Sent: Tuesday, May 20, 2008 1:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Right terminal residues for constructs. Dear friends and scientists, (A pre-Structural biological question.) I Have a multidomain protein , I know the domain boundaries, But am still not that rational to what residues a construct should start or end? But I have learned from people that changing one residue changes the fate of the construct. I will be greatful for the insights from the scientific community. I dont want to do any Directed evolution approach. -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
