November 7, 2011
Comparing Apples with Oranges: B&W
Identifying individual amino acid residues within a GPCR and comparing these across different receptors is a routine task that’s helped by a widely accepted nomenclature system: that of Ballesteros and Weinstein.
Juan A. Ballesteros, Harel Weinstein (1995). Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors Methods in Neurosciences, 25, 366-428 DOI: 10.1016/S1043-9471(05)80049-7
You could look up the nomenclature rules in the original paper or find the rules online and apply them to the particular amino acid sequence you’re working with. This is a bit cumbersome, isn’t it?
Good news: here’s a simple way to check the Ballesteros&Weinstein nomenclature with the Sequence Tool provided by http://www.gpcr.org. Just call up the target sequence and hover over a particular amino acid to extract the Ballesteros&Weinstein(B&W) code:
A simple way to call up the Ballesteros&Weinstein(B&W) code for a particular amino acid in a GPCR target
I like simple.
Peter