NEW ALIGNMENT STRATEGY FOR TRANSMEMBRANE PROTEINS

In this paper an algorithm which locates helical transmembrane segment s is described. It is shown that given the location of transmembrane h elices of a protein, corresponding helices in another membrane related protein can be pinpointed. The method seems to be extremely insensiti ve to sequence identity but highly sensitive to the property of a sequ ence to assume transmembrane helical structure. As an example, using t he present method, a sequence alignment between bacteriorhodopsin and human rhodopsin is carried out and it provides a good starting point f or homology modeling of this G-protein coupled receptor. It is difficu lt to obtain this particular alignment using the traditional methods b ecause of poor sequence homology. There are indications that hint at t he broader range of applicability of the presented method.