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New alignment strategy for transmembrane proteins.

Authors
  • Cserzö, M
  • Bernassau, J M
  • Simon, I
  • Maigret, B
Type
Published Article
Journal
Journal of molecular biology
Publication Date
Oct 28, 1994
Volume
243
Issue
3
Pages
388–396
Identifiers
PMID: 7966267
Source
Medline
License
Unknown

Abstract

In this paper an algorithm which locates helical transmembrane segments is described. It is shown that given the location of transmembrane helices of a protein, corresponding helices in another membrane related protein can be pinpointed. The method seems to be extremely insensitive to sequence identity but highly sensitive to the property of a sequence to assume transmembrane helical structure. As an example, using the present method, a sequence alignment between bacteriorhodopsin and human rhodopsin is carried out and it provides a good starting point for homology modeling of this G-protein coupled receptor. It is difficult to obtain this particular alignment using the traditional methods because of poor sequence homology. There are indications that hint at the broader range of applicability of the presented method.

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