New alignment strategy for transmembrane proteins.

M Cserzö; J M Bernassau; I Simon; B Maigret

doi:10.1006/jmbi.1994.1666

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New alignment strategy for transmembrane proteins.

M Cserzö·J M Bernassau·I Simon·B Maigret

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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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Algorithms Amino Acid Sequence Bacteriorhodopsins Humans Membrane Proteins Molecular Sequence Data Photosynthetic Reaction Center Complex Proteins Protein Structure, Secondary Rhodopsin Sequence Alignment Journal Article Research Support, Non-U.S. Gov't

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M Cserzö, J M Bernassau, I Simon, B Maigret. 1994-10-28. New alignment strategy for transmembrane proteins.. https://doi.org/10.1006/jmbi.1994.1666

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