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How to predict transmembrane protein topology?

David J. States states at newsreader.wustl.edu
Sat Sep 30 01:32:56 EST 1995

bclong at uxmail.ust.hk (Terence) wrote:
>I often read in journals that a certain transmembrane topology is
>determined/predicted for a certain transmemnrane protein. ...

There are two classes of transmembrane domains, single alpha helical
membrane spanning segments, and more complex intrinsic membrane proteins
such as the G-protein coupled receptors.  The former can be identified
as an non-random strectch of hydrophobic amino acids.  Kyte and Doolittle
developed one of the earlier hydrophobicity scales and dmonstrated the
utility of this method.  Many PD and commercial implementation are
available now.

More complex domain can be identified either through sequence similarity
searches of the protein sequence database, by looking for hydrophobic
and amphipathic helices, or by searching with more complex sequence motifs 
such as hidden Markov models.


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