pdb-l: minimal transmembrane helix length?

[Andrei Lomize]

Hi Mario,

A transmembrane helix can be as short as 11 residues, for example, 193-203
in Cl channel (1kpl PDB file) or 77-87 in aquaporin  (1h6i).  They
can be so short, because their folding and insertion into the membrane is
facilitated by interactions with the rest of the transmembrane protein.

At the same time, there are probably some minimum length requirements
for a SINGLE transmembrane helix to be inserted into bilayer
in vivo (i.e. via translocon).  At least, the insertion efficiency
decreases when the helix is broken by prolines (see recent paper in Nature
v. 433, p.377). As for insertion of a single helix in vitro, there are
also some very strict length limitations (see discussion
of negative hydrophobic mismatch in Molecular Membrane Biology v. 20.
p.271), in addition to the "hydrophobicity cutoff". However, you should
keep in mind that many individual TM helices are not required (and in fact
can not) be folded and inserted to the membrane independently
on others, i.e. as separate peptides. This was shown to be the
case for at least three TM helices from bacteriorhodopsin.
That is why the prediction of TM helices is not simple.

Andrei

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Andrei Lomize                            Phone: (734)615-7194
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On Wed, 9 Mar 2005, Mario Albrecht wrote:

> Dear all,
>
> Do you know what may be the minimal reasonable length
> (number of amino acids) of a transmembrane helix
> located in the cell membrane or ER membrane?
>
> Thanks a lot for your help,
>
>   Mario
>
>
>
>
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