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Transmembrane helix
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Within an integral membrane protein, a transmembrane helix is an alpha helix that passes through or "spans" a membrane such as that of a cell or an organelle.
Transmembrane helices are usually about 20 amino acids in length[citation needed], although they may be much longer or shorter. Whilst a lone transmembrane helix will contact the lipid bilayer all around, if a bundle of such helices are present the innermost ones may interact with the membrane little, if at all.
Transmembrane helices are visible in structures of membrane proteins determined by X-ray diffraction. They may be also predicted on the basis of hydrophobicity. Because the interior of the bilayer and the interiors of most proteins of known structure are hydrophobic, it is presumed to be a requirement of the amino acids that span a membrane that they be hydrophobic as well. However, membrane pumps and ion channels also contain numerous charged and polar residues within the generally non-polar transmembrane segments.
Using hydrophobicity analysis to predict transmembrane helices enables a prediction in turn of the "transmembrane topology" of a protein; i.e. prediction of what parts of it protrude into the cell, what parts protrude out, and how many times the protein chain crosses the membrane. Such prediction methods are commonly applied with a limited success.
The Bioinformatics package STRAP provides access to 15 different TM-helix prediction algorithms.