Editing Transmembrane domain (section)

==Identification of transmembrane helices==
Transmembrane helices are visible in structures of membrane proteins determined by [[X-ray crystallography|X-ray diffraction]]. They may also be predicted on the basis of [[hydrophobicity scales]]. Because the interior of the [[Lipid bilayer|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, [[Active transport|membrane pump]]s and [[ion channel]]s also contain numerous charged and polar residues within the generally non-polar transmembrane segments.

Using [[hydrophilicity plot|"hydrophobicity analysis"]] to predict transmembrane helices enables a prediction in turn of the [[membrane topology|"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.

Transmembrane helices can also be identified ''[[in silico]]'' using the [[Bioinformatics|bioinformatic]] tool, [https://services.healthtech.dtu.dk/service.php?TMHMM-2.0 TMHMM].<ref>{{cite journal | vauthors = Krogh A, Larsson B, von Heijne G, Sonnhammer EL | title = Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes | journal = Journal of Molecular Biology | volume = 305 | issue = 3 | pages = 567–80 | date = January 2001 | pmid = 11152613 | doi = 10.1006/jmbi.2000.4315 }}</ref>