Transmembrane helix
Encyclopedia
Transmembrane domain usually denotes a single transmembrane alpha helix
of a transmembrane protein
. It is called a "domain" because an alpha-helix in a membrane can fold independently from the rest of the protein, similar to domains of water-soluble proteins
. More broadly, a transmembrane domain is any three-dimensional protein structure which is thermodynamically stable in a membrane. This may be a single alpha helix, a stable complex of several transmembrane alpha helices, a transmembrane beta barrel
, a beta-helix of gramicidin A, or any other structure.
Transmembrane helices are usually about 20 amino acid
s in length, although they may be much longer or shorter.
. They may also be predicted on the basis of hydrophobicity scales
. 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.
Online transmembrane prediction algorithm servers are listed by Expasy
http://ca.expasy.org/tools/ under Topology prediction. The resulting predictions often differ and should be used with caution.
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
of a transmembrane protein
Transmembrane protein
A transmembrane protein is a protein that goes from one side of a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as...
. It is called a "domain" because an alpha-helix in a membrane can fold independently from the rest of the protein, similar to domains of water-soluble proteins
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
. More broadly, a transmembrane domain is any three-dimensional protein structure which is thermodynamically stable in a membrane. This may be a single alpha helix, a stable complex of several transmembrane alpha helices, a transmembrane beta barrel
Beta barrel
A beta barrel is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last.Beta-strands in beta-barrels are typically arranged in an antiparallel fashion...
, a beta-helix of gramicidin A, or any other structure.
Transmembrane helices are usually about 20 amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s in length, although they may be much longer or shorter.
Identification of transmembrane helices
Transmembrane helices are visible in structures of membrane proteins determined by X-ray diffractionCrystallography
Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...
. They may also be predicted on the basis of hydrophobicity scales
Hydrophobicity scales
Hydrophobicity scales are ranking lists for the relative hydrophobicity of amino acid residues. In general, the more positive the value, the more hydrophobic are the amino acids located in that region of the protein...
. 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"
Membrane topology
In biochemistry, the membrane topology of an transmembrane protein describes which portions of the amino-acid sequence of the protein lie within the plane of the surrounding lipid bilayer and which portions protrude into the watery environment on either side...
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.
Online transmembrane prediction algorithm servers are listed by Expasy
ExPASy
ExPASy is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences...
http://ca.expasy.org/tools/ under Topology prediction. The resulting predictions often differ and should be used with caution.