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A transmembrane domain (TMD, TM domain) is a membrane-spanning protein domain.TMDs may consist of one or several alpha-helices or a transmembrane beta barrel.Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues.
For example, the "unfolded" bacteriorhodopsin in SDS micelles has four transmembrane α-helices folded, while the rest of the protein is situated at the micelle-water interface and can adopt different types of non-native amphiphilic structures. Free energy differences between such detergent-denatured and native states are similar to stabilities ...
Tetraspanins are a family of membrane proteins found in all multicellular eukaryotes also referred to as the transmembrane 4 superfamily (TM4SF) proteins. These proteins have four transmembrane alpha-helices and two extracellular domains, one short (called the s mall e xtracellular d omain or l oop, SED/SEL or EC1) and one longer, typically 100 ...
The pore module is composed of the last two transmembrane helices, an extracellular cap domain, and an intracellular C-terminal domain. [6] [7] PIEZO1 functions as a non-selective cation channel capable of conducting both monovalent and divalent cations, including Na+, K+, and Ca2+. The mechanosensitivity of PIEZO1 is a defining characteristic.
The transmembrane domain is the smallest at around 25 amino acid residues and forms an alpha helix inserted into the membrane bilayer. The ECD is typically much larger than the ICD and is often globular, whereas many ICDs have relatively high disorder. [10] Some proteins in this class function as monomers, but dimerization or higher-order ...
The membrane-spanning segments, designated S1-S6, all take the form of alpha helices with specialized functions. The fifth and sixth transmembrane segments (S5 and S6) and pore loop serve the principal role of ion conduction, comprising the gate and pore of the channel, while S1-S4 serve as the voltage-sensing region.
In molecular biology, ATP-binding domain of ABC transporters is a water-soluble domain of transmembrane ABC transporters. ABC transporters belong to the ATP-Binding Cassette superfamily, which uses the hydrolysis of ATP to translocate a variety of compounds across biological membranes. ABC transporters are minimally constituted of two conserved ...
This causes the cross-prediction between them, which is a weakness of many transmembrane topology predictors. By predicting signal peptides and transmembrane helices simultaneously (Phobius [14]), the errors caused by cross-prediction are reduced and the performance is substantially increased. Another feature used to increase the accuracy of ...