| Content | |
|---|---|
| Description | Data aboutsingle-span (bitopic) transmembrane proteins in genomes |
| Data types captured | All bitopic proteins from six model organisms |
| Organisms | Homo sapiens,Arabidopsis thaliana,Dictyostelium discoideum,Saccharomyces cerevisiae,Escherichia coli,Methanococcus jannaschii |
| Contact | |
| Research center | University of Michigan College of Pharmacy |
| Primary citation | PMID 27510400 |
| Release date | 2017 |
| Access | |
| Website | http://membranome.org |
| Download URL | Archived 16 July 2018 at theWayback Machine |
| Tools | |
| Web | FMAP andTMDOCK |
| Miscellaneous | |
| Version | 3.0 |
| Curation policy | Curated |
Membranome database provides structural and functional information about more than 6000single-pass (bitopic) transmembrane proteins fromHomo sapiens,Arabidopsis thaliana,Dictyostelium discoideum,Saccharomyces cerevisiae,Escherichia coli andMethanocaldococcus jannaschii.[1] Bitopic membrane proteins consist of a single transmembrane alpha-helix connecting water-soluble domains of the protein situated at the opposite sides of a biological membrane. These proteins are frequently involved in thesignal transduction and communication between cells inmulticellular organisms.
The database provides information about the individual proteins including computationally generated three-dimensional models of their transmembranealpha-helices spatially arranged in the membrane,topology,intracellular localizations,amino acid sequences,domain architecture, functional annotation and availableexperimental structures from theProtein Data Bank. It also provides a classification of bitopic proteins into 15 functional classes, more than 700 structural superfamilies and 1400 families, along with 3D structures of bitopic proteincomplexes which are also classified to different families.[1]The second Membranome version[2] provides 3D models of more than 2000 parallel homodimers formed by TM α-helices of bitopic proteins from different organisms which were generated using TMDOCK program.[3] The models of the homodimers were verified through comparison with available experimental data for nearly 600 proteins.[4] The database includes downloadable coordinate files of transmembrane helices and their homodimers with calculated membrane boundaries. Membranome 3.0 version incorporates models generated byAlphaFold 2.[5]
The database website provides access to related webservers, FMAP[6] and TMDOCK which have been developed for modeling individual alpha-helices and their dimeric complexes in membranes. The database and webservers were used in experimental and bioinformatics studies of bitopic membrane proteins[7][8][9][10]