Membranome database
| Content | |
|---|---|
| Description | Data about single-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 the Wayback Machine |
| Tools | |
| Web | FMAP and TMDOCK |
| Miscellaneous | |
| Version | 3.0 |
| Curation policy | Curated |
Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus 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 the signal transduction and communication between cells in multicellular organisms.
The database provides information about the individual proteins including computationally generated three-dimensional models of their transmembrane alpha-helices spatially arranged in the membrane, topology, intracellular localizations, amino acid sequences, domain architecture, functional annotation and available experimental structures from the Protein 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 protein complexes 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 by AlphaFold 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]
References
[edit]- ^ a b Lomize, Andrei L; Lomize, Mikhail A; Krolicki, SR; Pogozheva, Irina D. (2017). "Membranome: a database for proteome-wide analysis of single-pass membrane proteins". Nucleic Acids Res. 45 (D1): D250–D255. doi:10.1093/nar/gkw712. PMC 5210604. PMID 27510400.
- ^ Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers, by: Lomize, Andrei L., Hage, Jacob M., Pogozheva, Irina D., Bioinformatics, volume: 34, issue: 6 pages: 1061-1062.
- ^ TMDOCK: An Energy -Based Method for Modeling alpha-Helical Dimers in Membranes, by Lomize, Andrei L. and Pogozheva, Irina D., J. Mol. Biol., Volume: 429 Issue: 3, pages: 390-398
- ^ Dimer verification page of Membranome
- ^ Lomize, A. L.; Schnitzer, K. A.; Todd, S. C.; Cherepanov, S.; Outeiral, C.; Deane, C. M.; Pogozheva, I. D. (2022). "Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models". Protein Science. 31 (5): e4318. doi:10.1002/pro.4318. PMC 9047035. PMID 35481632.
- ^ Thermodynamic model of secondary structure for alpha-helical peptides and proteins, by Lomize, AL and Mosberg, HI, Biopolymers, vol 42, issue: 2, pages: 239-269
- ^ Evolution and adaptation of single-pass transmembrane proteins, by: Pogozheva, Irina D. and Lomize, Andrei L., Biochimica et. Biophysica Acta Biomembranes, Volume: 1860 Issue: 2 Pages: 364-377
- ^ Membrane proteins structures: A review on computational modeling tools, by Almeida, Jose G.; Preto, Antonio J., Koukos, Panagiotis I., Bonvin, Alexandre M. J. J., Moreira, Irina S. Biochimica et. Biophysica Acta, vol. 1859, issue: 10, pages: 2021-2039
- ^ NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins, by Lesovoy, D. M., Mineev, K. S., Bragin, P. E., Bocharova, O. V., Bocharov, E. V., Arseniev, A. S., J. Biomol. NMR, vol. 69, issue: 3, pages 165-179
- ^ Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism, by Mineev, Konstantin S., Goncharuk, Sergey A., Goncharuk, Marina V., Volynsky, Pavel E., Novikova, Ekaterina V., Arseinev, Alexander S., Scientific Reports, vol. 7, article number: 6864