Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from ''

Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

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Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...

'', ''

Dictyostelium discoideum ''Dictyostelium discoideum'' is a species of soil-dwelling amoeba belonging to the phylum Amoebozoa, infraphylum Mycetozoa. Commonly referred to as slime mold, ''D. discoideum'' is a eukaryote that transitions from a collection of unicellular ...

'', ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

'', ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

'' and ''

Methanocaldococcus jannaschii ''Methanocaldococcus jannaschii'' (formerly ''Methanococcus jannaschii'') is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon to have its complete genome sequenced. The sequencing identified many genes u ...

''. 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 Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellula ...

and communication between cells in

multicellular organisms A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni- ...

. The database provides information about the individual proteins including computationally generated three-dimensional models of their transmembrane

alpha-helices The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...

spatially arranged in the membrane,

topology In mathematics, topology (from the Greek language, Greek words , and ) is concerned with the properties of a mathematical object, geometric object that are preserved under Continuous function, continuous Deformation theory, deformations, such ...

, intracellular localizations,

amino acid sequence Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...

s, domain architecture, functional annotation and available experimental structures from the

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

. 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. The second Membranome version''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 Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

'', volume: 34, issue: 6 pages: 1061-1062. 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.''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 The models of the homodimers were verified through comparison with available experimental data for nearly 600 proteins.Dimer verification page of Membranome
/ref> The database includes downloadable coordinate files of transmembrane helices and their homodimers with calculated membrane boundaries. The database website provides access to related webservers, FMAP''Thermodynamic model of secondary structure for alpha-helical peptides and proteins'', by Lomize, AL and Mosberg, HI,

Biopolymers Biopolymers are natural polymers produced by the cells of living organisms. Like other polymers, biopolymers consist of monomeric units that are covalently bonded in chains to form larger molecules. There are three main classes of biopolymers, cl ...

, vol 42, issue: 2, pages: 239-269 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 proteinsEvolution 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 ''Scientific Reports'' is a peer-reviewed open-access scientific mega journal published by Nature Portfolio, covering all areas of the natural sciences. The journal was established in 2011. The journal states that their aim is to assess solely th ...

, vol. 7, article number: 6864

References

{{reflist Model organism databases Biological databases Single-pass transmembrane proteins Protein classification