Membrane topology (original) (raw)
Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB, OPM, and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. It is also possible to predict beta-barrel membrane proteins' topology.
| Property | Value |
|---|---|
| dbo:abstract | Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB, OPM, and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. Several computational methods were developed, with a limited success, for predicting transmembrane alpha-helices and their topology. Pioneer methods utilized the fact that membrane-spanning regions contain more hydrophobic residues than other parts of the protein, however applying different hydrophobic scales altered the prediction results. Later, several statistical methods were developed to improve the topography prediction and a special alignment method was introduced. According to the positive-inside rule, cytosolic loops near the lipid bilayer contain more positively-charged amino acids. Applying this rule resulted in the first topology prediction methods. There is also a negative-outside rule in transmembrane alpha-helices from single-pass proteins, although negatively charged residues are rarer than positively charged residues in transmembrane segments of proteins. As more structures were determined, machine learning algorithms appeared. Supervised learning methods are trained on a set of experimentally determined structures, however, these methods highly depend on the training set. Unsupervised learning methods are based on the principle that topology depends on the maximum divergence of the amino acid distributions in different structural parts. It was also shown that locking a segment location based on prior knowledge about the structure improves the prediction accuracy. This feature has been added to some of the existing prediction methods. The most recent methods use consensus prediction (i.e. they use several algorithm to determine the final topology) and automatically incorporate previously determined experimental informations. HTP database provides a collection of topologies that are computationally predicted for human transmembrane proteins. Discrimination of signal peptides and transmembrane segments is an additional problem in topology prediction treated with a limited success by different methods. Both signal peptides and transmembrane segments contain hydrophobic regions which form α-helices. 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), the errors caused by cross-prediction are reduced and the performance is substantially increased. Another feature used to increase the accuracy of the prediction is the homology (PolyPhobius).” It is also possible to predict beta-barrel membrane proteins' topology. (en) |
| dbo:thumbnail | wiki-commons:Special:FilePath/Group_1_and_2_transmembrane_protein.png?width=300 |
| dbo:wikiPageID | 169448 (xsd:integer) |
| dbo:wikiPageLength | 10530 (xsd:nonNegativeInteger) |
| dbo:wikiPageRevisionID | 1112456915 (xsd:integer) |
| dbo:wikiPageWikiLink | dbr:Endomembrane_system dbr:Integral_membrane_protein dbr:Protein_topology dbr:Signal_peptide dbr:Orientations_of_Proteins_in_Membranes_database dbc:Integral_membrane_proteins dbc:Membrane_biology dbr:Transmembrane_protein dbr:Biological_membrane dbc:Molecular_topology dbr:Unsupervised_learning dbr:Uniprot dbr:Supervised_learning dbr:File:Group_1_and_2_transmembrane_protein.png |
| dbp:wikiPageUsesTemplate | dbt:Cleanup_bare_URLs dbt:Reflist |
| dcterms:subject | dbc:Integral_membrane_proteins dbc:Membrane_biology dbc:Molecular_topology |
| rdf:type | yago:Abstraction100002137 yago:Chemical114806838 yago:Compound114818238 yago:Macromolecule114944888 yago:Material114580897 yago:Matter100020827 yago:Molecule114682133 yago:OrganicCompound114727670 yago:Part113809207 yago:PhysicalEntity100001930 yago:Protein114728724 yago:Relation100031921 yago:WikicatIntegralMembraneProteins yago:Substance100019613 yago:Thing100002452 yago:Unit109465459 |
| rdfs:comment | Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB, OPM, and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. It is also possible to predict beta-barrel membrane proteins' topology. (en) |
| rdfs:label | Membrane topology (en) |
| owl:sameAs | freebase:Membrane topology yago-res:Membrane topology wikidata:Membrane topology https://global.dbpedia.org/id/4ragn |
| prov:wasDerivedFrom | wikipedia-en:Membrane_topology?oldid=1112456915&ns=0 |
| foaf:depiction | wiki-commons:Special:FilePath/Group_1_and_2_transmembrane_protein.png |
| foaf:isPrimaryTopicOf | wikipedia-en:Membrane_topology |
| is dbo:wikiPageDisambiguates of | dbr:Topology_(disambiguation) |
| is dbo:wikiPageRedirects of | dbr:Transmembrane_topology |
| is dbo:wikiPageWikiLink of | dbr:Anion_exchanger_family dbr:List_of_words_with_the_suffix_-ology dbr:UniProt dbr:Index_of_biochemistry_articles dbr:Index_of_biophysics_articles dbr:ORF7b dbr:Protein_topology dbr:Coronavirus_envelope_protein dbr:Coronavirus_membrane_protein dbr:Membranome_database dbr:Orientations_of_Proteins_in_Membranes_database dbr:Structural_biology dbr:CD36 dbr:Dispanin dbr:Cell_surface_receptor dbr:Transmembrane_protein dbr:Topology_(disambiguation) dbr:CD133 dbr:SLC46A3 dbr:Transmembrane_domain dbr:Transmembrane_topology |
| is foaf:primaryTopic of | wikipedia-en:Membrane_topology |
