Topology of a membrane protein refers to location of N-terminus of the protein at the cytosolic or non-cytosolic sides of the biological membrane occupied by the protein.1 For example, topology of a protein attached to the cell plasma membrane indicates location of its N-terminus at the cytoplasmic or extracellular side of the membrane. Every individual transmembrane segment of a protein also has topology, depending on location of its N-terminus on the inner or outer side of the membrane. There are several databases which provide topologies of membrane proteins including Uniprot, TOPDB23 and ExTopoDB.4 There are several computational methods for predicting transmembrane domains, both for helices and β-barrels.56
- Membrane-protein topology by Gunnar von Heijne
- TOPDB: topology data bank of transmembrane proteins
- TOPDB database
- ExTopoDB: a database of experimentally derived topological models of transmembrane proteins
- Links to topology prediction methods in Expasy
- Bagos, P.G. "PRED-TMBB, A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins.". Retrieved 4 August 2012.