Membrane topology

Topology of a transmembrane protein refers to orientations (locations of N- and C-termini) of membrane-spanning segments with respect to the inner or outer sides of the biological membrane occupied by the protein.^[1][2]

Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB,^[3][4][5] OPM, and ExTopoDB.^[6][7] There is also a database of domains located conservatively on a certain side of membranes, TOPDOM.^[8]

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 method was developed to improve the topography prediction, as well as a special alignment method was introduced.^[9] According to the positive-inside rule,^[10] cytoslic loops near the lipid bilayer contain more positively charged amino acids. Applying this information resulted in the first topology prediction methods. 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 used.^{[11][12][13][14]} Unsupervised learning methods are based on the principle that topology depends on the maximum divergence of the amino acid distributions in different structural parts.^[15][16] It was also shown that locking a segment location based on prior knowledge about the structure improves the prediction accuracy.^[17] This feature has been added to some of the existing prediction methods.^[18][19] The most recent methods use consensus prediction (i.e. they use several algorithm to determine the final topology) ^[20] and automatically incorporate previously determined experimental informations.^[21] HTP database^[22][23] provides a collection of topologies that are computationally predicted for human transmembrane proteins.

Discrimination of hydrophobic signal peptides and transmembrane segments is an additional problem in topology prediction treated with a limited success by different methods.^[24]

It is also possible to predict beta-barrel membrane proteins' topology.^[25]

See also

• Protein topology

References

1. Membrane-protein topology by Gunnar von Heijne
2. Membrane-protein topology by Gunnar von Heijne
3. TOPDB: topology data bank of transmembrane proteins
4. Expediting topology data gathering for the TOPDB database
5. TOPDB database
6. ExTopoDB: a database of experimentally derived topological models of transmembrane proteins
7. ExTopoDB
8. TOPDOM database
9. DAS
10. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology
11. Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
12. TMHMM server
13. Phobius server
14. OCTOPUS server
15. Principles governing amino acid composition of integral membrane proteins: application to topology prediction
16. HMMTOP server
17. The HMMTOP transmembrane topology prediction server
18. HMMTOP server
19. Phobius server
20. TOPCONS server
21. CCTOP server
22. The human transmembrane proteome
23. The human transmembrane proteome database
24. Topology Prediction of Helical Transmembrane Proteins: How Far HaveWe Reached?
25. Bagos, P.G. "PRED-TMBB, A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins.". Retrieved 4 August 2012.