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 methods were developed to improve the topography prediction and 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 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.[11] 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.[12][13][14][15] Unsupervised learning methods are based on the principle that topology depends on the maximum divergence of the amino acid distributions in different structural parts.[16][17] It was also shown that locking a segment location based on prior knowledge about the structure improves the prediction accuracy.[18] This feature has been added to some of the existing prediction methods.[19][20] The most recent methods use consensus prediction (i.e. they use several algorithm to determine the final topology) [21] and automatically incorporate previously determined experimental informations.[22] HTP database[23][24] 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.[25] 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[26]), 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.[27][28]

See also

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. ↑ Baker, James Alexander; Wong, Wing-Cheong; Eisenhaber, Birgit; Warwicker, Jim; Eisenhaber, Frank (2017). "Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"". BMC Biology. 15 (1): 66. doi:10.1186/s12915-017-0404-4.
  12. ↑ Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
  13. ↑ TMHMM server
  14. ↑ Phobius server
  15. ↑ OCTOPUS server
  16. ↑ Principles governing amino acid composition of integral membrane proteins: application to topology prediction
  17. ↑ HMMTOP server
  18. ↑ The HMMTOP transmembrane topology prediction server
  19. ↑ HMMTOP server
  20. ↑ Phobius server
  21. ↑ TOPCONS server
  22. ↑ CCTOP server
  23. ↑ The human transmembrane proteome
  24. ↑ The human transmembrane proteome database
  25. ↑ Topology Prediction of Helical Transmembrane Proteins: How Far HaveWe Reached? Archived 2016-02-06 at the Wayback Machine.
  26. ↑ http://phobius.sbc.su.se/
  27. ↑ Tsirigos, K.D. "PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins". Retrieved 4 August 2017.
  28. ↑ Savojardo C, Fariselli P, Casadio R (February 2013). "BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes". Bioinformatics. 29 (4): 504–5. doi:10.1093/bioinformatics/bts728. PMID 23297037.
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