Computational protocol: Prediction of β-barrel membrane proteins by searching for restricted domains

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Protocol publication

[…] In order to evaluate the prediction, the following sequence pools were created with a redundancy of maximal 50%. From the TMPDB [] databank we retrieved the file TMPDB_alpha_nr_PR.dat [] which contains a set of α-helical transmembrane proteins. We further collected all OM proteins from the experimentally verified ePSortdb dataset v2.0 [] and removed proteins that are clearly no integral OM proteins and proteins marked as hypothetical. From the same databank all available proteins of the cytoplasmic membrane and the cytoplasm of Gram-negative bacteria were downloaded.From PDB [,] (version 01/11/2005) we retrieved globular proteins. By SCOP [] classification we downloaded from PDB proteins with transmembrane helices and all available transmembrane β-barrels.As mentioned above, we removed all proteins with more than one transmembrane helix predicted by TMHMM and with less than 80 amino acids. Of the initially 1.235 proteins, 782 survived these steps.All proteins that are not β-barrel membrane proteins and are not from PDB were accumulated in one sequence pool. They are referred to as PSort NOM protein pool. The OM proteins of PSort and PDB were kept each in separate pools. [...] The BSHS value is derived by calculating the individual score for the β-strand starting at amino acid z. The β-strand position was assigned by the in here redesigned BSN algorithm. X strand ( aa = z ) = ∑ i = 0 4 ( aa ( z + ( i * 2 + 1 ) ) − aa ( z + ( i * 2 ) ) ) / 10       ( E 1 ) [email protected]@[email protected]@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=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[email protected][email protected] using the water/octanol transfer free energy scale [], multiplying the EBSS valueYstrand(aa=z) = |Xstrand (aa=z)| * EBSS(aa=z)     (E2)adding all values in a defined amino acid window (w) and normalize to that window B S H S ( w ) = ∑ aa = 1 w − 9 Y strand ( aa ) / w       ( E 3 ) [email protected]@[email protected]@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciGacaGaaeqabaqabeGadaaakeaaieaacqWFcbGqcqWFtbWucqWFibascqWFtbWudaWgaaWcbaGaeiikaGIaee4DaCNaeiykaKcabeaakiabg2da9maaqahabaGaeeywaK1aaSbaaSqaaiabbohaZjabbsha0jabbkhaYjabbggaHjabb6gaUjabbsgaKjabcIcaOiabbggaHjabbggaHjabcMcaPaqabaaabaGaeeyyaeMaeeyyaeMaeyypa0JaeGymaedabaGaee4DaCNaeyOeI0IaeGyoaKdaniabggHiLdGccqGGVaWlcqq[email protected][email protected] All scores were described earlier []. For transmembrane helix prediction TMHMM v. 2.0 was used [,]. […]

Pipeline specifications

Software tools TMHMM, PSORT, EMBOSS
Databases TMPDB
Applications Protein sequence analysis, Membrane protein analysis
Organisms Escherichia coli