PRED-TMBB: a web server for predicting the topology of  -barrel outer membrane proteins

Abstract

The beta-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for alpha-helical membrane proteins, currently there is no freely available prediction method for beta-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane beta-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer.

Paralogous Outer Membrane Proteins Mediate Uptake of Different Forms of Iron and Synergistically Govern Virulence in Francisella tularensis tularensis

“…The PRED-TMBB program (40,41) predicts that these proteins form ␤-barrels with large periplasmic plugs of 152 residues and 201 residues for FslE and FupA, respectively. Our studies with 55 Fe transport in conjunction with the predicted structure of the proteins have confirmed the role of FslE as the siderophore receptor and identified FupA as a high affinity ferrous iron transporter in Schu S4.…”

Identification of critical amino acid residues in the plague biofilm Hms proteins

“…HmsH is predicted to form a b-barrel protein with a large Nterminal periplasmic domain (Bagos et al, 2004;Kirillina et al, 2004). Our mutagenesis study concentrated on this periplasmic domain to avoid a loss of phenotype due to disruption of the b-barrel structure.…”

Membrane protein prediction methods

“…Bagos et al assessed the ability of the methods to predict the location of the TM regions of beta-strands, as determined by PDB_TM (94). With the above factors as caveats, the study made one major conclusion: the top three methods namely, HMM-B2TMR (95), ProfTMB (93) and PRED-TMBB (91), are HMM-based and far outperform NN-and SVM-based methods in predicting topology and number of strands correctly.…”

“…http://www.bioinfo.no/tools/bomp WP PRED-TMBB (91) http://bioinformatics2.biol.uoa.gr/PRED-TMBB PR3 PROFtmb (93) http://rostlab.org/services/proftmb PR3, WP TMB-HUNT (156,157) http://www.bioinformatics.leeds.ac.uk/ WP * The methods in this Table are recommended either because they stood out in independent assessments or because otherwise interesting. See Table 3 for legend.…”