Reliability of Nine Programs of Topological Predictions and Their Application to Integral Membrane Channel and Carrier Proteins

Abstract

We evaluated topological predictions for nine different programs, HMMTOP, TMHMM, SVMTOP, DAS, SOSUI, TOPCONS, PHOBIUS, MEMSAT-SVM (hereinafter referred to as MEMSAT), and SPOCTOPUS. These programs were first evaluated using four large topologically well-defined families of secondary transporters, and the three best programs were further evaluated using topologically more diverse families of channels and carriers. In the initial studies, the order of accuracy was: SPOCTOPUS > MEMSAT > HMMTOP > TOPCONS > PHOBIUS > TMHMM > SVMTOP > DAS > SOSUI. Some families, such as the Sugar Porter Family (2.A.1.1) of the Major Facilitator Superfamily (MFS; TC #2.A.1) and the Amino Acid/Polyamine/Organocation (APC) Family (TC #2.A.3), were correctly predicted with high accuracy while others, such as the Mitochondrial Carrier (MC) (TC #2.A.29) and the K⁺ transporter (Trk) families (TC #2.A.38), were predicted with much lower accuracy. For small, topologically homogeneous families, SPOCTOPUS and MEMSAT were generally most reliable, while with large, more diverse superfamilies, HMMTOP often proved to have the greatest prediction accuracy. We next developed a novel program, TM-STATS, that tabulates HMMTOP, SPOCTOPUS or MEMSAT-based topological predictions for any subdivision (class, subclass, superfamily, family, subfamily, or any combination of these) of the Transporter Classification Database (TCDB; www.tcdb.org) and examined the following subclasses: α-type channel proteins (TC subclasses 1.A and 1.E), secreted pore-forming toxins (TC subclass 1.C) and secondary carriers (subclass 2.A). Histograms were generated for each of these subclasses, and the results were analyzed according to subclass, family and protein. The results provide an update of topological predictions for integral membrane transport proteins as well as guides for the development of more reliable topological prediction programs, taking family-specific characteristics into account.

Mutational Analysis of the Shigella flexneri O-Antigen Polymerase Wzy: Identification of Wzz-Dependent Wzy Mutants

“…However, G130V is present in TM5, which was validated by all 5 of the programs. Recently, Reddy et al reported that different topology prediction programs are suitable for different families of proteins (37). Therefore, lack of prediction of TM7 to TM9 by some programs does not invalidate the presence of these regions in our model.…”

Brettanomyces bruxellensis SSU1Haplotypes Confer Different Levels of Sulfite Tolerance When Expressed in aSaccharomyces cerevisiae SSU1Null Mutant

“…To estimate if differences in the amino acid sequences of Ssu1p transporters were associated with protein topology, transmembrane domains were predicted using SPOCTOPUS (39). SPOCTOPUS is a method for the combined prediction of signal peptides and membrane protein topology suitable for whole-genome annotation, which has shown the highest accuracy prediction compared to similar methods (40).…”

Comparative genomic analyses of transport proteins encoded within the red algae Chondrus crispus, Galdieria sulphuraria, and Cyanidioschyzon merolae11

“…Though the WHAT program uses the HMMTOP program to highlight regions where predicted TMSs could be, this program sometimes predicts incorrectly, and it is ultimately up to the user to judge the actual TMS numbers (Reddy et al. ). An arbitrary criterion for a TMS would be a hydrophobic peak with a value of greater than 1 (Zhai and Saier ).…”