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.

Figure 1

Average hydropathy, amphipathicity and similarity plots using the AveHAS program for (A) the sugar porter family in the MFS, (B) The APC family in the APC superfamily, (C) the mitochondrial carrier (MC) family within the MC superfamily, (D) the Trk family in the VIC superfamily (see TCDB).

Figure 2

Comparative distribution of topological types predicted using the TMStats program for HMMTOP in black, MEMSAT in white and SPOCTOPUS in grey, for the proteins included in subclass 1.A of TCDB as of 5/29/2013.

Figure 3

Comparative distribution of topological types predicted using the TMStats program for HMMTOP in black, MEMSAT in white and SPOCTOPUS in grey, for the proteins included in subclass 1.E of TCDB as of 5/29/2013.

Figure 4

Comparative distribution of topological types predicted using the TMStats program for HMMTOP in black, MEMSAT in white and SPOCTOPUS in grey, for the proteins included in subclass 1.C of TCDB as of 5/29/2013.

Figure 5

Comparative distribution of topological types predicted using the TMStats program for HMMTOP in black, MEMSAT in white and SPOCTOPUS in grey, for the proteins included in subclass 2.A of TCDB as of 5/29/2013.

Figure 6

Schematic depiction of the proposed pathway for the evolution of transport proteins including different types of channel-forming proteins and secondary carriers. We further propose that primary active transport carriers and group translocators arose by the superimposition of energy coupling enzymes such as ATPases. Finally, the integration of these systems into metabolic pathways resulted in the physical construction of complex but coordinated metabolons.