Schematic of the topology of the SCP-fold, location of the <i>c</i>ysteine-rich secretory proteins, <i>a</i>ntigen 5, and <i>p</i>athogenesis-related 1 proteins (CAP) motifs and approximate position of conserved cysteine residues in the primary structure.

<p>The proposed classification of groups of trematode SCP/TAPS proteins is supported by the occurrence of conserved cysteine residues. The grouping of hookworm SCP/TAPS proteins has been reported recently <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031164#pone.0031164-Osman1" target="_blank">[63]</a>. For the hookworm SCP/TAPS proteins, the cysteine connectivity in the intra-molecular disulphide bonds is known from experimental three-dimensional structures and shown by colour-mapping. The likely cysteine connectivity for trematode SCP/TAPS is hypothetical and based on the modelling in this study.</p

The phylogenetic relationships of single-domain SCP/TAPS proteins (>120 amino acids in length) predicted from the transcriptomes of <i>Clonorchis sinensis</i>, <i>Opisthorchis viverrini</i>, <i>Fasciola hepatica</i> and <i>F. gigantica</i> (liver flukes) and the genomes of <i>Schistosoma mansoni</i>, <i>S. japonicum</i> and <i>S. haematobium</i> (blood flukes) based on Bayesian inference.

<p>Group 1 (a); group 2 (b); group 3 (c); group 4 (d). The posterior probability supporting each clade is indicated. The corresponding phylogenetic reconstructions conducted using Neighbour Joining analyses of single-domain SCP/TAPS proteins are available from the primary author upon request.</p

Homology models for the molecule c962 from <i>Opisthorchis viverrini</i>.

<p>Top row: the models are rendered in cartoon representation with cysteine side chains shown as bars in grey. The colour mapping ramps from blue (N-terminal end) to red (C-terminal end). Bottom row: surface representation of the models is in the same orientation as in the top row. The electrostatic surface potential is mapped by colour (blue: positive charge; red: negative charge). The left panel shows a homology model using <i>Na</i>-ASP-2 (PDB code: 1u53) as a template without restraint. For the model shown in the right panel, two restraints were applied to force disulphide bonds between the remaining cysteine residues. The comparison of both models highlights the significant differences in conformation and shape resulting from different template restraints applied. The images were generated using PyMOL [<a href="http://www.pymol.org/" target="_blank">http://www.pymol.org/</a>].</p