Discussion of SNAPG

The SNAP-gamma structure obtained Danio rerio possess 4 chains of alpha helical hairpins fold without any beta strands observed (Figure 1). Each chain was interconnected with one another via hydrogen bond and non-bonded contacts (PDBSum). The helices towards N-terminal end were connected by extended loops and those towards C-terminal end tend to form a globular bundle presumably forming a cleft. Two different types of ligand interact with SNAP-gamma differently. One of the ligand types, sulfanate ion (SO4), was found to from a distinct interaction with different residues in different chain (Figure 2 & 3). Meanwhile, selenomethione (MSE) ligands were integrated into protein structure as seem to appear as modified amino acid residues (Figure 2).

Although the protein structure of SNAP-gamma was already known, the function is still yet under investigations. Protein super families identification reveals that SNAP-gamma is made of 2 domains in which both of the domains had a soluble-NFS(N-ethylmaleimide-sensitive factor)-attachment-protein (SNAP) activity. The sequence conservation against the protein super families (Figure 15) suggests that SNAP proteins may have a conserved 3D shape. Structural alignment against a representative structure in PDB databases using Dali web server shows several proteins with acknowledged protein function and domains shares structure similarity with SNAP-gamma protein (Table 1). For this study purpose, two proteins with highest statistical significance of the match (Z-value) were chosen. A vesicular transport protein sec17 found in yeast and type 4 fimbrial biogenesis protein pili in Pseudomonas aeruginosa had a Z-value of 23.3 and 12.9; and shares 23 and 14 respectively %identity with SNAP-gamma. Structure-based alignment of these structures indicates similar secondary structure and motifs (Figure 5&6). In regards of SNAP-gamma and sec17 surface properties proximity (Figure 7&8), it suggest that both of these proteins may have similar protein-protein interaction. However, the amino acid conservation were not satisfying (Figure 5) suggesting the function can not be determined based on structure alignment alone.

The SNAP-gamma hydrophobicity and electrostatic potential properties were distributed throughout majority of SNAP-gamma residues. These features may be important for examination of possible SNAP-gamma biological function. Large hydrophobic surface area, as shown by Figure 7.A, may contributes to ligands recognition and binding. Vast majority of SNAP-gamma negative electrostatic potentials (Figure 9) and cleft binding predictions (Figure 10) towards C-terminal end gave an insight of protein possibility to bind with another protein, but not DNA, at this region. The DNA enveloped by negative electrostatic potential just like SNAP-gamma suggests its implausibility to form an interaction with one another . This also supported by ProFunc results of which there was no HTH (helix-turn-helix) motif, which resembles DNA-binding protein, found in the structure. These finding agrees with study done by Tani in 2003 that characterized SNAP-gamma interactions with NSF via its extreme C-terminal region.

Figure 1. Evolutionary analysis of the tree with radial view. Red dotted signs means bootstrap value more than 75% or 75.00

SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent the branching tree which has more than 75% bootstrap value. The value was to measure the consistently data compare with the branching tree patterns. As an example: in the diagram phylogenetic tree (see Figure 3), there is 39.0 boostrap value in branching Apis melifera and Tribolium castaneum. The boostrap value is below 75%, thus it could be concluded that the degree of confidence of branching tree in the correct order is far below 95%. On the other hand, boostrap value more than 75% or 75.00 means 95% confidence that the branching tree is in the correct order. It means, if in certain branch and the organism include in this branch have bootstrap value more than 95%, nearly all the informative sequence of this group agree that it is the group.

As indicated in diagram in Figure 1, SNAP-gamma protein was evolved in eukaryotes. There is no prokaryotes organism detected in the phylogenetic tree. The SNAPG protein was detected in lower eukaryotes until higher eukaryotes. Interestingly, SNAPG protein has similar function although it evolved in different organism. By comparison, the function of SNAPG in eukaryotes is to facilitate vesicular transport between Endoplasmic Reticulum and Golgi Apparatus. Unfortunately, the exact function of this protein is not yet known.