Result of SNAPG

SNAPG Structure

Structure architecture

In order to analyze protein structure of SNAPG, structural comparison to known protein structure is required. An insight to SNAPG structural arrangement provides various informative data on possible protein functions and interactions with another protein and/or DNA. Based on protein families database, Pfam at Sanger, it was found that SNAPG protein matched to Pfam-B protein families and consist of 2 domains, Pfam-B_7270 (PB007270) and Pfam-B_15198 (PB015189) respectively as shown in Figure 3. Both of 2 domains appears to be associated with NSF attachment protein activity (*dijelasin di discussion aja! NSF acivity dijelasin ga?)[1].

Figure 1. Ligands interaction to SNAPG chain A. A) Ligands position in the structure are highlighted; B) Secondary structure of SNAPG chain A with ligands interaction indicated; and C) Various ligand interactions with SNAPG by covalent bonds (shown in red color), hydrogen bonding (cyan) and van der waals (green)

Figure 2. Various interaction of sulfanate ions

Figure 3. Two domains of SNAPG protein (chain A)

. The sequence was also used against InterproScan generated by Profunc that gave an TFR (Tetratricopeptide-like helical) domain classification while that of protein family agrees with Pfam classification.

(interproscan)

Structural comparison

Dali webserver is one of the powerful tool to screen any protein that are structurally homologous with our query. Two structurally related proteins with highest Z-value generated by Dali server were chosen for SNAPG structure comparison analysis. These proteins were vesicular transport ptotein sec17 (1qqe) and type 4 fimbrial biogenesis protein (2f17) (refer to Table 1).alto

Table 1. Structure comparison based on Dali results

PDB-chain	Structure	Z-value	% identity	Protein
2IFU-A		37.8	100	Endocytosis/exocytosis. Gamma-SNAP (Danio rerio)
1QQE-A		23.3	23	Protein binding. Vesicular transport protein sec17(yeast)
2FI7-A		12.9	14	Protein transport. Type 4 fimbrial biogenesis protein pili (Pseudomonas aeruginosa)

2ifuA, 1qqeA and 2fi7 alignment

Figure 4. Superimposed structures of 2ifuA with 1qqeA (A) and 2ifuA with 2fi7A (B) generated by PyMOL. The 2ifuA is shown in green, 1qq3A in blue and 2fi7A in purple color.

Figure 5. Stucture and sequence alignment of 2ifuA, 1qqeA and 2fi7A generated by STRAP.

physical properties

Figure 6. Hydrophobic and hydrophilic residues of 2ifuA (A) and 1qqeA (B) in front and back view. Amino acid residues with hydrophobic properties such as Ala, Gly, Val, Ile, Phe, and Met were selected and colored in green while that with hydrophilic properties (= Arg, Lys, His, Glu, Asp, Asn, Gln, Thr, Ser, and Cys) were colored in orange

Figure 7. Charged residues of 2ifuA (A) and 1qqeA (B) in front and back view. The sidechains for charged residues indicated as red (negative; Glu and Asp) and blue (positive; Arg, Lys and His).

Figure 8. 2ifuA structures highlighted by chain color ramp (A), hydrophobicity (B) and conformation type (C). Legends are shown.

[[image:Electrostatic potential (molecular surface).png|thumb|left|500px|Figure 9. 2ifuA electrostatic potential map visualised by molecular surface. Computation method that were used are coulumb method.](red= -1.800; white= 0.000; blue= +1.800]

Figure 10 cleft

SNAPG Evolution

Background

-> This is the cladogram treeview of SNAP-gamma protein. However, this view is not suitable enough to represent the evolutionary gap between species but this is clearly shows the species name.

Final Tree Analysis

-> Evolutionary analysis of the tree with radial view (for professional viewer)

Legends:

• Red-dotted sign means boostrap value more than 75.00 or 75%
• any number (in red) located near branching tree indicated boostrap value of the branching tree
• Green Line: The species belongs to Plants group
• Brown Line: Amoeba group
• Purple Line: Parasite type
• Pink Line : The species belongs to Insects Group
• Light Green Line: Worms Group
• Dark Blue Line: Invertebrate
• Red Line: Vertebrate

Other version: Evolutionary analysis of the tree with radial view (for non-professional or common viewer)

Understanding the Tree

SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent more than 75% boostrap value. The value was indicated the degree of confidence about the branching order. As an example: in the diagram above, 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

As indicated in diagram above, SNAP-gamma protein was evolved in eukaryotes. There is no prokaryotes detected in the phylogenetic tree.

 Function (in various organism) = nunggu justine

Thus, it could be concluded that SNAP-gamma protein is important protein in eukaryotes animal.