Result of SNAPG: Difference between revisions

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(interproscan)
(interproscan)


[[Image:Ligand structure visualisation .jpg|thumb|500px|left|none||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) ]]
[[Image:Snap-gamm ligands.png|thumb|600px|left|none||Figure 1. SNAP-gamma ]]




[[Image:Ligand structure visualisation .jpg|thumb|600px|left|none||Figure 2. 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. Sulfanate ions interact mainly hy hydrogen bonding while MSE by covalent bonds (shown in red color), hydrogen bonding (cyan) and van der waals (green). ]]


[[Image:Sulfate ion ligand interactions.png|thumb|500px|left|none|Figure 2. Various interaction of sulfanate ions]]




[[Image:PFam domains.png|thumb|left|none|Figure 3. Two domains of SNAPG protein (chain A)]]  
[[Image:Sulfate ion ligand interactions.png|thumb|600px|left|none|Figure 3. Various interaction of sulfanate ions to different residues of SNAPG]]


[[Image:PFam domains.png|thumb|600px|left|none|Figure 4. Two domains of SNAPG protein (chain A) obtained from Pfam at Sanger. Residue 7-66 aligned with Pfam-B_7270 domain and that of 87-307 with Pfam-B_15198.]]


=== Structural comparison ===
=== 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
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).




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[[image:2ifu structure alognments.png|thumb|left|none|700px|[[Media:2ifu structure alognments.png|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.]]]]
[[image:2ifu structure alognments.png|thumb|left|none|700px|[[Media:2ifu structure alognments.png|Figure 5. 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.]]]]




[[image:2ifu 1qqe 2fi7 alignment.png|thumb|left|none|700px|[[Media:2ifu 1qqe 2fi7 alignment.png|Figure 5. Stucture and sequence alignment of 2ifuA, 1qqeA and 2fi7A generated by STRAP. ]]]]
[[image:2ifu 1qqe 2fi7 alignment.png|thumb|left|none|700px|[[Media:2ifu 1qqe 2fi7 alignment.png|Figure 6. Structure and sequence alignment of 2ifuA, 1qqeA and 2fi7A generated by STRAP. No gap assumed during alignment of these proteins. The 2ifuA appears to have a similar secondary structure motifs (highlighted in red blocks) and alternating amino acid residues conservation with other 2 proteins. Only one region that is conserved for all of the three proteins as shown by blue ball on both sequence and structure alignments.]]]]


==== physical properties ====
==== physical properties ====




[[image:2ifuA-1qqe hydrophobes and hydrophilics.png|thumb|left|none|500px|[[Media:2ifuA-1qqe hydrophobes and hydrophilics.png|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]]]]
[[image:2ifuA-1qqe hydrophobes and hydrophilics.png|thumb|left|none|500px|[[Media:2ifuA-1qqe hydrophobes and hydrophilics.png|Figure 7. 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]]]]
 
 
 
[[image:2ifuA-1qqe charged resi.png|thumb|left|none|500px|[[Media:2ifuA-1qqe charged resi.png|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). ]]]]






[[image:IfuA-structure.png|thumb|left|none|500px|[[Media:IfuA-structure.png|Figure 8. 2ifuA structures highlighted by chain color ramp (A), hydrophobicity (B) and conformation type (C). Legends are shown.]]]]
[[image:2ifuA-1qqe charged resi.png|thumb|left|none|500px|[[Media:2ifuA-1qqe charged resi.png|Figure 8. 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). ]]]]
 




[[image:Electrostatic potential.png|thumb|left|none|500px|[[Media:Electrostatic potential.png|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)]]]]
[[image:Electrostatic potential.png|thumb|left|none|500px|[[Media:Electrostatic potential.png|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)]]]]


[[image:Bindingsite 2ifuA.png|thumb|left|none|500px|[[Media:Bindingsite 2ifuA.png|Figure 10. ]]]]
[[image:Bindingsite 2ifuA.png|thumb|left|none|500px|[[Media:Bindingsite 2ifuA.png|Figure 10. Ligand binding site prediction generated by ProFunc]]]]
 


==SNAPG Function==
==SNAPG Function==
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===Function in the context of Structure===
===Function in the context of Structure===
====Fold Matching Analysis by ProFunc====
====Fold Matching Analysis by ProFunc====
SSM (Krissinel and Henrick, 2004) represents several protein that have similar structure to SNAPG associated with function prediction. The most closely related structure is 1qqeA shows 24% fold identity to 2ifuA. This results could be different from DALI results (refers to Table1).
SSM (Krissinel and Henrick, 2004) represents several protein that have similar structure to SNAP-gamma associated with function prediction. The most closely related structure is 1qqeA shows 24% fold identity to 2ifuA. This results could be different from DALI results (refers to Table1).


[[Image:Fold.jpg|thumb|700px|none||Figure 12. Fold match results for ay64 (chain A)]]
[[Image:Fold.jpg|thumb|700px|none||Figure 12. Fold match results for ay64 (chain A)]]
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====Sequence Motif====
====Sequence Motif====
Aromatic-di-Alanine (AdAR) repeat was found in NSF attachment proteins (SNAPG). Its structure is similar to that found in TPR-1 (belongs to Tetratrico peptide repeat family). Get the [http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF02071 link]
Aromatic-di-Alanine (AdAR) repeat was found in NSF attachment proteins (SNAP-gamma). Its structure is similar to that found in TPR-1 (belongs to Tetratrico peptide repeat family). Get the [http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF02071 link]


[[Image:TPR.jpg|thumb|700px|none||Figure 14. TPR family motif was linked to SNAPG]]
[[Image:TPR.jpg|thumb|700px|none||Figure 14. TPR family motif was linked to SNAP-gamma]]


===Genomic Context===  
===Genomic Context===  
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=== Background ===
=== Background ===


[[Image:Cladogram view.JPG|thumb|800px|Figure 18. Cladogram treeview of SNAP-gamma Protein]]
[[Image:Cladogram view.JPG|thumb|800px|none|Figure 18. Cladogram treeview of SNAP-gamma Protein]]


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.
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.
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=== Final Tree Analysis ===
=== Final Tree Analysis ===


[[Image:Rad.JPG|thumb|700px|Figure 13. Evolutionary analysis of the tree with radial view (for professional viewer)|left]]  
[[Image:Rad.JPG|thumb|700px|none|Figure 19. Evolutionary analysis of the tree with radial view (for professional viewer)|left]]  




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Other version: [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Rad2.JPG Evolutionary analysis of the tree with radial view (for non-professional or common viewer) ]
Other version: [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Rad2.JPG Evolutionary analysis of the tree with radial view (for non-professional or common viewer) ]


===Other Attributes ===
===Other Attributes ===
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[[Boostrap value]]
[[Boostrap value]]
Back to [[Scientific Report of N-ethylmaleide-sensitive factor attachment protein, gamma]]

Latest revision as of 03:51, 12 June 2007

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 [1]. 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)

Figure 1. SNAP-gamma


Figure 2. 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. Sulfanate ions interact mainly hy hydrogen bonding while MSE by covalent bonds (shown in red color), hydrogen bonding (cyan) and van der waals (green).


Figure 3. Various interaction of sulfanate ions to different residues of SNAPG


Figure 4. Two domains of SNAPG protein (chain A) obtained from Pfam at Sanger. Residue 7-66 aligned with Pfam-B_7270 domain and that of 87-307 with Pfam-B_15198.

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).


Table 1. Structure comparison based on Dali results
PDB-chain Structure RMSD Z-value % identity Protein
2IFU-A
2ifu.jpg
0.0 37.8 100 Endocytosis/exocytosis. Gamma-SNAP (Danio rerio)
1QQE-A
1qqe asym r 250.jpg
3.4 23.3 23 Protein binding. Vesicular transport protein sec17(yeast)
2FI7-A
2fi7 asym r 250.jpg
11.6 12.9 14 Protein transport. Type 4 fimbrial biogenesis protein pili (Pseudomonas aeruginosa)



2ifuA, 1qqeA and 2fi7 alignment


physical properties



SNAPG Function

Gene Ontology Annotation by Similarity

AmiGo has been used to find three structured controlled vocabularies that describe gene products of SNAPG in terms of their associated biological processes, cellular components and molecular functions. This protein function is not yet established therefore it is only by similarity (see the figure below).

Figure 11. Gene Ontology: Biological Process, Molecular Function and Cellular Component of SNAP gamma by similarity

Function in the context of Structure

Fold Matching Analysis by ProFunc

SSM (Krissinel and Henrick, 2004) represents several protein that have similar structure to SNAP-gamma associated with function prediction. The most closely related structure is 1qqeA shows 24% fold identity to 2ifuA. This results could be different from DALI results (refers to Table1).

Figure 12. Fold match results for ay64 (chain A)

Conserved Residue Domain

Figure 13. Sequences showing conserved residue between 2ifu, 1qqe and 2FI7 on chain A. Secondary structures are highlighted with red

Sequence Motif

Aromatic-di-Alanine (AdAR) repeat was found in NSF attachment proteins (SNAP-gamma). Its structure is similar to that found in TPR-1 (belongs to Tetratrico peptide repeat family). Get the link

Figure 14. TPR family motif was linked to SNAP-gamma

Genomic Context

Figure 15. SNAP gamma is conserved on several organisms genome

Cellular Context

Figure 16. Cellular localisation of human SNAPG on various tissue. Expression of SNAPG is highest in B lymphocytes and bone marrow
Figure 17. Cellular localisation of mouse SNAPG on various tissue. The highest expression of SNAPG is more distributed

SNAPG Evolution

Background

Figure 18. Cladogram treeview of SNAP-gamma Protein

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

Figure 19. 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)

Other Attributes

command BLAST

List IDs use as an batch entrez input

List of various alignments of protein

Boostrap value



Back to Scientific Report of N-ethylmaleide-sensitive factor attachment protein, gamma