DAP Structural Analysis: Difference between revisions
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'''Structure of 2ijz-A chain''' | '''Structure of 2ijz-A chain''' | ||
[[image:PDBsum.JPG | [[image:PDBsum.JPG|framed|<BR>'''Figure 3.1''' PDBsum Analysis of the secondary protein sequence giving rise to how the protein folds in the motifs of turns and hairpins.|none]]<BR> | ||
[[image:Topology.JPG]] | [[image:Topology.JPG|framed|<BR>'''Figure 3.2''' Topology of 2ijz-A chain giving a simplified understanding of how the protein folds.|none]]<BR> | ||
'''Structural Analysis of 2ijz-A chain''' | '''Structural Analysis of 2ijz-A chain''' | ||
[[image:2ijz-A.JPG]] | [[image:2ijz-A.JPG|framed|<BR>'''Figure 3.3''' A) Front view of 2ijz-A chain structure; B) Back view of 2ijz-A –chain Structure; | ||
Pictures showing the loops (pink), beta-sheet (magenta) and | |||
alpha helix (greenish blue) of the structure taken from PyMOL|none]]<BR> | |||
[[image:Dali_Results.JPG]] | [[image:Dali_Results.JPG|framed|<BR>'''Figure 3.4''' Part of DALI search results gathering structurally related proteins. The three marked proteins in orange were structurally aligned using PyMOL. Proteins 13 to 18 were not taken as no scientific evidence of the protein has been obtained yet.|none]]<BR> | ||
From here, the results of the conserved regions in the sequence is taken from the evolutionary analysis part. These conserved regions are then marked out in red in the following image below (Fig:X). | From here, the results of the conserved regions in the sequence is taken from the evolutionary analysis part. These conserved regions are then marked out in red in the following image below (Fig:X). | ||
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'''Positions of conserved regions''' | '''Positions of conserved regions''' | ||
[[image:Conserved_regions.JPG]] | [[image:Conserved_regions.JPG|framed|<BR>'''Figure 3.5''' Simon fill in here|none]]<BR> | ||
[[image:Conserved_regions_of_2ijz-A.JPG]] | [[image:Conserved_regions_of_2ijz-A.JPG|framed|<BR>'''Figure 3.6''' Simon fill in here|none]]<BR> | ||
Fig X: Structure of 2ijz-A with conserved regions colored in red. | Fig X: Structure of 2ijz-A with conserved regions colored in red. | ||
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'''Structural Comparison of 2ijz-A and Respective Proteins''' | '''Structural Comparison of 2ijz-A and Respective Proteins''' | ||
[[image:Comparison_2ijz_and_1vhe.JPG]] | [[image:Comparison_2ijz_and_1vhe.JPG|framed|<BR>'''Figure 3.7''' Simon fill in here|none]]<BR> | ||
Comparison of 2ijz-A chain (yellow) and 1vhe-A chain (blue) and both of the similar conserved regions are marked in red. | Comparison of 2ijz-A chain (yellow) and 1vhe-A chain (blue) and both of the similar conserved regions are marked in red. | ||
[[image:Comparison_2ijz_and_1xfo3.JPG]] | [[image:Comparison_2ijz_and_1xfo3.JPG|framed|<BR>'''Figure 3.8''' Simon fill in here|none]]<BR> | ||
Comparison of 2ijz-A chain (yellow) and 1xfo-A chain (blue) and both of the similar conserved regions are marked in red. | Comparison of 2ijz-A chain (yellow) and 1xfo-A chain (blue) and both of the similar conserved regions are marked in red. | ||
[[image:Comparison_2ijz_and_2cf4.JPG]] | [[image:Comparison_2ijz_and_2cf4.JPG|framed|<BR>'''Figure 3.9''' Simon fill in here|none]]<BR> | ||
Comparison of 2ijz-A chain (yellow) and 2cf4-A chain (blue) and both of the similar conserved regions are marked in red. | Comparison of 2ijz-A chain (yellow) and 2cf4-A chain (blue) and both of the similar conserved regions are marked in red. | ||
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http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bx52&code=035241 | http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bx52&code=035241 | ||
[[image:Jmol_analyse_of_H82site2.JPG]] | [[image:Jmol_analyse_of_H82site2.JPG|framed|<BR>'''Figure 3.10''' Simon fill in here|none]]<BR> | ||
Jmol picture taken with functional motif H(82)T(83)D(84) site. | Jmol picture taken with functional motif H(82)T(83)D(84) site. | ||
Amino acids involved in the catalytic mechanism of M18metallopeptidases are unknown, although histidines are likely involved in Zn2+ coordination (Wilk .et, al. 2002). Above shown is the histidine site at poisition 82 in the sequence and it is conserved in structural alignment with the other three proteins that are marked out in the DALI search. From literature review papers, the following results have been deduced and dicuss in the discussion. | Amino acids involved in the catalytic mechanism of M18metallopeptidases are unknown, although histidines are likely involved in Zn2+ coordination (Wilk .et, al. 2002). Above shown is the histidine site at poisition 82 in the sequence and it is conserved in structural alignment with the other three proteins that are marked out in the DALI search. From literature review papers, the following results have been deduced and dicuss in the discussion. | ||
Revision as of 04:58, 8 June 2008
Structure of 2ijz-A chain
Figure 3.1 PDBsum Analysis of the secondary protein sequence giving rise to how the protein folds in the motifs of turns and hairpins.
Figure 3.2 Topology of 2ijz-A chain giving a simplified understanding of how the protein folds.
Structural Analysis of 2ijz-A chain
Figure 3.3 A) Front view of 2ijz-A chain structure; B) Back view of 2ijz-A –chain Structure; Pictures showing the loops (pink), beta-sheet (magenta) and alpha helix (greenish blue) of the structure taken from PyMOL
Figure 3.4 Part of DALI search results gathering structurally related proteins. The three marked proteins in orange were structurally aligned using PyMOL. Proteins 13 to 18 were not taken as no scientific evidence of the protein has been obtained yet.
From here, the results of the conserved regions in the sequence is taken from the evolutionary analysis part. These conserved regions are then marked out in red in the following image below (Fig:X).
Positions of conserved regions
Figure 3.5 Simon fill in here
Figure 3.6 Simon fill in here
Fig X: Structure of 2ijz-A with conserved regions colored in red.
Structural Comparison of 2ijz-A and Respective Proteins
Figure 3.7 Simon fill in here
Comparison of 2ijz-A chain (yellow) and 1vhe-A chain (blue) and both of the similar conserved regions are marked in red.
Figure 3.8 Simon fill in here
Comparison of 2ijz-A chain (yellow) and 1xfo-A chain (blue) and both of the similar conserved regions are marked in red.
Figure 3.9 Simon fill in here
Comparison of 2ijz-A chain (yellow) and 2cf4-A chain (blue) and both of the similar conserved regions are marked in red.
Figure 3.10 Simon fill in here
Jmol picture taken with functional motif H(82)T(83)D(84) site.
Amino acids involved in the catalytic mechanism of M18metallopeptidases are unknown, although histidines are likely involved in Zn2+ coordination (Wilk .et, al. 2002). Above shown is the histidine site at poisition 82 in the sequence and it is conserved in structural alignment with the other three proteins that are marked out in the DALI search. From literature review papers, the following results have been deduced and dicuss in the discussion.
