Difference between revisions of "Part:BBa K1640024:Experience"

Latest revision as of 04:58, 26 October 2016

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Applications of BBa_K1640024

User Reviews

UNIQ299652b65789accd-partinfo-00000000-QINU

IngenuityLab_Canada 2016

Nafaa Haddou

As part of our gold medal requirement we further characterizes a pre-existing BioBrick in the registry. Part BBa_K1640024 was modeled using SwissModel to show the tertiary structure. The ribbon model was rendered using multiple templates of other highly characterized CP47 protein crystals found through Protein Data Bank. The sequences were aligned using the BLAST and the SwissModel script. Secondary structures were assigned based on homology and the alignment with the templates. Closer alignment allowed for better estimation of the structure. The secondary structures were then used to stack the image and develop the tertiary structure. Finally, energy minimization was done to render the most stable orientation and organization of the amino sequence in tertiary form. The model allows for a better understanding of how the protein interacts within the complex since function is derived from structure. The secondary structures also allow for comparison and identification of key domains and motifs that are necessary for protein function. Likewise these regions are usually conserved and thus the can be used in the identification of unknown functions or the characterization of similar proteins in the organism as well as others.

Ribbon Model

Tertiary Structure of the CP43 Protein Reaction Centre from Chlamydomonas reinhardtii. CP43 is a proximal antennae subunit protein of the PSII complex. It contains multiple binding sites for Chlorophyll derivatives, specialized lipids, and ligands that facilitate movement of electrons in the electron transport chain of the photosystem cycle. The protein also contains structures and ligands that form parts of the oxygen evolving complex of PSII.

Secondary Structure

Transmembrane Regions and Binding Sites

Key Domains of CP43:

-Part of the PsbB/PsbC Family

Transmembrane Regions

Position (aa) Description

61-76 Helical

127-141 Helical

168-184 Helical

250-264 Helical

280-295 Helical

440-456 Helical

Binding Sites:

Chlorophyll A

Chlorophyll B

Beta- Carotene and Derivatives

Digalactosyl Diacyl Glycerol

Fe (II) Ion

Protoporphyrin IX

1,2-Dipalmitoyl-Phosphatidyl-Glycerole

Cl- ion

Pheophytin A

Benzoquinone derivative

Calcium-manganese-oxide binding

Sources

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.

Remmert, M., Biegert, A., Hauser, A. and Soding, J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods, 9, 173-175.

Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.

Sali, A. and Blundell, T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol, 234, 779-815.

Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350.

Mariani, V., Kiefer, F., Schmidt, T., Haas, J. and Schwede, T. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, 79 Suppl 10, 37-58 Magrane M. and the UniProt consortium. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database, 2011: bar009 (2011). The UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res. 43: D204-D212 (2015)

UNIQ299652b65789accd-partinfo-00000001-QINU

@@ Line 8: / Line 8: @@
 ===User Reviews===
 <!-- DON'T DELETE --><partinfo>BBa_K1640024 StartReviews</partinfo>
-<!-- Template for a user review
-{|width='80%' style='border:1px solid gray'
+IngenuityLab_Canada 2016
-|-
-|width='10%'|
+Nafaa Haddou
-<partinfo>BBa_K1640024 AddReview number</partinfo>
-<I>Username</I>
+As part of our gold medal requirement we further characterizes a pre-existing BioBrick in the registry. Part BBa_K1640024 was modeled using SwissModel to show the tertiary structure. The ribbon model was rendered using multiple templates of other highly characterized CP47 protein crystals found through Protein Data Bank. The sequences were aligned using the BLAST and the SwissModel script. Secondary structures were assigned based on homology and the alignment with the templates. Closer alignment allowed for better estimation of the structure. The secondary structures were then used to stack the image and develop the tertiary structure. Finally, energy minimization was done to render the most stable orientation and organization of the amino sequence in tertiary form.
-|width='60%' valign='top'|
+The model allows for a better understanding of how the protein interacts within the complex since function is derived from structure. The secondary structures also allow for comparison and identification of key domains and motifs that are necessary for protein function. Likewise these regions are usually conserved and thus the can be used in the identification of unknown functions or the characterization of similar proteins in the organism as well as others.
-Enter the review inofrmation here.
-|};
+==Ribbon Model==
-<!-- End of the user review template -->
+[[File:Team_Ingenuity_Lab_CP43.png|thumb|400px|center|<strong>Tertiary Structure of the CP43 Protein Reaction Centre from Chlamydomonas reinhardtii.</strong> CP43 is a proximal antennae subunit protein of the PSII complex. It contains multiple binding sites for Chlorophyll derivatives, specialized lipids, and ligands that facilitate movement of electrons in the electron transport chain of the photosystem cycle. The protein also contains structures and ligands that form parts of the oxygen evolving complex of PSII.]]
+==Secondary Structure==
+[[File:Team Ingenuity_Lab_Secondary Structure Cp43.png|thumb|400px|centre]]
+==Transmembrane Regions and Binding Sites==
+Key Domains of CP43:
+-Part of the PsbB/PsbC Family
+Transmembrane Regions
+<strong>Position (aa)	Description </strong>
+-76	        Helical
+-141	        Helical
+-184  	Helical
+-264 	Helical
+-295 	Helical
+-456 	Helical
+<strong>Binding Sites:</strong>
+Chlorophyll A
+Chlorophyll B
+Beta- Carotene and Derivatives
+Digalactosyl Diacyl Glycerol
+Fe (II) Ion
+Protoporphyrin IX
+,2-Dipalmitoyl-Phosphatidyl-Glycerole
+Cl- ion
+Pheophytin A
+Benzoquinone derivative
+Calcium-manganese-oxide binding
+==Sources==
+Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
+Remmert, M., Biegert, A., Hauser, A. and Soding, J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods, 9, 173-175.
+Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
+Sali, A. and Blundell, T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol, 234, 779-815.
+Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350.
+Mariani, V., Kiefer, F., Schmidt, T., Haas, J. and Schwede, T. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, 79 Suppl 10, 37-58
+Magrane M. and the UniProt consortium. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database, 2011: bar009 (2011).
+The UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res. 43: D204-D212 (2015)
 <!-- DON'T DELETE --><partinfo>BBa_K1640024 EndReviews</partinfo>