Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

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(→Proteins)
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== Proteins ==
== Proteins ==
-
Information about our proteins goes here.
+
=== Superoxide dismutase 1 protein, SOD ===
 +
[http://partsregistry.org/Part:BBa_K380007 Part:BBa_K380007]
 +
 
 +
 
 +
Human soluble superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in E. coli by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
 +
 
 +
[[Image:SOD1_dimeric.png|400px|thumb|right|3D structure of human SOD1 in it's dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)] ]]
 +
 
 +
{|
 +
| '''Gene''' (cDNA)
 +
|
 +
|-
 +
| length
 +
| 465 bp
 +
|-
 +
| removed restriction site
 +
| PfeI
 +
|-
 +
| exchanged nt
 +
| nt331 A &rarr; G
 +
|-
 +
| '''Protein'''
 +
|
 +
|-
 +
| length
 +
| 154 aa
 +
|-
 +
| size
 +
| 15,936 Da
 +
|-
 +
| Fasta
 +
| [http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]
 +
|}
 +
 
 +
 
 +
GenBank:[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]
 +
 
 +
First reported by:[http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
=== copper chaperon protein for SOD, yCCS ===
 +
[http://partsregistry.org/Part:BBa_K380008 Part:BBa_K380008]
 +
 
 +
 
 +
Yeast copper chaperon protein (yCCS) is a help chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm.  yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage.
 +
 
 +
yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 ([http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al''. 2003]). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins.
 +
 +
[[Image:YSOD+yCCS_interaction.jpg‎|400px|thumb|right|3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [[http://www.ncbi.nlm.nih.gov/pubmed/11524675 Lamb ''et al''. 2001]] ]]
 +
 
 +
 
 +
 
 +
{|
 +
| '''Gene''' (cDNA)
 +
|
 +
|-
 +
| length
 +
| 750bp
 +
|-
 +
| removed restriction site
 +
| EcoRI
 +
|-
 +
| exchanged nt
 +
| nt257 T &rarr; C
 +
|-
 +
| '''Protein'''
 +
|
 +
|-
 +
| length
 +
| 249 aa
 +
|-
 +
| size
 +
| 27,330 Da
 +
|-
 +
| Fasta
 +
| [http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]
 +
|}
 +
 
 +
 
 +
GenBank:[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]
 +
 
 +
First reported by:[http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
----
 +
 
 +
 
 +
=== basic fibroblast growth factor, bFGF ===
 +
[http://partsregistry.org/Part:BBa_K380006 Part:BBa_K380006]
 +
 
 +
 
 +
 +
[[Image:BFGF.jpg|200px|thumb|right|3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010] ]]
 +
 
 +
 
 +
 
 +
{|
 +
| '''Gene''' (cDNA)
 +
|
 +
|-
 +
| length
 +
| 468 bp
 +
|-
 +
| removed restriction sites
 +
| AgeI
 +
|-
 +
| exchanged nt
 +
|
 +
|-
 +
| '''Protein'''
 +
|
 +
|-
 +
| length
 +
| 288 aa
 +
|-
 +
| size
 +
| 30,770 Da
 +
|-
 +
| Fasta
 +
| [http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]
 +
|}
 +
 
 +
 
 +
GenBank:
 +
 
 +
First reported by:
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
----
 +
 
 +
 
 +
=== Protein A, z domain ===
 +
[http://partsregistry.org/Part:BBa_K380009 Part:BBa_K380009]
 +
 
 +
 
 +
 +
[[Image:|300px|thumb|right|]]
 +
 
 +
 
 +
 
 +
{|
 +
| '''Genepart'''
 +
|
 +
|-
 +
| length
 +
| 174 bp
 +
|-
 +
| removed restriction sites
 +
| -
 +
|-
 +
| exchanged nt
 +
| -
 +
|-
 +
| '''Protein'''
 +
|
 +
|-
 +
| length
 +
| 58 aa
 +
|-
 +
| size
 +
|
 +
|-
 +
| Fasta
 +
|
 +
|}
 +
 
 +
 
 +
GenBank:
 +
 
 +
First reported by:
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
----
 +
 
 +
 
 +
=== IgG protease, IdeS ===
 +
[http://partsregistry.org/Part:BBa_K380010 Part:BBa_K380010]
 +
 
 +
 
 +
 +
[[Image:IdeS.jpg|200px|thumb|right|3D structure of IdeS. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004] ]]
 +
 
 +
 
 +
 
 +
{|
 +
| '''Gene''' (cDNA)
 +
|
 +
|-
 +
| length
 +
| 930 bp
 +
|-
 +
| removed restriction sites
 +
| -
 +
|-
 +
| exchanged nt
 +
| -
 +
|-
 +
| '''Protein'''
 +
|
 +
|-
 +
| length
 +
| 339 aa
 +
|-
 +
| size
 +
| 37,977 Da
 +
|-
 +
| Fasta
 +
| [http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]
 +
|}
 +
 
 +
 
 +
GenBank:
 +
 
 +
First reported by:
 +
 
 +
 
 +
 
 +
 
|}
|}
{{Stockholm/Footer}}
{{Stockholm/Footer}}

Revision as of 23:59, 26 October 2010

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↳  Introduction Pre-Study Proteins Future applications


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Contents

Proteins

Superoxide dismutase 1 protein, SOD

Part:BBa_K380007


Human soluble superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O-2 + O-2 + 2H+ → H2O2 + O2, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in E. coli by Hallewell et al., (1985).

3D structure of human SOD1 in it's dimeric form. Primary citation Leinartaite et al. (2010)
Gene (cDNA)
length 465 bp
removed restriction site PfeI
exchanged nt nt331 A → G
Protein
length 154 aa
size 15,936 Da
Fasta SOD1


GenBank:AY450286.1

First reported by:Hallewell et al., (1985).




copper chaperon protein for SOD, yCCS

Part:BBa_K380008


Yeast copper chaperon protein (yCCS) is a help chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm. yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage.

yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 (Ahl et al. 2003). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins.

3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [Lamb et al. 2001]


Gene (cDNA)
length 750bp
removed restriction site EcoRI
exchanged nt nt257 T → C
Protein
length 249 aa
size 27,330 Da
Fasta yCCS


GenBank:NM_001182535.1

First reported by:Culotta et al. (1997).





basic fibroblast growth factor, bFGF

Part:BBa_K380006


3D structure of bFGF. Primary citation Bae et al. 2010


Gene (cDNA)
length 468 bp
removed restriction sites AgeI
exchanged nt
Protein
length 288 aa
size 30,770 Da
Fasta bFGF


GenBank:

First reported by:





Protein A, z domain

Part:BBa_K380009


[[Image:|300px|thumb|right|]]


Genepart
length 174 bp
removed restriction sites -
exchanged nt -
Protein
length 58 aa
size
Fasta


GenBank:

First reported by:





IgG protease, IdeS

Part:BBa_K380010


3D structure of IdeS. Primary citation Wenig et al. 2004


Gene (cDNA)
length 930 bp
removed restriction sites -
exchanged nt -
Protein
length 339 aa
size 37,977 Da
Fasta IdeS


GenBank:

First reported by:







The Faculty of Science at Stockholm University Swedish Vitiligo association (Svenska Vitiligoförbundet) Geneious Fermentas/ Sigma-Aldrich/

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