Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

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== Proteins ==
== Proteins ==
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=== Superoxide dismutase 1 protein, SOD ===
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=== Superoxide dismutase 1 (SOD1) ===
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[http://partsregistry.org/Part:BBa_K380007 Part:BBa_K380007]
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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 ''Escherichia coli'' by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
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{|border="1" align="center" cellpadding="3" cellspacing="0"
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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)].
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!colspan="2"|Gene (cDNA)  
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|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]
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[[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)] ]]
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{|
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| '''Gene''' (cDNA)
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|
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|-
|-
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| length
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|width="130"|'''Length'''
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| 465 bp
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|width="130"|465 bp
|-
|-
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| removed restriction site
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|'''Edited nucleotide(s)'''
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| PfeI
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|nt331 A &rarr; G
|-
|-
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| exchanged nt
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|'''Removed restr. site(s)'''
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| nt331 A &rarr; G
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|PfeI
|-
|-
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| '''Protein'''
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|'''GenBank'''
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|  
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|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br />
|-
|-
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| length
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!colspan="2"|Protein
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| 154 aa
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|-
|-
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| size
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|'''Length'''
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| 15,936 Da
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|154 aa
|-
|-
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| Fasta
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|'''Size'''
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| [http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]
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|15,936 Da
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|-
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|'''Fasta'''
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|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br />
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|-
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|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
|}
|}
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GenBank:[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]
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----
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First reported by:[http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
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=== copper chaperon protein for SOD, yCCS ===
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[http://partsregistry.org/Part:BBa_K380008 Part:BBa_K380008]
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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.  
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=== Yeast copper chaperon (yCCS) ===
 +
Yeast copper chaperon protein (yCCS) is a helper 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.  
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.  
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[[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]] ]]
 
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{|border="1" align="center" cellpadding="3" cellspacing="0"
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!colspan="2"|Gene (cDNA)  
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{|  
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|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg‎|250px]]<br />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]
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| '''Gene''' (cDNA)
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|  
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|-
|-
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| length
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|width="130"|'''Length'''
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| 750bp
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|width="130"|750 bp
|-
|-
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| removed restriction site
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|'''Edited nucleotide(s)'''
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| EcoRI
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|nt257 T &rarr; C
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|-
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| exchanged nt
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|'''Removed restr. site(s)'''
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| nt257 T &rarr; C
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|EcoRI
|-
|-
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| '''Protein'''
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|'''GenBank'''
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|  
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|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br />
|-
|-
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| length
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!colspan="2"|Protein
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| 249 aa
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|-
|-
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| size
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|'''Length'''
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| 27,330 Da
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|249 aa
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|-
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| Fasta
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|'''Size'''
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| [http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]
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|27,330 Da
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|-
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|'''Fasta'''
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|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br />
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|-
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|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br />
|}
|}
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GenBank:[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]
 
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First reported by:[http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].
 
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=== Human basic fibroblast growth factor, bFGF ===
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=== Human basic fibroblast growth factor (bFGF) ===
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[http://partsregistry.org/Part:BBa_K380006 Part:BBa_K380006]
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[[Image:BFGF.jpg|200px|thumb|right|3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010] ]]
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{|  
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{|border="1" align="center" cellpadding="3" cellspacing="0"
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| '''Gene''' (cDNA)
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!colspan="2"|Gene (cDNA)  
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|  
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|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]
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|-
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| length
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|width="130"|'''Length'''
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| 468 bp
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|width="130"|468 bp
|-
|-
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| removed restriction sites
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|'''Edited nucleotide(s)'''
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| AgeI
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|nt341 C &rarr; T
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|-
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| exchanged nt 341 C → T
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|'''Removed restr. site(s)'''
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|  
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|AgeI
|-
|-
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| '''Protein'''
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|'''GenBank'''
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|  
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|&nbsp;<br />
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|-
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| length
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!colspan="2"|Protein
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| 155 aa
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|-
|-
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| size
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|'''Length'''
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| 17,353 Da
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|155 aa
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|-
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| Fasta
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|'''Size'''
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| [http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]
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|17,353 Da
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|-
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|'''Fasta'''
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|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br />
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|-
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|colspan="2"|First reported by <unknown><br />
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|}
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GenBank:
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First reported by:
 
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=== Protein A, z domain ===
=== Protein A, z domain ===

Revision as of 07:39, 27 October 2010

Home Project Idea Lab Work Results Modelling Team       Follow us on and        2010.igem.org

↳  Introduction Pre-Study Proteins Future applications


SU Modeling Icon 2.gif  

Contents

Proteins

Superoxide dismutase 1 (SOD1)

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 Escherichia coli by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell et al., (1985)].

Gene (cDNA) SOD1 dimeric.png
3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite et al. (2010)]
Length 465 bp
Edited nucleotide(s) nt331 A → G
Removed restr. site(s) PfeI
GenBank [http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]
Protein
Length 154 aa
Size 15,936 Da
Fasta [http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]
First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell et al., (1985)].



Yeast copper chaperon (yCCS)

Yeast copper chaperon protein (yCCS) is a helper 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.

Gene (cDNA) YSOD+yCCS interaction.jpg
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]
Length 750 bp
Edited nucleotide(s) nt257 T → C
Removed restr. site(s) EcoRI
GenBank [http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]
Protein
Length 249 aa
Size 27,330 Da
Fasta [http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]
First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta et al. (1997)].



Human basic fibroblast growth factor (bFGF)

Gene (cDNA) BFGF.jpg
3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae et al. 2010]
Length 468 bp
Edited nucleotide(s) nt341 C → T
Removed restr. site(s) AgeI
GenBank  
Protein
Length 155 aa
Size 17,353 Da
Fasta [http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]
First reported by <unknown>



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]


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:







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

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