Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

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|width="130"|'''Length'''
|width="130"|'''Length'''
|width="130"|465 bp
|width="130"|465 bp
-
|-
 
-
|'''Edited nucleotide(s)'''
 
-
|nt331 A → G
 
-
|-
 
-
|'''Removed restr. site(s)'''
 
-
|PfeI
 
|-
|-
|'''GenBank'''
|'''GenBank'''
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----
----
-
 
=== Yeast copper chaperon (yCCS) ===
=== Yeast copper chaperon (yCCS) ===
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|width="130"|'''Length'''
|width="130"|'''Length'''
|width="130"|750 bp
|width="130"|750 bp
-
|-
 
-
|'''Edited nucleotide(s)'''
 
-
|nt257 T → C
 
-
|-
 
-
|'''Removed restr. site(s)'''
 
-
|EcoRI
 
|-
|-
|'''GenBank'''
|'''GenBank'''
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|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br />
|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br />
|-
|-
-
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br />
+
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br><br><br><br><br>
|}
|}
----
----
-
 
=== Human basic fibroblast growth factor (bFGF) ===
=== Human basic fibroblast growth factor (bFGF) ===
Line 90: Line 76:
|width="130"|'''Length'''
|width="130"|'''Length'''
|width="130"|468 bp
|width="130"|468 bp
-
|-
 
-
|'''Edited nucleotide(s)'''
 
-
|nt341 C &rarr; T
 
-
|-
 
-
|'''Removed restr. site(s)'''
 
-
|AgeI
 
|-
|-
|'''GenBank'''
|'''GenBank'''
-
|&nbsp;<br />
+
|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br />
|-
|-
!colspan="2"|Protein
!colspan="2"|Protein
Line 108: Line 88:
|17,353 Da
|17,353 Da
|-
|-
-
|'''Fasta'''
+
|'''Fasta'''<br /><br><br><br><br>
-
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br />
+
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br><br><br><br>
-
|-
+
-
|colspan="2"|First reported by <unknown><br />
+
|}
|}
----
----
-
 
=== Protein A, z domain ===
=== Protein A, z domain ===
-
[http://partsregistry.org/Part:BBa_K380009 Part:BBa_K380009]
 
 +
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!colspan="2"|Genepart
 +
|rowspan="10" width="250"|[[Image:ProteinA_z_domain.jpg|250px]]<br />3D structure of the Z-domain of Protein A. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/9325113 Tashiro ''et al''. 2010]
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|174 bp
 +
|-
 +
|'''GenBank'''
 +
|[http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)<br />
 +
|-
 +
!colspan="2"|Protein
 +
|-
 +
|'''Length'''
 +
|58 aa
 +
(508 aa, full protein )
 +
|-
 +
|'''Size'''
 +
|55,439 Da (full protein)
 +
|-
 +
|'''Fasta'''<br /><br><br><br><br><br>
 +
|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br><br><br><br><br>
 +
|}
-
 
-
[[Image:|300px|thumb|right|]]
 
 +
----
 +
=== IgG protease (IdeS) ===
-
{|  
+
{|border="1" align="center" cellpadding="3" cellspacing="0"
-
| '''Genepart'''
+
!colspan="2"|Gene (cDNA)
-
|
+
|rowspan="10" width="250"|[[Image:IdeS.jpg|250px]]<br />Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004]
|-
|-
-
| length
+
|width="130"|'''Length'''
-
| 174 bp
+
|width="130"|930 bp
|-
|-
-
| removed restriction sites
+
|'''GenBank'''
-
| -
+
|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br />
|-
|-
-
| exchanged nt
+
!colspan="2"|Protein
-
| -
+
|-
|-
-
| '''Protein'''
+
|'''Length'''
-
|  
+
|339 aa
|-
|-
-
| length
+
|'''Size'''
-
| 58 aa
+
|37,977 Da
-
|-
+
-
| size
+
-
|  
+
|-
|-
-
| Fasta
+
|'''Fasta'''<br /><br><br><br><br><br>
-
|  
+
|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br><br><br><br><br>
|}
|}
-
GenBank:
 
-
First reported by:
+
----
 +
== Cell penetrating peptides ==
 +
These cell-penetrating peptides, (CPPs) may be used in N- and C-terminal fusions with full-length proteins to create transduction proteins with the ability to permeate the lipid bilayer of various cell types, making them potential gene or protein delivery vectors.
 +
=== TAT cell penetrating peptide (TAT) ===
 +
Purified full-length TAT fusion proteins expressed in ''Escherichia coli'' have been shown to successfully translocate into several human cell types, including all cells found in whole blood, as well as bone marrow stem cells and osteoblasts, while still retaining the fused protein's activity ([http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). The mechanism for transduction over the bilipid membrane is still a matter of debate, but has been suggested to occur through macropinocytosis, a specialized form of endocytosis ([http://www.ncbi.nlm.nih.gov/pubmed/17913584 Gump and Dowdy, 2007]).
 +
TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) ''trans''-activating transcriptional activator (Tat) ([http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green and Loewenstein, 1988]; [http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.
 +
 +
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!colspan="2"|Sequence
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|33 bp
 +
|-
 +
|'''Patent PCT'''
 +
|[http://v3.espacenet.com/publicationDetails/biblio;jsessionid=646EDA06997EDDFC0CC04CCE49F87F6B.espacenet_levelx_prod_5?CC=WO&NR=2005084158A2&KC=A2&FT=D&date=20050915&DB=EPODOC&locale=se_se WO 2005/084158 A2]<br />
 +
|-
 +
!colspan="2"|Peptide
 +
|-
 +
|'''Length'''
 +
|11 aa
 +
|-
 +
|'''Size'''
 +
|1,560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 +
|-
 +
|colspan="2" align="center"|YGRKKRRQRRR
 +
|-
 +
|colspan="2"|First reported by
 +
[http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green ''et al''. (1988)] and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel ''et al''. (1988)]<br />
 +
|}
----
----
 +
=== Low molecular weight protamine (LMWP) ===
 +
Enzymatically prepared LMWP chemically conjugated to ovalbumin (OVA) and bovine serum albumin (BSA) have previously been shown to penetrate the lipid bilayer of human keratinocytes, as well as to successfully permeate mouse skin epidermis ([http://www.ncbi.nlm.nih.gov/pubmed/20232417 Huang ''et al.'', 2010]). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells ([http://www.ncbi.nlm.nih.gov/pubmed/12898639 Park ''et al.'', 2003]). As LMWP has been shown to be neither toxic nor immunogenic ([http://www.ncbi.nlm.nih.gov/pubmed/11741268 Chang ''et al.'' a, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741269 Chang ''et al.'' b, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741270 Lee ''et al.'', 2001]), it may be used as a potential vaccine, drug or gene delivery vector.
 +
LMWP is a 14-amino acid derivative from Rainbow trout (''Oncorhynchus mykiss'') protamine, an arginine-rich protein that replaces histones in chromatin during spermatogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/3755398 McKay ''et al.'', 1986]; [http://www.ncbi.nlm.nih.gov/pubmed/10213181 Byun ''et al.'', 1999]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.
-
=== IgG protease, IdeS ===
+
{|border="1" align="center" cellpadding="3" cellspacing="0"
-
[http://partsregistry.org/Part:BBa_K380010 Part:BBa_K380010]
+
!colspan="2"|Sequence
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|42 bp
 +
|-
 +
|'''Patent Application'''
 +
|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677]<br />
 +
|-
 +
!colspan="2"|Peptide
 +
|-
 +
|'''Length'''
 +
|14 aa
 +
|-
 +
|'''Size'''
 +
|1,880 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 +
|-
 +
|colspan="2" align="center"|VSRRRRRRGGRRRR
 +
|-
 +
|colspan="2"|Patent application by Park et al. (2004)<br />
 +
|}
-
+
----
-
[[Image:IdeS.jpg|200px|thumb|right|3D structure of IdeS. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004] ]]
+
 +
=== Transportan 10 (Tp10) ===
 +
Chemically synthesized Tp10 peptides conjugated to different cargo, including pDNA and protein, have been shown to efficiently penetrate the lipid bilayer of both human and mouse cells ([http://www.ncbi.nlm.nih.gov/pubmed/15763630 Kilk ''et al.'', 2005]). Membrane permeation is both energy and temperature independent ([http://www.ncbi.nlm.nih.gov/pubmed/11718666 H&auml;llbrink ''et al.'', 2001]). The exact mechanism for penetration is still unclear ([http://www.ncbi.nlm.nih.gov/pubmed/17218466 Yandek ''et al.'', 2007]).
 +
Tp10 is a 21-amino acid derivative from the parent peptide transportan (originally known as galparan), which is a peptide chimera of the neuropeptide galanin and the wasp venom peptide mastoparan ([http://www.ncbi.nlm.nih.gov/pubmed/10930519 Soomets ''et al.'', 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/8738882 Langel ''et al.'', 1996]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.
-
 
+
{|border="1" align="center" cellpadding="3" cellspacing="0"
-
{|  
+
!colspan="2"|Sequence
-
| '''Gene''' (cDNA)
+
|rowspan="8" width="250"|[[Image:Transportan.jpg‎|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]
-
|  
+
|-
|-
-
| length
+
|width="130"|'''Length'''
-
| 930 bp
+
|width="130"|63 bp
|-
|-
-
| removed restriction sites
+
|'''Patent Application'''
-
| -
+
|[http://www.freepatentsonline.com/y2008/0234183.html 20080234183]<br />
|-
|-
-
| exchanged nt
+
!colspan="2"|Peptide
-
| -
+
|-
|-
-
| '''Protein'''
+
|'''Length'''
-
|  
+
|21 aa
|-
|-
-
| length
+
|'''Size'''
-
| 339 aa
+
|2,183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
|-
|-
-
| size
+
|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL
-
| 37,977 Da
+
|-
|-
-
| Fasta
+
|colspan="2"|Patent application by Hallbrink et al. (2003)<br />
-
| [http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]
+
|}
|}
-
 
+
<!--|-
-
GenBank:
+
|rowspan="8" width="250"|[[Image:Tp10_prediction.png‎|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]-->
-
 
+
----
-
First reported by:
+
-
 
+
-
 
+
-
 
+
|}
|}
{{Stockholm/Footer}}
{{Stockholm/Footer}}

Latest revision as of 01:19, 28 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
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
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
GenBank (full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]
Protein
Length 155 aa
Size 17,353 Da
Fasta




[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]





Protein A, z domain

Genepart ProteinA z domain.jpg
3D structure of the Z-domain of Protein A. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/9325113 Tashiro et al. 2010]
Length 174 bp
GenBank [http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)
Protein
Length 58 aa

(508 aa, full protein )

Size 55,439 Da (full protein)
Fasta





[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)






IgG protease (IdeS)

Gene (cDNA) IdeS.jpg
Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig et al. 2004]
Length 930 bp
GenBank [http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]
Protein
Length 339 aa
Size 37,977 Da
Fasta





[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]






Cell penetrating peptides

These cell-penetrating peptides, (CPPs) may be used in N- and C-terminal fusions with full-length proteins to create transduction proteins with the ability to permeate the lipid bilayer of various cell types, making them potential gene or protein delivery vectors.


TAT cell penetrating peptide (TAT)

Purified full-length TAT fusion proteins expressed in Escherichia coli have been shown to successfully translocate into several human cell types, including all cells found in whole blood, as well as bone marrow stem cells and osteoblasts, while still retaining the fused protein's activity ([http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara et al. 1998]). The mechanism for transduction over the bilipid membrane is still a matter of debate, but has been suggested to occur through macropinocytosis, a specialized form of endocytosis ([http://www.ncbi.nlm.nih.gov/pubmed/17913584 Gump and Dowdy, 2007]). TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) trans-activating transcriptional activator (Tat) ([http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green and Loewenstein, 1988]; [http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara et al. 1998]). This part was back translated from the corresponding amino acid sequence and optimized for expression in Escherichia coli. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.

Sequence
Length 33 bp
Patent PCT [http://v3.espacenet.com/publicationDetails/biblio;jsessionid=646EDA06997EDDFC0CC04CCE49F87F6B.espacenet_levelx_prod_5?CC=WO&NR=2005084158A2&KC=A2&FT=D&date=20050915&DB=EPODOC&locale=se_se WO 2005/084158 A2]
Peptide
Length 11 aa
Size 1,560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
YGRKKRRQRRR
First reported by

[http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green et al. (1988)] and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel et al. (1988)]


Low molecular weight protamine (LMWP)

Enzymatically prepared LMWP chemically conjugated to ovalbumin (OVA) and bovine serum albumin (BSA) have previously been shown to penetrate the lipid bilayer of human keratinocytes, as well as to successfully permeate mouse skin epidermis ([http://www.ncbi.nlm.nih.gov/pubmed/20232417 Huang et al., 2010]). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells ([http://www.ncbi.nlm.nih.gov/pubmed/12898639 Park et al., 2003]). As LMWP has been shown to be neither toxic nor immunogenic ([http://www.ncbi.nlm.nih.gov/pubmed/11741268 Chang et al. a, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741269 Chang et al. b, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741270 Lee et al., 2001]), it may be used as a potential vaccine, drug or gene delivery vector. LMWP is a 14-amino acid derivative from Rainbow trout (Oncorhynchus mykiss) protamine, an arginine-rich protein that replaces histones in chromatin during spermatogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/3755398 McKay et al., 1986]; [http://www.ncbi.nlm.nih.gov/pubmed/10213181 Byun et al., 1999]). This part was back translated from the corresponding amino acid sequence and optimized for expression in Escherichia coli. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.

Sequence
Length 42 bp
Patent Application [http://www.freepatentsonline.com/y2007/0071677.html 20070071677]
Peptide
Length 14 aa
Size 1,880 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
VSRRRRRRGGRRRR
Patent application by Park et al. (2004)


Transportan 10 (Tp10)

Chemically synthesized Tp10 peptides conjugated to different cargo, including pDNA and protein, have been shown to efficiently penetrate the lipid bilayer of both human and mouse cells ([http://www.ncbi.nlm.nih.gov/pubmed/15763630 Kilk et al., 2005]). Membrane permeation is both energy and temperature independent ([http://www.ncbi.nlm.nih.gov/pubmed/11718666 Hällbrink et al., 2001]). The exact mechanism for penetration is still unclear ([http://www.ncbi.nlm.nih.gov/pubmed/17218466 Yandek et al., 2007]). Tp10 is a 21-amino acid derivative from the parent peptide transportan (originally known as galparan), which is a peptide chimera of the neuropeptide galanin and the wasp venom peptide mastoparan ([http://www.ncbi.nlm.nih.gov/pubmed/10930519 Soomets et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/8738882 Langel et al., 1996]). This part was back translated from the corresponding amino acid sequence and optimized for expression in Escherichia coli. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.

Sequence Transportan.jpg
3D structure of transportan
[http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]
Length 63 bp
Patent Application [http://www.freepatentsonline.com/y2008/0234183.html 20080234183]
Peptide
Length 21 aa
Size 2,183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
AGYLLGKINLKALAALAKKIL
Patent application by Hallbrink et al. (2003)





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

Retrieved from "http://2010.igem.org/Team:Stockholm/Project_Idea/Proteins"