Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

(Difference between revisions)

Latest revision as of 01:19, 28 October 2010

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)].

Protein
Gene (cDNA)		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]
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.

Protein
Gene (cDNA)		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]
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)

Protein
Gene (cDNA)		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]
Length	155 aa
Size	17,353 Da
Fasta	[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]

Protein A, z domain

Protein
Genepart		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)
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)

Protein
Gene (cDNA)		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]
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.

Peptide
Sequence		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]
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)

@@ Line 15: / Line 15: @@
 |width="130"|'''Length'''
 |width="130"|465 bp
-|-
-|'''Edited nucleotide(s)'''
-|nt331 A &rarr; G
-|-
-|'''Removed restr. site(s)'''
-|PfeI
 |-
 |'''GenBank'''
@@ Line 53: / Line 47: @@
 |width="130"|'''Length'''
 |width="130"|750 bp
-|-
-|'''Edited nucleotide(s)'''
-|nt257 T &rarr; C
-|-
-|'''Removed restr. site(s)'''
-|EcoRI
 |-
 |'''GenBank'''
@@ Line 74: / Line 62: @@
 |[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>
 |}
@@ Line 88: / Line 76: @@
 |width="130"|'''Length'''
 |width="130"|468 bp
-|-
-|'''Edited nucleotide(s)'''
-|nt341 C &rarr; T
-|-
-|'''Removed restr. site(s)'''
-|AgeI
 |-
 |'''GenBank'''
-|&nbsp;<br />
+|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br />
 |-
 !colspan="2"|Protein
@@ Line 106: / Line 88: @@
 |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 />
 |}
@@ Line 123: / Line 103: @@
 |width="130"|'''Length'''
 |width="130"|174 bp
-|-
-|'''Edited nucleotide(s)'''
-| -
-|-
-|'''Removed restr. site(s)'''
-| -
 |-
 |'''GenBank'''
-|&nbsp;<br />
+|[http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)<br />
 |-
 !colspan="2"|Protein
 |-
 |'''Length'''
-|58 aa (full protein 508 aa)
+|58 aa
+(508 aa, full protein )
 |-
 |'''Size'''
-|(full protein 55,439 Da)
+|55,439 Da (full protein)
-|-
-|'''Fasta'''
-|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br />
 |-
-|colspan="2"|First reported by <unknown><br />
+|'''Fasta'''<br /><br><br><br><br><br>
+|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br><br><br><br><br>
 |}
@@ Line 158: / Line 131: @@
 |width="130"|'''Length'''
 |width="130"|930 bp
-|-
-|'''Edited nucleotide(s)'''
-| -
-|-
-|'''Removed restr. site(s)'''
-| -
 |-
 |'''GenBank'''
-|&nbsp;<br />
+|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br />
 |-
 !colspan="2"|Protein
@@ Line 176: / Line 143: @@
 |37,977 Da
 |-
-|'''Fasta'''
+|'''Fasta'''<br /><br><br><br><br><br>
-|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br />
+|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br><br><br><br><br>
-|-
-|colspan="2"|First reported by <unknown><br />
 |}
@@ Line 188: / Line 153: @@
 == Cell penetrating peptides ==
-This 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 it a potential gene or protein delivery vector.
+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.
@@ Line 201: / Line 166: @@
 |width="130"|33 bp
 |-
-|'''GenBank'''
+|'''Patent PCT'''
-|<br />
+|[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
@@ Line 210: / Line 175: @@
 |-
 |'''Size'''
-|
+|1,560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 |-
 |colspan="2" align="center"|YGRKKRRQRRR
 |-
-|colspan="2"|Original protein first reported by [http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green ''et al''. (1988)]<br />
+|colspan="2"|First reported by
-and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel ''et al''. (1988)] independently
+[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 />
 |}
@@ Line 232: / Line 197: @@
 |-
 |'''Patent Application'''
-|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677
+|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677]<br />
-]<br />
 |-
 !colspan="2"|Peptide
@@ Line 241: / Line 205: @@
 |-
 |'''Size'''
-|
+|1,880 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 |-
 |colspan="2" align="center"|VSRRRRRRGGRRRR
 |-
-|colspan="2"|First reported by <unknown><br />
+|colspan="2"|Patent application by Park et al. (2004)<br />
 |}
@@ Line 257: / Line 221: @@
 {|border="1" align="center" cellpadding="3" cellspacing="0"
 !colspan="2"|Sequence
-|rowspan="10" 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]
+|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]
 |-
 |width="130"|'''Length'''
@@ Line 271: / Line 235: @@
 |-
 |'''Size'''
-|
+|2,183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 |-
 |colspan="2" align="center"|AGYLLGKINLKALAALAKKIL
 |-
-|colspan="2"|First reported by <unknown><br />
+|colspan="2"|Patent application by Hallbrink et al. (2003)<br />
 |}
-{|border="1" align="right" cellpadding="3" cellspacing="0"
+<!--|-
-|rowspan="10" 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]
+|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]-->
-|}
 ----
-|}
-== Cell penetrating peptides ==
-This 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 it a potential gene or protein delivery vector.
-=== 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
-|-
-|'''GenBank'''
-|<br />
-|-
-!colspan="2"|Peptide
-|-
-|'''Length'''
-|11 aa
-|-
-|'''Size'''
-|
-|-
-|colspan="2" align="center"|YGRKKRRQRRR
-|-
-|colspan="2"|First reported by <unknown><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.
-{|border="1" align="center" cellpadding="3" cellspacing="0"
-!colspan="2"|Sequence
-|-
-|width="130"|'''Length'''
-|width="130"|42 bp
-|-
-|'''GenBank'''
-|<br />
-|-
-!colspan="2"|Peptide
-|-
-|'''Length'''
-|14 aa
-|-
-|'''Size'''
-|
-|-
-|colspan="2" align="center"|VSRRRRRRGGRRRR
-|-
-|colspan="2"|First reported by <unknown><br />
-|}
-----
-=== 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
-|rowspan="10" 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]
-|-
-|width="130"|'''Length'''
-|width="130"|63 bp
-|-
-|'''GenBank'''
-|<br />
-|-
-!colspan="2"|Peptide
-|-
-|'''Length'''
-|21 aa
-|-
-|'''Size'''
-|
-|-
-|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL
-|-
-|colspan="2"|First reported by <unknown><br />
-|}
-----
 |}
 {{Stockholm/Footer}}