Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

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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 />
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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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|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br><br><br><br><br>
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|'''Fasta'''
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|'''Fasta'''<br /><br><br><br><br>
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|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br />
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|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br><br><br><br>
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|colspan="2"|First reported by <unknown><br />
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|55,439 Da (full protein)
|55,439 Da (full protein)
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|'''Fasta'''<br /><br><br><br><br><br>
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|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br />
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|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br><br><br><br><br>
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|'''Fasta'''
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|'''Fasta'''<br /><br><br><br><br><br>
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|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br />
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|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br><br><br><br><br>
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|colspan="2"|First reported by <unknown><br />
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== Cell penetrating peptides ==
== Cell penetrating peptides ==
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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.
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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.

Latest revision as of 01:19, 28 October 2010


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 Hallewell et al., (1985).

Gene (cDNA) SOD1 dimeric.png
3D structure of human SOD1 in its dimeric form. Primary citation Leinartaite et al. (2010)
Length 465 bp
GenBank AY450286.1
Protein
Length 154 aa
Size 15,936 Da
Fasta SOD1
First reported by 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 (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 Lamb et al. 2001
Length 750 bp
GenBank NM_001182535.1
Protein
Length 249 aa
Size 27,330 Da
Fasta yCCS
First reported by Culotta et al. (1997).







Human basic fibroblast growth factor (bFGF)

Gene (cDNA) BFGF.jpg
3D structure of bFGF. Primary citation Bae et al. 2010
Length 468 bp
GenBank (full mRNA) 153285460
Protein
Length 155 aa
Size 17,353 Da
Fasta




bFGF






Protein A, z domain

Genepart ProteinA z domain.jpg
3D structure of the Z-domain of Protein A. Primary citation Tashiro et al. 2010
Length 174 bp
GenBank 2859152 (full protein)
Protein
Length 58 aa

(508 aa, full protein )

Size 55,439 Da (full protein)
Fasta





Protein A (full protein)







IgG protease (IdeS)

Gene (cDNA) IdeS.jpg
Primary citation Wenig et al. 2004
Length 930 bp
GenBank 6985687
Protein
Length 339 aa
Size 37,977 Da
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 (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 (Gump and Dowdy, 2007). TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) trans-activating transcriptional activator (Tat) (Green and Loewenstein, 1988; 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 WO 2005/084158 A2
Peptide
Length 11 aa
Size 1,560 Da (calculated)
YGRKKRRQRRR
First reported by

Green et al. (1988) and 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 (Huang et al., 2010). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells (Park et al., 2003). As LMWP has been shown to be neither toxic nor immunogenic (Chang et al. a, 2001; Chang et al. b, 2001; 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 (McKay et al., 1986; 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 20070071677
Peptide
Length 14 aa
Size 1,880 Da (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 (Kilk et al., 2005). Membrane permeation is both energy and temperature independent (Hällbrink et al., 2001). The exact mechanism for penetration is still unclear (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 (Soomets et al., 2000; 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
www.dbb.su.se
Length 63 bp
Patent Application 20080234183
Peptide
Length 21 aa
Size 2,183 Da (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/