Team:Stockholm/Project Idea/Proteins

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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
Edited nucleotide(s) nt331 A → G
Removed restr. site(s) PfeI
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
Edited nucleotide(s) nt257 T → C
Removed restr. site(s) EcoRI
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
Edited nucleotide(s) nt341 C → T
Removed restr. site(s) AgeI
GenBank  
Protein
Length 155 aa
Size 17,353 Da
Fasta bFGF
First reported by <unknown>



Protein A, z domain

Genepart [[Image:|250px]]
Primary citation et al. 2010]
Length 174 bp
Edited nucleotide(s) -
Removed restr. site(s) -
GenBank  
Protein
Length 58 aa
Size
Fasta ProteinA
First reported by <unknown>



IgG protease (IdeS)

Gene (cDNA) IdeS.jpg
Primary citation Wenig et al. 2004
Length 930 bp
Edited nucleotide(s) -
Removed restr. site(s) -
GenBank  
Protein
Length 339 aa
Size 37,977 Da
Fasta IdeS
First reported by <unknown>




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 (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 [[Image:‎|250px]]
Primary citation [ et al. 2001]
Length 33 bp
GenBank
Peptide
Length 11 aa
Size
YGRKKRRQRRR
First reported by <unknown>



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 [[Image:‎|250px]]
Primary citation [ et al. 2001]
Length 42 bp
GenBank
Peptide
Length 14 aa
Size
VSRRRRRRGGRRRR
First reported by <unknown>



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 [[Image:‎|250px]]
Primary citation [ et al. 2001]
Length 63 bp
GenBank
Peptide
Length 21 aa
Size
AGYLLGKINLKALAALAKKIL
First reported by <unknown>







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