Team:Stockholm/Project Idea/Proteins

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)		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)		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)		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		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)		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.

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.

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		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)