Team:Stockholm/Project Idea/Proteins

From 2010.igem.org

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== Network analysis and prove of concept ==
+
== Proteins ==
-
[[Image:Net_Image_confidence_View_igem_stockholm_modelling_report.png|590px|thumb|center|Figure 1 Produced by STRING database Jensen et al. Nucleic Acids Res. 2009, 37(Database issue):D412-6]]
+
-
Currently Wet-lab members are working on several proteins that according to previous research have been pointed out to have a positive effect on repigmentation of vitiligo affected skin areas. The idea behind why we chose the biomolecules of interest is presented under the section planning on our wiki homepage. In this section we try to explain a simple interaction network of the specific genes coding the biomolecules. The goal is to give a clear picture of how the genes interact with other potential genes in a way that could result a restroring of the affected skin color.  
+
=== 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<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, 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)].  
-
As a starting point, we began with the article [http://www.ncbi.nlm.nih.gov/pubmed/18426409 Strömberg S et al. (2008)]. In this paper they identified some 859 genes as differentially regulated genes in pigment skin cells called melanocytes. These genes can be classified in several groups based on their possible cellular role (Strömberg et al. 2008). These groups are:
+
{|border="1" align="center" cellpadding="3" cellspacing="0"
-
# Developing melanocytes
+
!colspan="2"|Gene (cDNA)
-
# Melanin synthesis (melanogenesis) and transport of melanosomes to keratinocytes
+
|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]
-
# Cell adhesion
+
|-
-
# Antigen presenting
+
|width="130"|'''Length'''
 +
|width="130"|465 bp
 +
|-
 +
|'''GenBank'''
 +
|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br />
 +
|-
 +
!colspan="2"|Protein
 +
|-
 +
|'''Length'''
 +
|154 aa
 +
|-
 +
|'''Size'''
 +
|15,936 Da
 +
|-
 +
|'''Fasta'''
 +
|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br />
 +
|-
 +
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].
 +
|}
-
In fig. 1, a summarized regulatory network of some candidate genes are illustated. We intentionally chose to present interactions that have currently been investigated in order to support our study.
 
-
[[Image:SU_igem_mitf_regulatory_site.jpg|200px|thumb|left|Figure 2 Regulators and transcription-factor binding sites on the MITF promoter. Levy et al., 2006]]
+
----
-
out of those genes, it seemed that [http://www.ncbi.nlm.nih.gov/gene/4286 MITF] is one of the most regulated and regulating genes in vitiligo disease. This was the first block of the map. . The MITF promoter is targeted by several transcription factors that are important in neural-crest development and signaling. Transcription factors implicated in the regulation of the MITF promoter include PAX3, cAMP-responsive element binding protein (CREB), SOX10, LEF1 (also known as TCF), one cut domain 2 (ONECUT-2) and MITF itself, Fig. 2 (Levy et al., 2006). It also regulates both the survival and differentiation of melanocytes, and enzymes which are necessary for melanin production. (Levy et al., 2006; T.J. Hemesath et al., 1994; N.J. Bentley et al., 1994;  K. Yasumoto et al., 1994; C. Bertolotto et al., 1998). So, the regulation of multiple pigmentation and differentiation related genes by MITF (Levy et al., 2006) convinced us that MITF is a central regulator of melanogenesis.
+
 +
=== 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.
-
There are evidences for the accumulation of H2O2 in vitiliginous skin  (K. U. Schallreuter et al., 1999, 2001, 2006) and low levels of SOD and CAT (A. Jalel et. al., 2008; Koca R et. al., 2004; K. U. Schallreuter et al. 1991; Maresca V et. al. , 1997; ). It was also shown that calcium uptake is defective in vitiliginous skin in keratocytes (K. U. Schallreuter et al. 1988) as well as Melanocytes(K.U. Schallreuter et al., 1996), later the effect of accumulation of H2O2 in the epidermis of patients with vitiligo which leads to disruption calcium homeostasis in the skin was observed (K. U. Schallreuter et al. ,2007). This suggests that an oxidative stress is a pathogenic event in the degeneration of melanocytes (Strömberg S et al. ,2008).
+
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.  
-
We hypothesized that extra levels of SOD could improve the Melanocytes survivability and help re-pigmentation.
+
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!colspan="2"|Gene (cDNA)
 +
|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg‎|250px]]<br />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]
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|750 bp
 +
|-
 +
|'''GenBank'''
 +
|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br />
 +
|-
 +
!colspan="2"|Protein
 +
|-
 +
|'''Length'''
 +
|249 aa
 +
|-
 +
|'''Size'''
 +
|27,330 Da
 +
|-
 +
|'''Fasta'''
 +
|[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 /><br><br><br><br><br>
 +
|}
-
When thinking about re-pigmentation in vitiliginous skin, the first thing comes to mind is lack of melanin. There are evidences that melanocytes are still available in depigmented epidermis of patients with vitiligo even after 25 years (Tobin DJ et. al., 2000). So if melanocytes can't deliver melanin to keratinocytes or they are producing very low amount, it is possible to produce melanin using synthetic biology and deliver it to help re-pigmentation.
+
----
-
[http://www.nature.com/jid/journal/v125/n2/full/5603495a.html ]
+
=== Human basic fibroblast growth factor (bFGF) ===
 +
 
 +
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!colspan="2"|Gene (cDNA)
 +
|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|468 bp
 +
|-
 +
|'''GenBank'''
 +
|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br />
 +
|-
 +
!colspan="2"|Protein
 +
|-
 +
|'''Length'''
 +
|155 aa
 +
|-
 +
|'''Size'''
 +
|17,353 Da
 +
|-
 +
|'''Fasta'''<br /><br><br><br><br>
 +
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br><br><br><br>
 +
|}
 +
 
 +
 
 +
----
 +
 
 +
=== Protein A, z domain ===
 +
 
 +
{|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>
 +
|}
 +
 
 +
 
 +
----
 +
 
 +
=== IgG protease (IdeS) ===
 +
 
 +
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!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]
 +
|-
 +
|width="130"|'''Length'''
 +
|width="130"|930 bp
 +
|-
 +
|'''GenBank'''
 +
|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br />
 +
|-
 +
!colspan="2"|Protein
 +
|-
 +
|'''Length'''
 +
|339 aa
 +
|-
 +
|'''Size'''
 +
|37,977 Da
 +
|-
 +
|'''Fasta'''<br /><br><br><br><br><br>
 +
|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br><br><br><br><br>
 +
|}
 +
 
 +
 
 +
 
 +
----
 +
 
 +
== 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.
 +
 
 +
{|border="1" align="center" cellpadding="3" cellspacing="0"
 +
!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 />
 +
|}
 +
 
 +
 
 +
----
 +
 
 +
=== 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="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'''
 +
|width="130"|63 bp
 +
|-
 +
|'''Patent Application'''
 +
|[http://www.freepatentsonline.com/y2008/0234183.html 20080234183]<br />
 +
|-
 +
!colspan="2"|Peptide
 +
|-
 +
|'''Length'''
 +
|21 aa
 +
|-
 +
|'''Size'''
 +
|2,183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])
 +
|-
 +
|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL
 +
|-
 +
|colspan="2"|Patent application by Hallbrink et al. (2003)<br />
 +
|}
 +
 
 +
<!--|-
 +
|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]-->
 +
----
 +
 
 +
|}
{{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"