Data sources

During our project, we required many data. We used the data of protein-protein interactions for signal transduction pathway deciding, protein sequence and domain description for modified FGFR design, gene sequence for modified FGFR sequence synthesis, structures or sequences of antibodies and FGF binding domain of FGFR for structural alignment. These data are from Uniprot, PID, NCBI and RCSB PDB.

Uniprot

Uniprot provides sequences of many proteins and domain description of well-researched proteins. Key advantage to use Uniprot is domain description. Without knowledge of function of each parts of protein, to design engineered protein for detecting Mycobacterium. Tubeculosis antigen MPT51 is impossible. Uniprot provided the information of location of FGF binding domain of FGFR which is replaced by our single-chain antibody 16A1. Uniprot also provided sequences of some antibodies to make single chain antibody sequences.

PID

PID(Pathway Interaction Database) provides the interaction networks between protein and protein or protein and DNA through certain signal transduction pathway. This Protein-protein interaction(PPI) and protein-DNA interaction(PDI) data helped us to port Human signal transduction pathway which is activated by FGF to fission yeast. Without knowledge of PPI and PDI through FGF signal pathway, we must undergo many trial and error of adding and removing of proteins and promoters to form working signal transduction pathway. With the data from PID, we decided to port the FGF->FGFR1->STAT1->GAS pathway from human to fission yeast.

NCBI

NCBI provides many data for biologists. We used protein sequence and DNA sequence from NCBI nucleotide database and protein database. DNA sequence is very important to us because gene sequence of original protein is required to synthesize novel engineered protein. Even we don't synthesize gene, we should know the sequence of gene because biobrick require not only nucleotide material, but also its sequence information. NCBI also provided sequences of some antibodis to make single chain antibody sequence, and many Journals through PubMed service.

RCSB PDB

RCSB PDB(Protein Data Bank) provides the data of structure of protein or other biomolecules. Key feature of data from PDB is the structure. NCBI or Uniprot provide the sequence of proteins, but it don't shows us the 3D-structure of them. With the structural similarity between FGF binding domain of FGFR and single chain antibody 16A1, we can sure that the replacement of FGF binding domain with 16A1 to detect MPT51 is appropriate.

References

Fig 1. Estimated TB incidence rates, 2008 WHO Library Cataloguing-in-Publication Data,

Global tuberculosis control: a short update to the 2009 report

Fig 2. People suffering from malaria and TB

Mother nature network, article “New form of malaria threatens Thai-Cambodia border”

Fig 3. Researching disease

Fondation Merieux Research Programs

http://www.fondation-merieux.org/-research-programmes.html

Fig 4. Antibody

Cytomx http://cytomx.com/technologies.html

Fig 5. MPT51

RCSB Protein Database, "The crystal structure of Mycobacterium tuberculosis MPT51"

Fig 6. E.coli Statistics

http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi

Fig 7. Yeast homologous recombinant

Bioneer http://pombe.bioneer.co.kr/technic_infomation/construction.jsp

Fig 8. CRYSTAL STRUCTURE OF A TERNARY FGF2-FGFR1-HEPARIN COMPLEX

RCSB Protein Database, "CRYSTAL STRUCTURE OF A TERNARY FGF2-FGFR1-HEPARIN COMPLEX"

Fig 9. FGF signaling pathway

Nature Pathway Interation Database, "FGF signaling pathway"

http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=fgf_pathway&source=NCI-Nature%20curated&what=graphic&jpg=on&ppage=1

Fig 10. Unneccesary Syndecan-2 Function

http://www.kaomp.org/new/board_view.htm?table_name=photo_0&currPage=6&aq_id=92&aq_type=&aq_value

Fig 11. Structural bases of unphosphorylated STAT1 association and receptor binding

RCSB Protein Database, "Structural bases of unphosphorylated STAT1 association and receptor binding"

Fig 12. Roberto, Proteína fluorescente verde – história e perspectivas, Química de Produtos Naturais (2009)

Fig 13. KAIST success!

http://imperfectaction.com/blog/2009/03/04/entrepreneurship/definition-of-success/

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