IGEM:MIT/2007/Ideas3

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Contents

Inbox

  • Put Links and Papers you find for another category here
  • Put your initials next to a link if you're in the process of analyzing it

Sticky Proteins

Adhesive Properties of Pla

Metal Pumps and Metal Specific Promoters

Arsenic binding

Mussel Protein

Expressing proteins on E coli cell membranes

Water Purification Methods

Metal Pumps and Metal Specific Promoters

Mussel Protein

Error fetching PMID 15184131:
Error fetching PMID 15932281:
Error fetching PMID 17507090:
Error fetching PMID 16979252:
Error fetching PMID 16920796:
Error fetching PMID 17360430:
Error fetching PMID 17475323:
Error fetching PMID 16600968:
Error fetching PMID 16448666:
Error fetching PMID 15531628:
Error fetching PMID 11698382:
Error fetching PMID 17469847:
Error fetching PMID 12039531:
Error fetching PMID 15035661:
Error fetching PMID 9048419:
Error fetching PMID 16873017:
Error fetching PMID 7737512:
Error fetching PMID 15620878:
Error fetching PMID 10021411:
Error fetching PMID 10998254:
Error fetching PMID 9206011:
Error fetching PMID 3089286:
Error fetching PMID 6298211:
Error fetching PMID 11258900:
Error fetching PMID 7650037:
  1. Error fetching PMID 15184131: [Hwang04]
  2. Error fetching PMID 15932281: [Hwang05]
  3. Error fetching PMID 17507090: [Hwang07]
  4. Error fetching PMID 16979252: [Hwang07a]
  5. Error fetching PMID 16920796: [Lee06]
  6. Error fetching PMID 17360430: [Lin07]
  7. Error fetching PMID 17475323: [Wang07]
  8. Error fetching PMID 16600968: [Rice07]
  9. Error fetching PMID 16448666: [Dane06]
  10. Error fetching PMID 15531628: [Bessette04]
  11. Error fetching PMID 11698382: [Etz01]
  12. Error fetching PMID 17469847: [Hall07]
  13. Error fetching PMID 12039531: [Samuelson02]
  14. Error fetching PMID 15035661: [Wernerus04]
  15. Error fetching PMID 9048419: [Gebhart96]
  16. Error fetching PMID 16873017: [Kenan06]
  17. Error fetching PMID 7737512: [Adey95]
  18. Error fetching PMID 15620878: [Menendez05]
  19. Error fetching PMID 10021411: [Deming99]
  20. Error fetching PMID 10998254: [Burzio00]
  21. Error fetching PMID 9206011: [Burzio97]
  22. Error fetching PMID 3089286: [Marumo86]
  23. Error fetching PMID 6298211: [Waite83]
  24. Error fetching PMID 11258900: [Waite01]
  25. Error fetching PMID 7650037: [Papov95]
All Medline abstracts: PubMed HubMed


Mgfp-5 Amino Acid Sequence

 1 sseeykggyy pgntyhyhsg gsyhgsgyhg gykgkyygka kkyyykykns gkykylkkar
61 kyhrkgykky ygggss

/lue


6.20.07

KNOWN PEPTIDES/PROTEINS AND CHARACTERISTICS (please update!)

  • Name of peptide/protein
    • Paper/Reference
    • Length in amino acids
    • Obstacles for synthesis?
    • Relevant characteristics/Other pertinent information

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

  • Mgfp-5/Mefp-5
    • Hwang, et al
    • 75 aa
    • Obstacles AGK
      • "However, these attempts have failed to express functional and economical mussel adhesive proteins for several reasons, including a highly biased amino acid composition (5 amino acid types comprised �89% of the total amino acids), different codon usage preference between mussel and other expression systems (tRNA utilization problem), and small amount of adhesive produced" - Hwang
      • Presence of fp-5 has adverse effects on cell growth.
    • Positives AGK
      • Known sequence
      • Very adhesive
      • Has a 30% DOPA level, which no other foot protein comes close to
      • From M. galloprovincialis; Very adhesive; Low purification yield (but this last fact may not matter for us?)
  • Mgfp-1
    • Hwang, et al
    • … aa
  • Mgfp-3
    • Hwang, et al
    • … aa


  • Mefp-1
    • Hwang, et al
    • 10 aa ?
    • Not very adhesive
  • Mefp-5
  • Mefp-1

Water Purification Methods

OmpX

Error fetching PMID 7836315:
  1. Error fetching PMID 7836315: [Mecsas95]

[OmpX sequence]

Sequence for CPX

  • Total length is 558 bp + length of passenger peptide
  1. Native SS - 69 bp
     MKKIACLSALAAVLAFTAGTSVA 
  2. Embedded SfiI restriction site - 15 bp
     GQSGQ 
  3. Passenger Peptide
     XXXXXXXXXXXXXX 
  4. Sequence - 18 bp
     GGQSGQ  
  5. S54-F148 - 285 bp
     SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 
  6. Join native C and N - 12 bp
     GGSG 
  7. A1-S53 - 159 bp
     ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS 

Papers!

Error fetching PMID 10698802:
Error fetching PMID 10049868:
Error fetching PMID 9758845:
Error fetching PMID 7608087:
Error fetching PMID 10931321:
  1. Error fetching PMID 10698802: [Samuelson00]
  2. Error fetching PMID 10049868: [Kotrba99]
  3. Error fetching PMID 9758845: [Biosorbants]
  4. Error fetching PMID 7608087: [pBAD33]
  5. Error fetching PMID 10931321: [koebnik00]
All Medline abstracts: PubMed HubMed


FhuA

Error fetching PMID 6315686:
Error fetching PMID 11698382:
Error fetching PMID 9856937:
Error fetching PMID 8939430:
Error fetching PMID 9353297:
Error fetching PMID 9865695:
Error fetching PMID 3079747:
Error fetching PMID 9822833:
  1. Error fetching PMID 11698382: [Etz01]
  2. Error fetching PMID 6315686: [Coulton83]
  3. Error fetching PMID 9856937: [Ferguson91]
  4. Error fetching PMID 8939430: [Moeck96]
  5. Error fetching PMID 9353297: [Moeck97]
  6. Error fetching PMID 9865695: [Locher98]
  7. Error fetching PMID 3079747: [Coulton86]
  8. Error fetching PMID 9822833: [Hashemzadeh98]
All Medline abstracts: PubMed HubMed


OmpC

[OmpC Sequence]

Error fetching PMID 10543834:
  1. Error fetching PMID 10543834: [Xu99]


New ideas for stickiness from Drew

NEW IDEAS: how do we use conditional stickiness???

  • baby machines??? but reason for it? applications?
  • yeast surface attachement
  • coli background -- non-sticky / non-biofilm forming (indole deficient)
  • attacking diseased cells: low oxygen-induced stickiness
    • quorum sensing stickiness
    • cancer surface markers
  • contact: roy curtis (arizona state) -- salmonella as vaccine platform (have you ever wanted salmonella to stick to things)
  • stickiness as amplifier of rare phenotypes
  • fuel cell (zinc binding)
  • magnetotactic
  • geobacter (metal pilus -- iron oxide)
  • benign (neutral) biocoating for medical grade stuff
  • self-assembling bacteria (form 3d structure)
  • micron scale assembly (M13 phage factories...)
  • spatial polarity? (bacteria -- old poles and new poles!) markers?
    • yeast-- bud scar?
    • M13 easy
  • photogluing: 3D printing (what to use for?)
  • checkpoint driven stickiness: (cell cycle synchronization)
  • sticks to arterial plaque and eats it  :)
  • competant bacteria (snarfs up and integrates environmental DNA)


Heavy Metals

Error fetching PMID 3056525:
Error fetching PMID 15109722:
Error fetching PMID 15734556:
Error fetching PMID 12829276:
Error fetching PMID 2530602:
Error fetching PMID 17475501:
Error fetching PMID 16294830:
Error fetching PMID 16307789:
Error fetching PMID 16028496:
Error fetching PMID 12119168:
Error fetching PMID 17306392:
Error fetching PMID 11092247:
  1. Error fetching PMID 3056525: [Hou88]
  2. Error fetching PMID 15109722: [DeMarco04]
  3. Error fetching PMID 15734556: [Paul05]
  4. Error fetching PMID 12829276: [Mergeay03]
  5. Error fetching PMID 2530602: [Weinberg89]
  6. Error fetching PMID 17475501: [Mizuno07]
  7. Error fetching PMID 16294830: [Mehta05]
  8. Error fetching PMID 16307789: [Munoz06]
  9.  ://water.usgs.gov/wid/html/bioremed.html

    [http]

  10. Error fetching PMID 16028496: [Yang05]
  11. Error fetching PMID 12119168: [Clemes02]
  12. Error fetching PMID 17306392: [Tripathi07]
  13. Error fetching PMID 11092247: [Kamnev00]
All Medline abstracts: PubMed HubMed
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