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

  1. Hwang DS, Yoo HJ, Jun JH, Moon WK, and Cha HJ. . pmid:15184131. PubMed HubMed [Hwang04]
  2. Hwang DS, Gim Y, and Cha HJ. . pmid:15932281. PubMed HubMed [Hwang05]
  3. Hwang DS, Gim Y, Yoo HJ, and Cha HJ. . pmid:17507090. PubMed HubMed [Hwang07]
  4. Hwang DS, Gim Y, Kang DG, Kim YK, and Cha HJ. . pmid:16979252. PubMed HubMed [Hwang07a]
  5. Lee H, Scherer NF, and Messersmith PB. . pmid:16920796. PubMed HubMed [Lee06]
  6. Lin Q, Gourdon D, Sun C, Holten-Andersen N, Anderson TH, Waite JH, and Israelachvili JN. . pmid:17360430. PubMed HubMed [Lin07]
  7. Wang J, Liu C, Lu X, and Yin M. . pmid:17475323. PubMed HubMed [Wang07]
  8. Rice JJ, Schohn A, Bessette PH, Boulware KT, and Daugherty PS. . pmid:16600968. PubMed HubMed [Rice07]
  9. Dane KY, Chan LA, Rice JJ, and Daugherty PS. . pmid:16448666. PubMed HubMed [Dane06]
  10. Bessette PH, Rice JJ, and Daugherty PS. . pmid:15531628. PubMed HubMed [Bessette04]
  11. Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. . pmid:11698382. PubMed HubMed [Etz01]
  12. Hall SS, Mitragotri S, and Daugherty PS. . pmid:17469847. PubMed HubMed [Hall07]
  13. Samuelson P, Gunneriusson E, Nygren PA, and Ståhl S. . pmid:12039531. PubMed HubMed [Samuelson02]
  14. Wernérus H and Ståhl S. . pmid:15035661. PubMed HubMed [Wernerus04]
  15. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. . pmid:9048419. PubMed HubMed [Gebhart96]
  16. Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. . pmid:16873017. PubMed HubMed [Kenan06]
  17. Adey NB, Mataragnon AH, Rider JE, Carter JM, and Kay BK. . pmid:7737512. PubMed HubMed [Adey95]
  18. Menendez A and Scott JK. . pmid:15620878. PubMed HubMed [Menendez05]
  19. Deming TJ. . pmid:10021411. PubMed HubMed [Deming99]
  20. Burzio LA and Waite JH. . pmid:10998254. PubMed HubMed [Burzio00]
  21. Burzio LO, Burzio VA, Silva T, Burzio LA, and Pardo J. . pmid:9206011. PubMed HubMed [Burzio97]
  22. Marumo K and Waite JH. . pmid:3089286. PubMed HubMed [Marumo86]
  23. Waite JH. . pmid:6298211. PubMed HubMed [Waite83]
  24. Waite JH and Qin X. . pmid:11258900. PubMed HubMed [Waite01]
  25. Papov VV, Diamond TV, Biemann K, and Waite JH. . pmid:7650037. PubMed HubMed [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

  1. Mecsas J, Welch R, Erickson JW, and Gross CA. . pmid:7836315. PubMed HubMed [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!

  1. Samuelson P, Wernérus H, Svedberg M, and Ståhl S. . pmid:10698802. PubMed HubMed [Samuelson00]
  2. Kotrba P, Dolecková L, de Lorenzo V, and Ruml T. . pmid:10049868. PubMed HubMed [Kotrba99]
  3. Pazirandeh M, Wells BM, and Ryan RL. . pmid:9758845. PubMed HubMed [Biosorbants]
  4. Guzman LM, Belin D, Carson MJ, and Beckwith J. . pmid:7608087. PubMed HubMed [pBAD33]
  5. Koebnik R, Locher KP, and Van Gelder P. . pmid:10931321. PubMed HubMed [koebnik00]
All Medline abstracts: PubMed HubMed


FhuA

  1. Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. . pmid:11698382. PubMed HubMed [Etz01]
  2. Coulton JW, Mason P, and DuBow MS. . pmid:6315686. PubMed HubMed [Coulton83]
  3. Ferguson AD, Hofmann E, Coulton JW, Diederichs K, and Welte W. . pmid:9856937. PubMed HubMed [Ferguson91]
  4. Moeck GS, Tawa P, Xiang H, Ismail AA, Turnbull JL, and Coulton JW. . pmid:8939430. PubMed HubMed [Moeck96]
  5. Moeck GS, Coulton JW, and Postle K. . pmid:9353297. PubMed HubMed [Moeck97]
  6. Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, and Moras D. . pmid:9865695. PubMed HubMed [Locher98]
  7. Coulton JW, Mason P, Cameron DR, Carmel G, Jean R, and Rode HN. . pmid:3079747. PubMed HubMed [Coulton86]
  8. Hashemzadeh-Bonehi L, Mehraein-Ghomi F, Mitsopoulos C, Jacob JP, Hennessey ES, and Broome-Smith JK. . pmid:9822833. PubMed HubMed [Hashemzadeh98]
All Medline abstracts: PubMed HubMed


OmpC

[OmpC Sequence]

  1. Xu Z and Lee SY. . pmid:10543834. PubMed HubMed [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)
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