IGEM:MIT/2007/Ideas3

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(OmpX)
Current revision (23:28, 24 June 2007) (view source)
 
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Line 3: Line 3:
*Put your initials next to a link if you're in the process of analyzing it
*Put your initials next to a link if you're in the process of analyzing it
-
===Metal Pumps and Metal Specific Promoters===
+
===Sticky Proteins===
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16923070&ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Adhesive Properties of Pla]
 +
===Metal Pumps and Metal Specific Promoters===
 +
Arsenic binding
===Mussel Protein===
===Mussel Protein===
Line 10: Line 13:
===Water Purification Methods===
===Water Purification Methods===
-
 
-
 
==Metal Pumps and Metal Specific Promoters==
==Metal Pumps and Metal Specific Promoters==
Line 17: Line 18:
==Mussel Protein==
==Mussel Protein==
 +
<biblio>
 +
# Hwang04 pmid=15184131
 +
# Hwang05 pmid=15932281
 +
# Hwang07 pmid=17507090
 +
# Hwang07a pmid=16979252
 +
# Lee06 pmid=16920796
 +
# Lin07 pmid=17360430
 +
# Wang07 pmid=17475323
 +
# Rice07 pmid=16600968
 +
# Dane06 pmid=16448666
 +
# Bessette04 pmid=15531628
 +
# Etz01 pmid=11698382
 +
# Hall07 pmid=17469847
 +
# Samuelson02 pmid=12039531
 +
# Wernerus04 pmid=15035661
 +
# Gebhart96 pmid=9048419 
 +
# Kenan06 pmid=16873017
 +
# Adey95 pmid=7737512
 +
# Menendez05 pmid=15620878
 +
# Deming99 pmid=10021411
 +
# Burzio00 pmid=10998254
 +
# Burzio97 pmid=9206011
 +
# Marumo86 pmid=3089286
 +
# Waite83 pmid=6298211
 +
# Waite01 pmid=11258900
 +
# Papov95 pmid=7650037
 +
</biblio>
 +
Mgfp-5 Amino Acid Sequence
Mgfp-5 Amino Acid Sequence
Line 26: Line 55:
/lue
/lue
-
==Water Purification Methods==
 
 +
6.20.07
-
==OmpX==
+
===KNOWN PEPTIDES/PROTEINS AND CHARACTERISTICS (please update!)===
-
<biblio>
+
-
# Mecsas95 pmid=7836315
+
-
</biblio>
+
-
[[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=559693 OmpX sequence]]
+
*Name of peptide/protein
 +
**Paper/Reference
 +
**Length in amino acids
 +
**Obstacles for synthesis?
 +
**Relevant characteristics/Other pertinent information
 +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-
===Sequence for CPX===
+
*Mgfp-5/Mefp-5
-
*Total length is 558 bp + length of passenger peptide
+
**Hwang, et al
-
#Native SS - 69 bp <pre> MKKIACLSALAAVLAFTAGTSVA </pre>
+
**75 aa
-
#Embedded SfiI restriction site - 15 bp<pre> GQSGQ </pre>
+
**Obstacles AGK
-
#Passenger Peptide <pre> XXXXXXXXXXXXXX </pre>
+
***"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
-
#Sequence - 18 bp<pre> GGQSGQ  </pre>
+
***Presence of fp-5 has adverse effects on cell growth.
-
#S54-F148 - 285 bp<pre> SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF </pre>
+
**Positives AGK
-
#Join native C and N - 12 bp<pre> GGSG </pre>
+
***Known sequence
-
#A1-S53 - 159 bp<pre> ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS </pre>
+
***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?)
-
==Papers!==
+
*fp-151
 +
**Hwang, et al 2007
 +
** fp-5 flanked by six decapeptide repeats from fp-1 AGK
 +
*** [http://www.biolbull.org/cgi/reprint/190/2/213?view=long&pmid=8652732 | fp-1 sequence: Ala-Lys-Pro-Ser-Tyr-diHyp-Hyp-Thr-DOPA-Lys]
 +
*** diHyp = 3,4 Dihydroxyproline; Hyp= 4 hydroxyproline
 +
**Positives AGK
 +
*** Purifies more easily than fp-5
 +
*** Not harmful to cells
 +
 
 +
*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==
 +
 
 +
==FhuA==
<biblio>
<biblio>
-
#Samuelson00 pmid=10698802
+
#Coulton83 pmid=6315686
-
#Kotrba99 pmid=10049868
+
#Etz01 pmid=11698382
 +
#Ferguson91 pmid=9856937
 +
#Moeck96 pmid=8939430
 +
#Moeck97 pmid=9353297
 +
#Locher98 pmid=9865695
 +
#Coulton86 pmid=3079747
 +
#Hashemzadeh98 pmid=9822833
</biblio>
</biblio>
 +
 +
 +
==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)

Current revision

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

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


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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