IGEM:MIT/2007/Ideas3

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*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>
-
==Water Purification Methods==
+
Mgfp-5 Amino Acid Sequence
 +
<pre>
 +
1 sseeykggyy pgntyhyhsg gsyhgsgyhg gykgkyygka kkyyykykns gkykylkkar
 +
61 kyhrkgykky ygggss
 +
</pre>
 +
/lue
-
==OmpX==
 
-
[[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=176659&blobtype=pdf|Mecsas, J., Welch, R., Erickson, J.W., and Gross, C.A. 1995. Identification and characterization of an outer membrane protein, OmpX, in Escherichia coli that is homologous to a family of outer membrane proteins including Ail of Yersinia enterocolitica. J. Bacteriol. 177: 799–804.Acad. Sci. 98: 3750–3755. Wittrup, K.D. 2001. Protein engineering by cell-surface display. Curr. Opin. Biotechnol. 12: 395–399.]]
 
-
[[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=559693 |OmpX sequence]]
+
6.20.07
-
===Sequence===
+
===KNOWN PEPTIDES/PROTEINS AND CHARACTERISTICS (please update!)===
-
#Native SS
+
-
<pre>
+
-
MKKIACLSALAAVLAFTAGTSVA
+
-
</pre>
+
-
#Embedded SfiI restriction site
+
-
<pre>
+
-
GQSGQ
+
-
</pre>
+
-
#Passenger Peptide
+
-
<pre>
+
-
XXXXXXXXXXXXXX
+
-
</pre>
+
-
#Sequence
+
-
<pre>
+
-
GGQSGQ
+
-
</pre>
+
-
#S54-F148
+
-
<pre>
+
-
SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
+
-
</pre>
+
-
Join native C and N
+
-
GGSG
+
-
A1-S53
+
*Name of peptide/protein
-
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS
+
**Paper/Reference
 +
**Length in amino acids
 +
**Obstacles for synthesis?
 +
**Relevant characteristics/Other pertinent information
 +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-
==Papers!==
+
*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?)
 +
 
 +
*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

  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

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


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)
Retrieved from "http://www.openwetware.org/wiki/IGEM:MIT/2007/Ideas3"
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