Difference between revisions of "IGEM:MIT/2007/Ideas3"

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*Put Links and Papers you find for another category here
 
*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
 
*Put your initials next to a link if you're in the process of analyzing it
 +
 +
===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===
 
===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 111: Line 112:
  
 
==Water Purification Methods==
 
==Water Purification Methods==
 
 
==OmpX==
 
<biblio>
 
# Mecsas95 pmid=7836315
 
</biblio>
 
 
[[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=559693 OmpX sequence]]
 
 
===Sequence for CPX===
 
*Total length is 558 bp + length of passenger peptide
 
#Native SS - 69 bp <pre> MKKIACLSALAAVLAFTAGTSVA </pre>
 
#Embedded SfiI restriction site - 15 bp<pre> GQSGQ </pre>
 
#Passenger Peptide <pre> XXXXXXXXXXXXXX </pre>
 
#Sequence - 18 bp<pre> GGQSGQ  </pre>
 
#S54-F148 - 285 bp<pre> SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF </pre>
 
#Join native C and N - 12 bp<pre> GGSG </pre>
 
#A1-S53 - 159 bp<pre> ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS </pre>
 
 
==Papers!==
 
<biblio>
 
#Samuelson00 pmid=10698802
 
#Kotrba99 pmid=10049868
 
#Biosorbants pmid=9758845
 
#pBAD33 pmid=7608087
 
#koebnik00 pmid=10931321
 
</biblio>
 
 
  
 
==FhuA==
 
==FhuA==
Line 153: Line 126:
  
  
==OmpC==
+
==New ideas for stickiness from Drew==
[[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=15832358 OmpC Sequence]]
+
NEW IDEAS:
<biblio>
+
how do we use conditional stickiness???
#Xu99 pmid=10543834
+
 
</biblio>
+
*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)

Latest revision as of 20:28, 24 June 2007

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. Expression of functional recombinant mussel adhesive protein Mgfp-5 in Escherichia coli. Appl Environ Microbiol. 2004 Jun;70(6):3352-9. DOI:10.1128/AEM.70.6.3352-3359.2004 | PubMed ID:15184131 | HubMed [Hwang04]
  2. Hwang DS, Gim Y, and Cha HJ. Expression of functional recombinant mussel adhesive protein type 3A in Escherichia coli. Biotechnol Prog. 2005 May-Jun;21(3):965-70. DOI:10.1021/bp050014e | PubMed ID:15932281 | HubMed [Hwang05]
  3. Hwang DS, Gim Y, Yoo HJ, and Cha HJ. Practical recombinant hybrid mussel bioadhesive fp-151. Biomaterials. 2007 Aug;28(24):3560-8. DOI:10.1016/j.biomaterials.2007.04.039 | PubMed ID:17507090 | HubMed [Hwang07]
  4. Hwang DS, Gim Y, Kang DG, Kim YK, and Cha HJ. Recombinant mussel adhesive protein Mgfp-5 as cell adhesion biomaterial. J Biotechnol. 2007 Jan 20;127(4):727-35. DOI:10.1016/j.jbiotec.2006.08.005 | PubMed ID:16979252 | HubMed [Hwang07a]
  5. Lee H, Scherer NF, and Messersmith PB. Single-molecule mechanics of mussel adhesion. Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):12999-3003. DOI:10.1073/pnas.0605552103 | PubMed ID:16920796 | HubMed [Lee06]
  6. Lin Q, Gourdon D, Sun C, Holten-Andersen N, Anderson TH, Waite JH, and Israelachvili JN. Adhesion mechanisms of the mussel foot proteins mfp-1 and mfp-3. Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3782-6. DOI:10.1073/pnas.0607852104 | PubMed ID:17360430 | HubMed [Lin07]
  7. Wang J, Liu C, Lu X, and Yin M. Co-polypeptides of 3,4-dihydroxyphenylalanine and L-lysine to mimic marine adhesive protein. Biomaterials. 2007 Aug;28(23):3456-68. DOI:10.1016/j.biomaterials.2007.04.009 | PubMed ID:17475323 | HubMed [Wang07]
  8. Rice JJ, Schohn A, Bessette PH, Boulware KT, and Daugherty PS. Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci. 2006 Apr;15(4):825-36. DOI:10.1110/ps.051897806 | PubMed ID:16600968 | HubMed [Rice07]
  9. Dane KY, Chan LA, Rice JJ, and Daugherty PS. Isolation of cell specific peptide ligands using fluorescent bacterial display libraries. J Immunol Methods. 2006 Feb 20;309(1-2):120-9. DOI:10.1016/j.jim.2005.11.021 | PubMed ID:16448666 | HubMed [Dane06]
  10. Bessette PH, Rice JJ, and Daugherty PS. Rapid isolation of high-affinity protein binding peptides using bacterial display. Protein Eng Des Sel. 2004 Oct;17(10):731-9. DOI:10.1093/protein/gzh084 | PubMed ID:15531628 | HubMed [Bessette04]
  11. Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. Bacterial phage receptors, versatile tools for display of polypeptides on the cell surface. J Bacteriol. 2001 Dec;183(23):6924-35. DOI:10.1128/JB.183.23.6924-6935.2001 | PubMed ID:11698382 | HubMed [Etz01]
  12. Hall SS, Mitragotri S, and Daugherty PS. Identification of peptide ligands facilitating nanoparticle attachment to erythrocytes. Biotechnol Prog. 2007 May-Jun;23(3):749-54. DOI:10.1021/bp060333l | PubMed ID:17469847 | HubMed [Hall07]
  13. Samuelson P, Gunneriusson E, Nygren PA, and Ståhl S. Display of proteins on bacteria. J Biotechnol. 2002 Jun 26;96(2):129-54. PubMed ID:12039531 | HubMed [Samuelson02]
  14. Wernérus H and Ståhl S. Biotechnological applications for surface-engineered bacteria. Biotechnol Appl Biochem. 2004 Dec;40(Pt 3):209-28. DOI:10.1042/BA20040014 | PubMed ID:15035661 | HubMed [Wernerus04]
  15. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. Adhesive peptides selected by phage display: characterization, applications and similarities with fibrinogen. Pept Res. 1996 Nov-Dec;9(6):269-78. PubMed ID:9048419 | HubMed [Gebhart96]
  16. Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. Peptide-PEG amphiphiles as cytophobic coatings for mammalian and bacterial cells. Chem Biol. 2006 Jul;13(7):695-700. DOI:10.1016/j.chembiol.2006.06.013 | PubMed ID:16873017 | HubMed [Kenan06]
  17. Adey NB, Mataragnon AH, Rider JE, Carter JM, and Kay BK. Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene. 1995 Apr 14;156(1):27-31. PubMed ID:7737512 | HubMed [Adey95]
  18. Menendez A and Scott JK. The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal Biochem. 2005 Jan 15;336(2):145-57. DOI:10.1016/j.ab.2004.09.048 | PubMed ID:15620878 | HubMed [Menendez05]
  19. Deming TJ. Mussel byssus and biomolecular materials. Curr Opin Chem Biol. 1999 Feb;3(1):100-5. PubMed ID:10021411 | HubMed [Deming99]
  20. Burzio LA and Waite JH. Cross-linking in adhesive quinoproteins: studies with model decapeptides. Biochemistry. 2000 Sep 12;39(36):11147-53. PubMed ID:10998254 | HubMed [Burzio00]
  21. Burzio LO, Burzio VA, Silva T, Burzio LA, and Pardo J. Environmental bioadhesion: themes and applications. Curr Opin Biotechnol. 1997 Jun;8(3):309-12. PubMed ID:9206011 | HubMed [Burzio97]
  22. Marumo K and Waite JH. Optimization of hydroxylation of tyrosine and tyrosine-containing peptides by mushroom tyrosinase. Biochim Biophys Acta. 1986 Jul 25;872(1-2):98-103. PubMed ID:3089286 | HubMed [Marumo86]
  23. Waite JH. Evidence for a repeating 3,4-dihydroxyphenylalanine- and hydroxyproline-containing decapeptide in the adhesive protein of the mussel, Mytilus edulis L. J Biol Chem. 1983 Mar 10;258(5):2911-5. PubMed ID:6298211 | HubMed [Waite83]
  24. Waite JH and Qin X. Polyphosphoprotein from the adhesive pads of Mytilus edulis. Biochemistry. 2001 Mar 6;40(9):2887-93. PubMed ID:11258900 | HubMed [Waite01]
  25. Papov VV, Diamond TV, Biemann K, and Waite JH. Hydroxyarginine-containing polyphenolic proteins in the adhesive plaques of the marine mussel Mytilus edulis. J Biol Chem. 1995 Aug 25;270(34):20183-92. PubMed ID:7650037 | 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. Bacterial phage receptors, versatile tools for display of polypeptides on the cell surface. J Bacteriol. 2001 Dec;183(23):6924-35. DOI:10.1128/JB.183.23.6924-6935.2001 | PubMed ID:11698382 | HubMed [Etz01]
  2. Coulton JW, Mason P, and DuBow MS. Molecular cloning of the ferrichrome-iron receptor of Escherichia coli K-12. J Bacteriol. 1983 Dec;156(3):1315-21. PubMed ID:6315686 | HubMed [Coulton83]
  3. Ferguson AD, Hofmann E, Coulton JW, Diederichs K, and Welte W. Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. Science. 1998 Dec 18;282(5397):2215-20. PubMed ID:9856937 | HubMed [Ferguson91]
  4. Moeck GS, Tawa P, Xiang H, Ismail AA, Turnbull JL, and Coulton JW. Ligand-induced conformational change in the ferrichrome-iron receptor of Escherichia coli K-12. Mol Microbiol. 1996 Nov;22(3):459-71. DOI:10.1046/j.1365-2958.1996.00112.x | PubMed ID:8939430 | HubMed [Moeck96]
  5. Moeck GS, Coulton JW, and Postle K. Cell envelope signaling in Escherichia coli. Ligand binding to the ferrichrome-iron receptor fhua promotes interaction with the energy-transducing protein TonB. J Biol Chem. 1997 Nov 7;272(45):28391-7. PubMed ID:9353297 | HubMed [Moeck97]
  6. Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, and Moras D. Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell. 1998 Dec 11;95(6):771-8. PubMed ID:9865695 | HubMed [Locher98]
  7. Coulton JW, Mason P, Cameron DR, Carmel G, Jean R, and Rode HN. Protein fusions of beta-galactosidase to the ferrichrome-iron receptor of Escherichia coli K-12. J Bacteriol. 1986 Jan;165(1):181-92. PubMed ID:3079747 | HubMed [Coulton86]
  8. Hashemzadeh-Bonehi L, Mehraein-Ghomi F, Mitsopoulos C, Jacob JP, Hennessey ES, and Broome-Smith JK. Importance of using lac rather than ara promoter vectors for modulating the levels of toxic gene products in Escherichia coli. Mol Microbiol. 1998 Nov;30(3):676-8. PubMed ID:9822833 | 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)