IGEM:MIT/2007/Ideas3

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

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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
13. Samuelson P, Gunneriusson E, Nygren PA, and Ståhl S. Display of proteins on bacteria. J Biotechnol. 2002 Jun 26;96(2):129-54. DOI:10.1016/s0168-1656(02)00043-3 |
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 |
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.
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 |
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. DOI:10.1016/0378-1119(95)00058-e |
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 |
19. Deming TJ. Mussel byssus and biomolecular materials. Curr Opin Chem Biol. 1999 Feb;3(1):100-5. DOI:10.1016/s1367-5931(99)80018-0 |
20. Burzio LA and Waite JH. Cross-linking in adhesive quinoproteins: studies with model decapeptides. Biochemistry. 2000 Sep 12;39(36):11147-53. DOI:10.1021/bi0002434 |
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. DOI:10.1016/s0958-1669(97)80008-0 |
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. DOI:10.1016/0167-4838(86)90152-4 |
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.
24. Waite JH and Qin X. Polyphosphoprotein from the adhesive pads of Mytilus edulis. Biochemistry. 2001 Mar 6;40(9):2887-93. DOI:10.1021/bi002718x |
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. DOI:10.1074/jbc.270.34.20183 |

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?)

• fp-151
  • Hwang, et al 2007
  • fp-5 flanked by six decapeptide repeats from fp-1 AGK
    • | 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

FhuA

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 |
26. 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. DOI:10.1128/jb.156.3.1315-1321.1983 |
27. 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. DOI:10.1126/science.282.5397.2215 |
28. 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 |
29. 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. DOI:10.1074/jbc.272.45.28391 |
30. 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. DOI:10.1016/s0092-8674(00)81700-6 |
31. 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. DOI:10.1128/jb.165.1.181-192.1986 |
32. 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. DOI:10.1046/j.1365-2958.1998.01116.x |

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)