IGEM:MIT/2007/Ideas3
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==Heavy Metals== | ==Heavy Metals== | ||
<biblio> | <biblio> | ||
| + | #Silver05 pmid=16133099 | ||
| + | #Bruins00 pmid=10702338 | ||
#Hou88 pmid=3056525 | #Hou88 pmid=3056525 | ||
#DeMarco04 pmid=15109722 | #DeMarco04 pmid=15109722 | ||
Revision as of 15:45, 23 June 2007
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
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
- Hwang DS, Yoo HJ, Jun JH, Moon WK, and Cha HJ. . pmid:15184131.
- Hwang DS, Gim Y, and Cha HJ. . pmid:15932281.
- Hwang DS, Gim Y, Yoo HJ, and Cha HJ. . pmid:17507090.
- Hwang DS, Gim Y, Kang DG, Kim YK, and Cha HJ. . pmid:16979252.
- Lee H, Scherer NF, and Messersmith PB. . pmid:16920796.
- Lin Q, Gourdon D, Sun C, Holten-Andersen N, Anderson TH, Waite JH, and Israelachvili JN. . pmid:17360430.
- Wang J, Liu C, Lu X, and Yin M. . pmid:17475323.
- Rice JJ, Schohn A, Bessette PH, Boulware KT, and Daugherty PS. . pmid:16600968.
- Dane KY, Chan LA, Rice JJ, and Daugherty PS. . pmid:16448666.
- Bessette PH, Rice JJ, and Daugherty PS. . pmid:15531628.
- Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. . pmid:11698382.
- Hall SS, Mitragotri S, and Daugherty PS. . pmid:17469847.
- Samuelson P, Gunneriusson E, Nygren PA, and Ståhl S. . pmid:12039531.
- Wernérus H and Ståhl S. . pmid:15035661.
- Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. . pmid:9048419.
- Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. . pmid:16873017.
- Adey NB, Mataragnon AH, Rider JE, Carter JM, and Kay BK. . pmid:7737512.
- Menendez A and Scott JK. . pmid:15620878.
- Deming TJ. . pmid:10021411.
- Burzio LA and Waite JH. . pmid:10998254.
- Burzio LO, Burzio VA, Silva T, Burzio LA, and Pardo J. . pmid:9206011.
- Marumo K and Waite JH. . pmid:3089286.
- Waite JH. . pmid:6298211.
- Waite JH and Qin X. . pmid:11258900.
- Papov VV, Diamond TV, Biemann K, and Waite JH. . pmid:7650037.
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
Water Purification Methods
OmpX
- Mecsas J, Welch R, Erickson JW, and Gross CA. . pmid:7836315.
Sequence for CPX
- Total length is 558 bp + length of passenger peptide
- Native SS - 69 bp
MKKIACLSALAAVLAFTAGTSVA
- Embedded SfiI restriction site - 15 bp
GQSGQ
- Passenger Peptide
XXXXXXXXXXXXXX
- Sequence - 18 bp
GGQSGQ
- S54-F148 - 285 bp
SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
- Join native C and N - 12 bp
GGSG
- A1-S53 - 159 bp
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS
Papers!
- Samuelson P, Wernérus H, Svedberg M, and Ståhl S. . pmid:10698802.
- Kotrba P, Dolecková L, de Lorenzo V, and Ruml T. . pmid:10049868.
- Pazirandeh M, Wells BM, and Ryan RL. . pmid:9758845.
- Guzman LM, Belin D, Carson MJ, and Beckwith J. . pmid:7608087.
- Koebnik R, Locher KP, and Van Gelder P. . pmid:10931321.
FhuA
- Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. . pmid:11698382.
- Coulton JW, Mason P, and DuBow MS. . pmid:6315686.
- Ferguson AD, Hofmann E, Coulton JW, Diederichs K, and Welte W. . pmid:9856937.
- Moeck GS, Tawa P, Xiang H, Ismail AA, Turnbull JL, and Coulton JW. . pmid:8939430.
- Moeck GS, Coulton JW, and Postle K. . pmid:9353297.
- Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, and Moras D. . pmid:9865695.
- Coulton JW, Mason P, Cameron DR, Carmel G, Jean R, and Rode HN. . pmid:3079747.
- Hashemzadeh-Bonehi L, Mehraein-Ghomi F, Mitsopoulos C, Jacob JP, Hennessey ES, and Broome-Smith JK. . pmid:9822833.
OmpC
- Xu Z and Lee SY. . pmid:10543834.
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)
Heavy Metals
- Silver S and Phung le T. . pmid:16133099.
- Bruins MR, Kapil S, and Oehme FW. . pmid:10702338.
- Hou YM, Kim R, and Kim SH. . pmid:3056525.
- De Marco P, Pacheco CC, Figueiredo AR, and Moradas-Ferreira P. . pmid:15109722.
- Paul D, Pandey G, Pandey J, and Jain RK. . pmid:15734556.
- Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, and Wattiez R. . pmid:12829276.
- Weinberg ED. . pmid:2530602.
- Mizuno T, Usui K, Nishida S, Unno T, and Obata H. . pmid:17475501.
- Mehta SK and Gaur JP. . pmid:16294830.
- Muñoz R, Alvarez MT, Muñoz A, Terrazas E, Guieysse B, and Mattiasson B. . pmid:16307789.
- http://water.usgs.gov/wid/html/bioremed.html
- Yang X, Feng Y, He Z, and Stoffella PJ. . pmid:16028496.
- Clemens S, Palmgren MG, and Krämer U. . pmid:12119168.
- Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392.
- Kamnev AA and van der Lelie D. . pmid:11092247.
