Difference between revisions of "Talk:Protein domains"

(→‎Parts that have been designed)
(→‎Parts that have been designed)
 
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*From Ron: KT3, His, VSV-G, S-tag, V5, HSV, T7, DDDK, Glu-Glu, HA, E-tag, Myc
 
*From Ron: KT3, His, VSV-G, S-tag, V5, HSV, T7, DDDK, Glu-Glu, HA, E-tag, Myc
 
**Of these tags, I think the widely used ones are FLAG, His, Myc, HA, and V5.
 
**Of these tags, I think the widely used ones are FLAG, His, Myc, HA, and V5.
 +
 +
*linkers - Andreas Nature paper
 +
*N end rule - Kevin Wang
  
 
==Parts that have been designed==
 
==Parts that have been designed==
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*Strep-tag II: [[Part:BBa_T2013]] | [[Part:BBa_T2014]] (WSHPQFEK)
 
*Strep-tag II: [[Part:BBa_T2013]] | [[Part:BBa_T2014]] (WSHPQFEK)
 
*S-tag: [[Part:BBa_T2015]] | [[Part:BBa_T2016]] | [[Part:BBa_T2017]] (KETAAAKFERQHMDS)
 
*S-tag: [[Part:BBa_T2015]] | [[Part:BBa_T2016]] | [[Part:BBa_T2017]] (KETAAAKFERQHMDS)
 +
*V5: [[Part:BBa_T2018]] | [[Part:BBa_T2019]] | [[Part:BBa_T2020]] (GKPIPNPLLGLDST)
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*VSV-G: [[Part:BBa_T2021]] | no head domain | [[Part:BBa_T2022]] (YTDIEMNRLGK)
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*GST: | | [[Part:BBa_T2025]]
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*Chitin Binding Domain: | | [[Part:BBa_T2028]]
  
 
==Codon selection==
 
==Codon selection==

Latest revision as of 18:01, 17 September 2009

Categories

  • //proteintags/affinity
  • //proteintags/cleavage
  • //proteintags/degradation
  • //proteintags/localization

Tables

  • protein_affinity_tags
    • //proteintags/affinity
  • protein_cleavage_sites
    • //proteintags/cleavage
  • protein_degradation_tags
    • //proteintags/degradation
  • protein_localization_sequences
    • //proteintags/localization

Columns for general protein tag tables

  • Available/Working
  • Part number (left aligned)
  • Description (left aligned)
  • AA sequence (most of these sequences are very short, courier or other fixed width font, left aligned) <- auto-generated by the computer
  • Length (centered) <- auto-generated by the computer

Columns for protein cleavage site tables

  • Available/Working
  • Part number (left aligned)
  • Description (left aligned)
  • Protease (centered, ideally should include links to coding sequences of the protease entered in the Registry)
  • AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
  • Length (centered)

Columns for protein degradation tag tables

  • Available/Working
  • Part number (left aligned)
  • Description (left aligned)
  • Chassis (center)
  • Half-life (centered)
  • AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
  • Length (centered)

Columns for protein affinity tag tables

  • Available/Working
  • Part number (left aligned)
  • Description (left aligned)
  • Column/resin (centered)
  • AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
  • Length (centered)

Parts to make

  • [http://openwetware.org/wiki/Protein_purification_tags Protein purification tags]
  • [http://openwetware.org/wiki/BBRFC14 Protein domains parts]
  • [http://openwetware.org/wiki/SynBERC:MIT/Calendar/2007-8-8 Wishlist of wanted parts]
  • [http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html ExPASy PeptideCutter]: The cleavage specificities of selected enzymes and chemicals
  • From Ron: KT3, His, VSV-G, S-tag, V5, HSV, T7, DDDK, Glu-Glu, HA, E-tag, Myc
    • Of these tags, I think the widely used ones are FLAG, His, Myc, HA, and V5.
  • linkers - Andreas Nature paper
  • N end rule - Kevin Wang

Parts that have been designed

The optimal second codon is AAA (Lys) in E. coli. So perhaps make all head domains start with Met-Lys?

Codon selection

Rare is defined as less than 5%. Also checked Xenopus, human, mouse, B. subtilis, Drosophila, C. elegans, Pichia, Trichoplusia.

Ala/A GCC, GCG, GCU (rare in Rhodobacter/Streptomyces), GCA (rare in Rhodobacter/Streptomyces)
Leu/L CUC (rare in Plasmodium), CUG (rare in Plasmodium), UUA (rare in E. coli/Rhodobacter/Streptomyces/Trichoderma/Sf9 insect cells), UUG (rare in Rhodobacter/Streptomyces), CUU (rare in Streptomyces), CUA (rare in E. coli/Chicken/Rhodobacter/Streptomyces/Trichoderma/Sf9 insect cells)
Arg/R CGC (rare in Plasmodium), CGU (rare in Sf9 insect cells), CGA (rare in E. coli/Rhodobacter/Streptomyces/Sf9 insect cells), CGG (rare in E. coli/Yeast/Plasmodium/Sf9 insect cells), AGA (rare in E. coli/Rhodobacter/Streptomyces), AGG (rare in E. coli/Rhodobacter/Streptomyces)
Lys/K AAA, AAG
Asn/N AAC, AAU (rare in Streptomyces)
Met/M AUG
Asp/D GAU, GAC
Phe/F UUC, UUU (rare in Streptomyces)
Cys/C UGU, UGC
Pro/P CCG, CCU (rare in Rhodobacter/Streptomyces), CCC (rare in E. coli), CCA (rare in Rhodobacter/Streptomyces)
Gln/Q CAA, CAG
Ser/S UCC, AGC, UCU (rare in Rhodobacter/Streptomyces), UCA (rare in Rhodobacter/Streptomyces), UCG (rare in Chicken/Sf9 insect cells), AGU (rare in E. coli/Rhodobacter/Streptomyces)
Glu/E GAA, GAG
Thr/T ACC, ACG, ACU (rare in Rhodobacter/Streptomyces), ACA (rare in E. coli/Streptomyces)
Gly/G GGU, GGC, GGA (rare in E. coli), GGG (rare in E. coli/Sf9 insect cells)
Trp/W UGG
His/H CAU, CAC
Tyr/Y UAU, UAC
Ile/I AUC, AUU (rare in Streptomyces), AUA (rare in E. coli/Rhodobacter/Streptomyces)
Val/V GUC, GUG, GUU (rare in Rhodobacter/Streptomyces), GUA (rare in Rhodobacter/Streptomyces/Trichoderma)
START AUG
STOP UAA, UGA, UAG (rare in Chicken)