Difference between revisions of "Talk:Protein domains"

(→‎Codon selection)
(→‎Parts that have been designed)
 
(14 intermediate revisions by the same user not shown)
Line 55: Line 55:
 
*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==
Line 65: Line 68:
 
*Strep-tag: [[Part:BBa_T2012]] (WRHPQFGG, originally selected as AWRHPQFGG; can only be a tail domain)
 
*Strep-tag: [[Part:BBa_T2012]] (WRHPQFGG, originally selected as AWRHPQFGG; can only be a tail domain)
 
*Strep-tag II: [[Part:BBa_T2013]] | [[Part:BBa_T2014]] (WSHPQFEK)
 
*Strep-tag II: [[Part:BBa_T2013]] | [[Part:BBa_T2014]] (WSHPQFEK)
−
*S-tag: (KETAAAKFERQHMDS)
+
*S-tag: [[Part:BBa_T2015]] | [[Part:BBa_T2016]] | [[Part:BBa_T2017]] (KETAAAKFERQHMDS)
 +
*V5: [[Part:BBa_T2018]] | [[Part:BBa_T2019]] | [[Part:BBa_T2020]] (GKPIPNPLLGLDST)
 +
*VSV-G: [[Part:BBa_T2021]] | no head domain | [[Part:BBa_T2022]] (YTDIEMNRLGK)
 +
*GST: | | [[Part:BBa_T2025]]
 +
*Chitin Binding Domain: | | [[Part:BBa_T2028]]
  
 
==Codon selection==
 
==Codon selection==
  
−
Rare is defined as less than 5%.
+
Rare is defined as less than 5%.  Also checked Xenopus, human, mouse, B. subtilis, Drosophila, C. elegans, Pichia, Trichoplusia.
  
 
{| style="border:#c9c9c9 1px solid; margin: 2em 2em 2em 0; border-collapse: collapse;"
 
{| style="border:#c9c9c9 1px solid; margin: 2em 2em 2em 0; border-collapse: collapse;"
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ala/A'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ala/A'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GCU (rare in Rhodobacter/Streptomyces), GCC, GCA (rare in Rhodobacter/Streptomyces), GCG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''GCC''', '''GCG''', GCU (rare in Rhodobacter/Streptomyces), GCA (rare in Rhodobacter/Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Leu/L'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Leu/L'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UUA (rare in E. coli/Rhodobacter/Streptomyces/Trichoderma), UUG (rare in Rhodobacter/Streptomyces), CUU (rare in Streptomyces), CUC (rare in Plasmodium), CUA (rare in E. coli/Chicken/Rhodobacter/Streptomyces/Trichoderma), CUG (rare in Plasmodium)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''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)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Arg/R'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Arg/R'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CGU, CGC (rare in Plasmodium), CGA (rare in E. coli/Rhodobacter/Streptomyces), CGG (rare in E. coli/Yeast/Plasmodium), AGA (rare in E. coli/Rhodobacter/Streptomyces), AGG (rare in E. coli/Rhodobacter/Streptomyces)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''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)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Lys/K'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Lys/K'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AAA, AAG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''AAA''', '''AAG'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asn/N'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asn/N'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AAU (rare in Streptomyces), AAC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''AAC''', AAU (rare in Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Met/M'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Met/M'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''AUG'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asp/D'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asp/D'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GAU, GAC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''GAU''', '''GAC'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Phe/F'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Phe/F'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UUU (rare in Streptomyces), UUC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''UUC''', UUU (rare in Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Cys/C'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Cys/C'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UGU, UGC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''UGU''', '''UGC'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Pro/P'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Pro/P'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CCU (rare in Rhodobacter/Streptomyces), CCC (rare in E. coli), CCA (rare in Rhodobacter/Streptomyces), CCG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''CCG''', CCU (rare in Rhodobacter/Streptomyces), CCC (rare in E. coli), CCA (rare in Rhodobacter/Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gln/Q'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gln/Q'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CAA, CAG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''CAA''', '''CAG'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ser/S'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ser/S'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UCU (rare in Rhodobacter/Streptomyces), UCC, UCA (rare in Rhodobacter/Streptomyces), UCG (rare in Chicken), AGU (rare in E. coli/Rhodobacter/Streptomyces), AGC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''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)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Glu/E'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Glu/E'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GAA, GAG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''GAA''', '''GAG'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Thr/T'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Thr/T'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | ACU (rare in Rhodobacter/Streptomyces), ACC, ACG, ACA (rare in E. coli/Streptomyces)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''ACC''', '''ACG''', ACU (rare in Rhodobacter/Streptomyces), ACA (rare in E. coli/Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gly/G'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gly/G'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GGU, GGC, GGA (rare in E. coli), GGG (rare in E. coli)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''GGU''', '''GGC''', GGA (rare in E. coli), GGG (rare in E. coli/Sf9 insect cells)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Trp/W'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Trp/W'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UGG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''UGG'''
 
|-----
 
|-----
−
| '''His/H'''
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''His/H'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CAU, CAC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''CAU''', '''CAC'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Tyr/Y'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Tyr/Y'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" |  UAU, UAC
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" |  '''UAU''', '''UAC'''
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ile/I'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ile/I'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUU (rare in Streptomyces), AUC, AUA (rare in E. coli/Rhodobacter/Streptomyces)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''AUC''', AUU (rare in Streptomyces), AUA (rare in E. coli/Rhodobacter/Streptomyces)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Val/V'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Val/V'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GUU (rare in Rhodobacter/Streptomyces), GUC, GUA (rare in Rhodobacter/Streptomyces/Trichoderma), GUG
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''GUC''', '''GUG''', GUU (rare in Rhodobacter/Streptomyces), GUA (rare in Rhodobacter/Streptomyces/Trichoderma)
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''START'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''START'''
Line 136: Line 143:
 
|-----
 
|-----
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''STOP'''
 
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''STOP'''
−
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UAA, UGA, UAG (rare in Chicken)
+
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''UAA''', UGA, UAG (rare in Chicken)
 
|}
 
|}

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)