Talk:Protein domains

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?

• His tag: Part:BBa_T2000 | Part:BBa_T2001 | Part:BBa_T2002 (7xHis)
• FLAG tag: Part:BBa_T2003 | Part:BBa_T2004 | Part:BBa_T2005 (DYKDDDDK)
• C-Myc: Part:BBa_T2006 | Part:BBa_T2007 | Part:BBa_T2008 (EQKLISEEDL)
• HA tag: Part:BBa_T2009 | Part:BBa_T2010 | Part:BBa_T2011 (YPYDVPDYA)
• 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)
• 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)

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)