Help:Protein coding

Revision as of 21:09, 13 April 2007 by Scmohr (Talk | contribs)

Part icon cds.png Browse protein coding parts!

Protein coding parts are parts which create functional proteins. Most of the parts presented on this page are protein coding regions only--however, a few of them currently also contain RBS sites.

Regulations for Protein Coding Parts

Every BioBrick coding region consists of the following structure:

  • It begins with a standard start codon: "ATG"
  • It ends with two "stop" codons: "TAA","TAA".

The actual protein coding sequence is sandwiched between the start codon and two stop codons. Thus the structure of a BioBricks protein coding region sequence looks like: "ATG-[your coding region]-TAATAA " (Note that ATG ---> AUG in the mRNA transcript, and AUG codes for methionine. Depending on which protein you have, the methionine may or may not remain as the first residue in your expressed amino acid sequence.)

Direction

A coding region can point RNA polymerase in either the forward or reverse direction depending on which strand of the double-stranded DNA molecule it binds to. Currently most BioBrick parts transcribe DNA in the forward direction.

References and Sources for Protein Coding Information

There are a number of excellent sources for protein coding sequence. Some of them include:

  • Pubmed (Entrez Protein) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein&itool=toolbar link]
  • UniProt [http://www.pir.uniprot.org/ link]
  • UniProt-SwissProt/TrEMBL [http://www.ebi.ac.uk/swissprot/ link]
  • Protein Data Bank (PDB) [http://www.rcsb.org/pdb/Welcome.do link]


Protein Barcodes

a BioBrick Barcode, shown under Part Design:Features, ssDNA viewing mode
 Many protein coding parts in the Registry are trackable through the use of pieces of DNA which are:

non-coding (no "start" codon), rare, and about 25 base pairs in length. These sequences are known as Barcodes.

Tags

Often, protein coding parts have tags attached to their ends in order to add functionalities such as fast degradation. The lengths of these tags depend on their function (the predominant LVA, AAV, ASV, etc. degradation tags are 11 amino acids or 33 base pairs in length).

Because protein coding parts currently all end in the double stop codon "TAATAA", we currently cannot add on Tag parts in the manner of Biobricks Standard Assembly method.

For more information, visit Part icon tag.pngHelp:Tag.