Help:Protein domains/Design

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Protein domain parts are DNA sequences that encode a portion of a protein. Protein domain parts can be assembled together to make translational units that express a protein. Translational units are composed of 3 types of protein domains, a Head Domain, one or more Internal Domains including Special Internal Domains, and a Tail Domain. For more details, see the Protein domains page.

Before you design a new protein domain, you might check if your protein domain already exists in the Registry. Many commonly used protein domains like affinity tags, localization sequences, cleavage sites, and degradation tags are already available in the Registry.

Here are some basic things to consider when designing a protein domain.

  1. The sequence of all protein domains should ideally be codon optimized for the chassis in which the part will be used.
  2. Protein domain part sequences should not have any BioBrick sites in it (EcoRI, XbaI, SpeI, or PstI).
  3. New Head domains in the Registry should include at least the first three codons of the protein coding sequence.
  4. The start codon in a Head domain should generally by ATG.
  5. Since in E. coli, the rate of translational initiation depends not only on the sequence of the ribosome start site and start codon, but also on the second and third codon as well, we suggest that you also specify the second and third codon in the Head domain as well.
  6. The stop codon in a Tail domain should generally be the double stop codon TAATAA.
  7. If you are planning on synthesizing the protein domain part sequence either alone or in the context of a full-length protein coding sequence or translational unit via commercial gene synthesis, design your protein domain part sequence to remove useful restriction enzyme sites. See a list of suggested sites for removal at OpenWetWare.
  8. If you are planning on constructing individual protein domain parts and assembling them, then you'll need to choose one of the Assembly standards that support in-frame protein assembly like Assembly standard 23, Assembly standard 25 or Assembly standard 21. You'll also need to consider any additional constraints the standard may impose on the protein domain sequence.

Regardless of which standard you use to assemble protein domain parts, the full-length protein coding sequence should ideally adhere to the original BioBrick assembly standard (Assembly standard 10) so that it is compatible with most of the parts in the Registry.