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JoVE Journal
Chemistry

This content is Open Access.

Optimization of Synthetic Proteins
 

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Article doi: 10.3791/52878
July 14th, 2015 Usage Statistics

Summary July 14th, 2015

Synthetic protein sequences based on consensus motifs typically ignore co-evolving residues, that imply interpositional dependencies (IPDs). IPDs can be essential to activity, and designs that disregard them may result in suboptimal results. This protocol uses StickWRLD to identify IPDs and help inform rational protein design, resulting in more efficient results.

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