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Optimization of Synthetic Proteins

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

Article DOI: 10.3791/52878-v 07:08 min July 14th, 2015
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.


Keywords: Protein Alignment Consensus Sequence Interpositional Dependencies Covariation Protein Folding Thermostability Functional Sites Synthetic Proteins Visual Analytics StickWRLD Adenylate Kinase Endonuclease Target Sites
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