The Effects of p-Azidophenylalanine Incorporation on Protein Structure and Stability

JW Wilkerson and AK Smith and KM Wilding and BC Bundy and TA Knotts, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60, 5117-5125 (2020).

DOI: 10.1021/acs.jcim.0c00725

Functionalization is often needed to harness the power of proteins for beneficial use but can cause losses to stability and/or activity. State of the art methods to limit these deleterious effects accomplish this by substituting an amino acid in the wildtype molecule into an unnatural amino acid, such as pazidophenylalanine (pAz), but selecting the residue for substitution a priori remains an elusive goal of protein engineering. The results of this work indicate that all-atom molecular dynamics simulation can be used to determine whether substituting pAz for a natural amino acid will be detrimental to experimentally determined protein stability. These results offer significant hope that local deviations from wild-type structure caused by pAz incorporation observed in simulations can be a predictive metric used to reduce the number of costly experiments that must be done to find active proteins upon substitution with pAz and subsequent functionalization.

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