Protein Engineering Study of Protein L by Simulation

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Abstract
We examine the ability of our recently introduced minimalist protein model to reproduce experimentally measured thermodynamic and kinetic changes upon sequence mutation in the well-studied immunoglobulin-binding protein L. We have examined five different sequence mutations of protein L that are meant to mimic the same mutation type studied experimentally: two different mutations which disrupt the natural preference in the β-hairpin #1 and β-hairpin #2 turn regions, two different helix mutants where a surface polar residue in the α-helix has been mutated to a hydrophobic residue, and a final mutant to further probe the role of nonnative hydrophobic interactions in the folding process. These simulated mutations are analyzed in terms of various kinetic and thermodynamic changes with respect to wild type, but in addition we evaluate the structure-activity relationship of our model protein based on the φ-value calculated from both the kinetic and thermodynamic perspectives. We find that the simulated thermodynamic φ-values reproduce the experimental trends in the mutations studied and allow us to circumvent the difficult interpretation of the complicated kinetics of our model. Furthermore, the level of resolution of the model allows us to directly predict what experiments seek in regard to protein engineering studies of protein folding - namely the residues or portions of the polypeptide chain that contribute to the crucial step in the folding of the wild-type protein.