Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins

• DOI: 10.1021/acs.biochem.0c00533
• Publication Date: 2020-09-24T16:07:31Z
• Authors: Joseph G. Plaks; Jeff A. Brewer; Nicole K. Jacobsen; Michael McKenna; Joshua R. Uzarski; Timothy J. Lawton; Shaun F. Filocamo; Joel L. Kaar
• Keywords: Tensin; Protein Engineering; Loop modeling

While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel domains remains limited. In the absence rational approaches, incorporation often destabilizes proteins, thereby requiring massive screening and selection identify sites that can accommodate insertion. We developed computational strategy for rapidly scanning entire structure scaffold determine impact insertion at all possible amino acid positions. This approach is based on Rosetta kinematic modeling protocol was demonstrated by identifying lipase were permissive LAP peptide. Interestingly, identification dependent contribution residues near-loop environment score did not correlate conventional structural features (e.g., B-factors). As evidence this, several following 17, 47–49, 108), which predicted confirmed be permissive, interrupted helices, while others 43, 67, 116, 119, 121), are situated regions, nonpermissive. further shown predictive β-glucosidase human phosphatase tensin homologue (PTEN), facilitate engineering through silico mutagenesis. By enabling design loop-containing libraries high probabilities soluble expression, this has broad implications many areas engineering, including antibody design, improving enzyme activity, modification.