Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis

Abstract

Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.

First Principles Calculation of Protein–Protein Dimer Affinities of ALS-Associated SOD1 Mutants

“…Both disulfide reduction and D101N mutations are either within the loops or close to the loop regions, so the anti-cooperative effect may be due to the loop structures having conformational ensembles that are modified by mutation or disulfide reduction. Previous studies have shown that mutation could affect cooperative folding ( Batey et al, 2005 ; Rogers, 2020 ) and that disordered structures (such as disordered loops) could affect long-range ( 10 nm) cooperative folding ( Gruszka et al, 2016 ). In the disulfide-reduced and D101N variants, well-structured loops in chain A may strain the native structure of chain B so that loop disorder is enhanced for chain B in the context of the dimer.…”

Enfuvirtide biosynthesis in thermostable chaperone-based fusion

“…The cyanogen bromide treatment in 70% formic acid provides fully denaturing conditions, which may cause peptide folding issues. It can be expected that soluble peptide would fold properly on its substrate [37] , especially if it is acysteine-free peptide. Enfuvirtide is exceptionally well-studied peptide.…”