Stopped-Flow Kinetic Techniques for Studying Binding Reactions of Intrinsically Disordered Proteins

Measuring and Analyzing Binding Kinetics of Coupled Folding and Binding Reactions Under Pseudo-First-Order Conditions

Many intrinsically disordered proteins (IDPs) adopt a well-defined structure upon binding to their interaction partners. Kinetic characterization is a requirement for the investigation of the dynamics and mechanisms of these folding-upon-binding reactions. Here a protocol is described for the investigation of binding kinetics of bimolecular binding and folding reactions of IDPs to their ligand partner under pseudo-first-order conditions using stopped-flow mixing and fluorescence detection.

Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis

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.