Heterogeneous folding and stretched kinetics

Abstract

It has been over half a century since Anfinsen et al. (1) outlined in a series of papers their groundbreaking discovery that the amino acid sequence of a globular protein determines its native structure. This hypothesis laid the foundation for a thermodynamic view of protein folding, where the native state is energetically favored over all other conformations of the protein. One question left open, however, was the process by which this occurred: How did proteins arrive at their native conformation on a biologically practical timescale? A broad area of kinetic investigations in a 50+-y journey of kinetic studies uncovered a wealth of insights into protein structure, dynamics, and kinetics that has had a tremendous impact on our current understanding of biological machinery and regulation at the molecular level. Early pioneers in protein science studying how proteins spontaneously transformed from what appeared to be a spaghetti-like self-avoiding random walk chain to a specific native conformation noticed that the process did not necessarily occur in a single kinetic step (2). A reaction with a single kinetic step (i.e., kinetically limited by one dominant energy barrier) exhibits a time course described by a single exponential function. However, the folding kinetics for a number of proteins required two (or more) exponentials to describe the data. This result was both exciting, because of the opportunity for gaining insights into the folding process, and also a source of debate: Did the additional steps correspond to obligatory intermediates along the folding process, as in a chemical reaction, or did they suggest the presence of traps? In kinetic studies, it is often possible for multiple kinetic models to adequately describe the data, and often the experimenter can only rule out inconsistent models. For ensemble experiments, a combination of experimental techniques sensitive to more than a few molecular properties … [↵][1]1Email: osman.bilsel{at}gmail.com. [1]: #xref-corresp-1-1