Mass Spectrometry‐Based Approaches to Study Biomolecular Dynamics: Equilibrium Intermediates

Abstract

In the preceding chapter, we surveyed various MS-based approaches to study higher-order structure of proteins under native conditions. For many decades, such well-defined and highly organized structures were thought of as the most important (if not the only) determinants of protein function. Protein folding was often considered a linear process leading from fully unstructured (and, therefore, dysfunctional) states to the highly organized native (function-competent) state. The advent of NMR has changed our perception of what "functional" protein states are, with the realization that native proteins are very dynamic species. Perhaps the most illustrious examples of the intimate link between protein dynamics and function were found in enzyme catalysis, where the chemical conversion of substrate to product is often driven by relatively small-scale dynamic events within (and often beyond) the active site. It became clear in recent years that large-scale macromolecular dynamics may also be an important determinant of protein function. A growing number of proteins are found to be either partially or fully unstructured under native conditions, and such flexibility (intrinsic disorder) appears to be vital for their function. Proteins that do have native folds under physiological conditions can also exhibit dynamic behavior via local structural fluctuations or by sampling alternative (higher-energy or "activated") conformations transiently. In many cases, such activated (non-native) states are functionally important despite their low Boltzmann weight. Realization of the importance of transient non-native protein structures for their function not only greatly advanced our understanding of processes as diverse as recognition, signaling, and transport Mass