How fast are the motions of tertiary-structure elements in proteins?

Gilad Haran,Hisham Mazal

doi:10.1063/5.0024972

Abstract

Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e., domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including nuclear magnetic resonance and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs functional cycles is a general design principle in proteins remains to be determined.

Highlights

Proteins are the key functional molecules in the living system, governing most cellular functions and biochemical tasks
We will introduce these methods, with some emphasis on single-molecule fluorescence resonance energy transfer spectroscopy, and provide several examples from our work and others’ to demonstrate how fast motions can be probed, how they might be coupled to slower protein functional cycles, and, more generally, what we can learn from them on protein machine function
nuclear magnetic resonance (NMR) and single-molecule fluorescence resonance energy transfer (smFRET) methods mentioned in this Perspective are useful for probing fast dynamics and may be seen as complementary to each other

Summary

INTRODUCTION

Proteins are the key functional molecules in the living system, governing most cellular functions and biochemical tasks. Experimental methods that can measure and trace large-scale (as opposed to local) motions on very short times have only appeared in recent years We will introduce these methods, with some emphasis on single-molecule fluorescence resonance energy transfer (smFRET) spectroscopy, and provide several examples from our work and others’ to demonstrate how fast motions can be probed, how they might be coupled to slower protein functional cycles, and, more generally, what we can learn from them on protein machine function. There is a good reason to believe based both on theoretical work and somewhat indirect experimental observations that large-scale conformational changes in proteins should take place on the nanosecond-microsecond time scale We will discuss some examples from the literature and from our work, and comment, where possible, on potential answers to the second question

METHODS

CONCLUSIONS AND PROSPECTS