A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Abstract

The synergy between structure and dynamics is essential to the function of biological macromolecules. Thermally driven dynamics on different timescales have been experimentally observed or simulated, and a direct link between micro- to milli-second domain motions and enzymatic function has been established. However, very little is understood about the connection of these functionally relevant, collective movements with local atomic fluctuations, which are much faster. Here we show that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state. The fast, local mobilities differ between a mesophilic and hyperthermophilic adenylate kinase, but are strikingly similar at temperatures at which enzymatic activity and free energy of folding are matched. The connection between different timescales and the corresponding amplitudes of motions in adenylate kinase and their linkage to catalytic function is likely to be a general characteristic of protein energy landscapes.

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

“…2), into the Nterminal region of BtuB (see Methods). The X-band EPR spectra from spin labels placed at positions [1][2][3][4][5] in BtuB are shown in Figure 3, along with the position of these sites in the BtuB meso structure. These spectra are similar to those published previously, 22 and are composed of two components resulting from populations of spin labels that have different dynamics.…”

“…[3][4][5] Dynamics also underlies protein-protein recognition, which is often mediated by conserved and highly dynamic or unstructured regions of proteins. 6,7 It is not precisely understood how structural fluctuations facilitate and mediate recognition, but there is considerable interest in characterizing the dynamics and conformation substates in regions that function in recognition.…”

Single Enzyme Studies Reveal the Existence of Discrete Functional States for Monomeric Enzymes and How They Are “Selected” upon Allosteric Regulation

“…Under this assumption, we conclude that regulation of TLL is achieved by simultaneous and equal energetic stabilization of the active state and of the energy barrier between the two states ( Figure 4, regulatory coordinate). 5,38 An additional control experiment would be to introduce additional mutations that shift the conformational equilibrium toward one of the states. 39 However, these mutations would also alter the enzyme's energy landscape, prohibiting us from directly comparing the free energy difference between the two variants.…”

Cross-Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta

“…Figure 11c states [1,31] that play important roles in protein folding [21], enzymology [72][73][74] and molecular recognition [75]. Further, the work demonstrates the utility in using a combined NMR relaxation dispersion/CSRosetta approach for studies of "invisible" excited protein states, providing structural data at a level of detail not possible using other biophysical techniques.…”

“…It also provides a method for studying other types of functional excited states, such as transiently populated catalytic [72][73][74] or ligandbinding conformations [75]. However, for this method to continue to be employed, one must be confident that the excited state structure is accurate.…”