Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back

105

This study aimed to shed light on the long debate over whether conformational selection (CS) or induced fit (IF) is the governing mechanism for protein-ligand binding. The main difference between the two scenarios is whether the conformational transition of the protein from the unbound form to the bound form occurs before or after encountering the ligand. Here we introduce the IF fraction (i.e., the fraction of binding events achieved via IF), to quantify the binding mechanism. Using simulations of a model protein-ligand system, we demonstrate that both the rate of the conformational transition and the concentration of ligand molecules can affect the IF fraction. CS dominates at slow conformational transition and low ligand concentration. An increase in either quantity results in a higher IF fraction. Despite the many-body nature of the system and the involvement of multiple, disparate types of dynamics (i.e., ligand diffusion, protein conformational transition, and binding reaction), the overall binding kinetics over wide ranges of parameters can be fit to a single exponential, with the apparent rate constant exhibiting a linear dependence on ligand concentration. The present study may guide future kinetics experiments and dynamics simulations in determining the IF fraction.protein-ligand complex | conformational dynamics | diffusion-influenced bimolecular reaction | induced-fit fraction

Section: Discussioncontrasting

confidence: 99%

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

Greives

Zhou

2014

105

“…This observation is consistent with theoretical simulations that reveal energetic and motional coupling between the active site and the adenosine binding site in E. coli DHFR (31)(32)(33)(34)(35). Interestingly, the coupling between these sites is lost in the binary and ternary product complexes E:THF and E:THF:NADP þ (Fig.…”

Section: Discussionsupporting

confidence: 90%

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

Boehr

McElheny

Dyson

et al. 2010

131

171

Enzyme catalysis can be described as progress over a multidimensional energy landscape where ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle. We applied NMR relaxation dispersion to investigate the role of bound ligands in modulating the dynamics and energy landscape of Escherichia coli dihydrofolate reductase to obtain insights into the mechanism by which the enzyme efficiently samples functional conformations as it traverses its reaction pathway. Although the structural differences between the occluded substrate binary complexes and product ternary complexes are very small, there are substantial differences in protein dynamics. Backbone fluctuations on the μs-ms timescale in the cofactor binding cleft are similar for the substrate and product binary complexes, but fluctuations on this timescale in the active site loops are observed only for complexes with substrate or substrate analog and are not observed for the binary product complex. The dynamics in the substrate and product binary complexes are governed by quite different kinetic and thermodynamic parameters. Analogous dynamic differences in the E:THF:NADPH and E:THF:NADP þ product ternary complexes are difficult to rationalize from ground-state structures. For both of these complexes, the nicotinamide ring resides outside the active site pocket in the ground state. However, they differ in the structure, energetics, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupies the active site. Overall, our results suggest that dynamics in dihydrofolate reductase are exquisitely "tuned" for every intermediate in the catalytic cycle; structural fluctuations efficiently channel the enzyme through functionally relevant conformational space. catalysis | energy landscape | enzyme dynamics | NMR | relaxation

“…Another important advance has been made in the use of CG simulations to explore the dynamics of protein structural changes (11), but these works have not explored the coupling to the chemical process.…”

mentioning

confidence: 99%

Enzyme millisecond conformational dynamics do not catalyze the chemical step

Pisliakov

Cao

Kamerlin

et al. 2009

198

220

The idea that enzymes catalyze reactions by dynamical coupling between the conformational motions and the chemical coordinates has recently attracted major experimental and theoretical interest. However, experimental studies have not directly established that the conformational motions transfer energy to the chemical coordinate, and simulating enzyme catalysis on the relevant timescales has been impractical. Here, we introduce a renormalization approach that transforms the energetics and dynamics of the enzyme to an equivalent low-dimensional system, and allows us to simulate the dynamical coupling on a ms timescale. The simulations establish, by means of several independent approaches, that the conformational dynamics is not remembered during the chemical step and does not contribute significantly to catalysis. Nevertheless, the precise nature of this coupling is a question of great importance.adenylate kinase ͉ coarse-grained model ͉ renormalization ͉ simplified model ͉ enzyme catalysis