Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

Abstract

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics and catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.enzyme dynamics ͉ population shift ͉ phosphoenolpyruvate carboxykinase I t has been 50 years since the original presentation of the induced fit hypothesis by Daniel Koshland (1) that built upon Emil Fisher's key-lock principle (2) and introduced the idea that the inherent dynamic properties of enzymes play an essential role in the processes of molecular recognition and catalysis. Over the last decade, with the advent of new instrumentation and novel experimental approaches there has been a resurgence in investigations focused upon understanding the specific ways in that these dynamic properties influence the ability of enzymes to achieve enormous levels of selectivity and catalytic power (refs. 3-6 and references therein).Presently there are two primary models used to explain the mechanism by which an enzyme can move toward adopting the final key-lock state ( Fig. 1): (i) the induced fit model and (ii) the conformational selection/population shift model (7-14). As defined originally by Koshland (1), the induced fit model states that the achievement of the final key-lock state, that is, the precise orientation of catalytic groups and residues necessary for catalysis, occurs only after changes in protein structure that are induced by the binding of a substrate. This pathway is represented by the equilibrium constants K 1 and K 2 in Fig. 1. Intrinsic to this model is the ability of the enzyme to form an ''encounter complex'' † (Fig. 1B). In this complex the enzyme is liganded identically to the eventual catalytically competent key-lock state; however, the conformational change leading to the active key-lock state has not yet occurred. In contrast, the conformational selection model states that the enzyme exists in multiple conformational states, of which the substrate has a high affinity for the active or key-lock state. In this model the ligand is suggested to bind to this lowly populated high-energy ...

Theory and simulation on the kinetics of protein–ligand binding coupled to conformational change

“…Two common features of most protein-ligand systems are that the energy surface switches from favoring nonreactive conformations while the ligand is away to favoring reactive conformations while the ligand is near and the reactive region is highly localized. 25,26 We have also presented a method for calculating the binding rate constant from Brownian dynamics simulations.…”

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

“…Despite such successes, there are many examples of systems that cannot be explained by conformational selection. For example, Sullivan and Holyoak (35) showed that in phosphoenolpyruvate carboxykinase (PEPCK) formation of the catalytic active complex is combined with a closure of the active site. This means that, even if in the unbound state PEPCK samples bound conformations, they would simply not be available for the substrate.…”

Two Lysine Residues in the Bacterial Luciferase Mobile Loop Stabilize Reaction Intermediates

“…The enediol intermediate is susceptible to loss of phosphate by ␤-elimination (46). To avoid this side reaction, triosephosphate isomerase uses a mobile loop as a lid to sequester the active site following ligand binding (47) Similar lid gating mechanisms are common, making those with uncommon properties particularly interesting (48) Luciferase is unusual because of its distinct reaction chemistry and an unusually long mobile loop consisting of ϳ30 residues. The first aim of this study was to determine whether any labile intermediates might be protected by the bacterial luciferase mobile loop.…”