Conformational selection or induced fit? 50 years of debate resolved

Abstract

Exactly 50 years ago, biochemists raised the question of the mechanism of the conformational change that mediates "allosteric" interactions between regulatory sites and biologically active sites in regulatory/receptor proteins. Do the different conformations involved already exist spontaneously in the absence of the regulatory ligands (Monod-Wyman-Changeux), such that the complementary protein conformation would be selected to mediate signal transduction, or do particular ligands induce the receptor to adopt the conformation best suited to them (Koshland-Nemethy-Filmer-induced fit)? This is not just a central question for biophysics, it also has enormous importance for drug design. Recent advances in techniques have allowed detailed experimental and theoretical comparisons with the formal models of both scenarios. Also, it has been shown that mutated receptors can adopt constitutively active confirmations in the absence of ligand. There have also been demonstrations that the atomic resolution structures of the same protein are essentially the same whether ligand is bound or not. These and other advances in past decades have produced a situation where the vast majority of the data using different categories of regulatory proteins (including regulatory enzymes, ligand-gated ion channels, G protein-coupled receptors, and nuclear receptors) support the conformational selection scheme of signal transduction.

Figure 1.. Conformational selection for hypothetical monomeric and dimeric proteins

(A) Monomer. (B) Dimer. T and R states are presented on a vertical free energy scale and include the transition state (TS) kinetic barriers for their interconversion, estimated according to linear free energy principles for the dimer [17]. Subscripts correspond to the number of ligand molecules (X) bound. The T–R transitions follow the Monod-Wyman-Changeux principles for the dimer [6] or those of Changeux et al. [8] for the monomer. The pathway for the induced-fit mechanism [14] is presented by the dashed arrows in yellow and includes an intermediate (I) state for the dimer.

Figure 2.. Co-crystal of T and R states of bacterial L-lactate dehydrogenase (LDH)

Left panel: Ribbon representation of the crystal showing alternating rows of molecules in the T and R states. Middle panel: Individual molecules in the T and R states complexed with NADH (the reduced form of nicotinamide adenine dinucleotide), 1,6-fructose-bisphosphate (FBP), or oxamate (analogue of the substrate pyruvate). Oxamate is present at a concentration that shifts the allosteric equilibrium 50% to the R state. Right panel: Schematic sketch of a T-state dimer (dashed outline) superimposed on the R-state tetramer (solid outline) showing the rotations for interconversion between the two states. Adapted from images supplied by So Iwata.