Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
Highlights
This review focuses on the analysis and interpretation of the kinetics of ligand binding mechanisms that are key to establishing a correlation with structure and any linked conformational transition
Interpretations of molecular recognition in biology have evolved from the rigid body association of the lock-and-key mechanism to the recognition of conformational transitions through the allosteric concept
This view has further expanded recently to embrace the role of dynamics and molecular ensembles[43,129,130] unraveled by advanced techniques such as single molecule detection,[132] nuclear magnetic resonance (NMR),[131,138,180] and cryo-EM.[133,134]
Summary
The phenomenological approach to ligand binding to a biological macromolecule at equilibrium, in a closed system under conditions of constant temperature and pressure, is based on the formulation of a partition function as a polynomial expansion in the ligand activity x of degree N, equal to the number of binding sites.[25,30] All relevant thermodynamic quantities are related to this “binding polynomial”[31,32] by simple transformations and offer a rigorous interpretation of the underlying energetics, yet provide little insight into the molecular mechanism of recognition. A stopped flow is restricted by the dead time of the instrument to values < 500 sÀ1 but a continuous flow apparatus can detect much faster rates, in the 2000–20 000 sÀ1 range.[49] Even faster ranges in the 105–106 sÀ1 range can be detected by temperature jump if the reaction is linked to sufficient perturbation of affinity linked to temperature changes.[4,15] An example of the plot in Eq (10) is given in Fig. 2 for the case of the tripeptide H-D-Phe-Pro-Arg-p-nitroanilide (FPR) binding to the active site of the mutant D194A of the clotting protease thrombin.[50] The binding mechanism is consistent with a lock-and-key, rigid body type of association with values of kon 1⁄4 1.3 6 0.1 Â 106 MÀ1sÀ1 in the diffusion-limited rate range and a relatively fast koff 1⁄4 8.5 6 0.5 sÀ1, corresponding to a value of the equilibrium constant Kd 1⁄4 6.5 6 0.6 lM. The widely accepted importance of protein flexibility in biomolecular recognition suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.[52] a (x) (s–1)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
