Protein recognition and selection through conformational and mutually induced fit

Abstract

Protein-protein interactions drive most every biological process, but in many instances the domains mediating recognition are disordered. How specificity in binding is attained in the absence of defined structure contrasts with well-established experimental and theoretical work describing ligand binding to protein. The signaling protein calmodulin presents a unique opportunity to investigate mechanisms for target recognition given that it interacts with several hundred different targets. By advancing coarsegrained computer simulations and experimental techniques, mechanistic insights were gained in defining the pathways leading to recognition and in how target selectivity can be achieved at the molecular level. A model requiring mutually induced conformational changes in both calmodulin and target proteins was necessary and broadly informs how proteins can achieve both high affinity and high specificity.coarse-grained molecular simulations | stopped-flow fluorescence techniques | conformational flexibility | hydrophobic motif | calmodulin binding target T he ubiquitous protein calmodulin (CaM) interacts with a vast selection of binding targets (CaMBTs); however, the molecular mechanisms that underlie target selectivity are not known despite an enormous wealth of structural information (1, 2). What emerges from this is the remarkable conformational flexibility of CaM, which exists in highly dynamic structures in the Ca 2+ free and bound forms (3-6) and will adopt distinct conformations when bound to protein targets. These distinct modes of binding are encoded by CaM-recognition motifs of targets that display impressive variability in amino acid sequence and are often partially or largely disordered in the absence of CaM. These data indicate that CaM-CaMBT interactions lie at the opposite end of the spectrum from the classic "lock and key" mechanism (7) initially proposed for rigid ligand binding to proteins, and require adopting more dynamic models, such as induced fit (8) or conformational selection (9). The induced-fit mechanism posits that productive binding occurs because the rigid ligand can alter the conformation of the enzyme, and that the final conformation exists only in the presence of ligand. Conformational selection assumes that the enzyme naturally samples a variety of conformational states and that the ligand binds to one, or a small subset, of these states. However, newer theories-termed extended conformational selection (10), mutually induced fit (11), fly-casting (12), or folding and binding (13, 14)-have begun to integrate molecule dynamics to describe folding and binding involving flexible molecules in protein-protein interactions, especially for the intrinsically disordered proteins (15-17) for which folding and binding are concomitant.The goal of the present study is to provide mechanistic insights at a molecular level into the time-dependent conformational adjustments between CaM and CaMBT for the binding mechanism. Results show that although CaM visits conformations similar to a target-boun...

Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

“…It is expected that different targets are able to select the most suitable ways to bind to CaM, benefiting from the multispecificity binding. There has been increasing evidence recently to support our proposal (40,47,58,59). The experiment has shown that CaM selects the partly rather than entirely compact structure to embrace the peptide, followed by conformational adaption to the bound structure induced by peptide.…”

“…This leads to a mixture of the two conventional binding scenarios (40). A mutually induced-fit scenario for binding between CaM and CaMKI peptide was proposed for CaM and CaMKI peptide (58,59), which is essentially a simultaneous binding-folding mechanism and is different from our mixture mechanism for the skMLCK. iv) It is expected that different targets can select the most suitable ways to bind to CaM, according to their structural features.…”

Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions

“…Its two globular domains are connected by a flexible linker, each containing a pair of EF-hand motifs to accommodate the reversible binding of four total Ca 2þ ions (13). CaM exists as an ensemble of conformers (14)(15)(16) fluctuating around a large flat energy minimum, where conformational sampling permits a continuum of structures with similar energies (17)(18)(19)(20). CaM function depends on dynamics occurring on various spatial scales, where backbone dynamics have been shown to drive Ca 2þ affinity (13) and accommodation of a target requires large rearrangements of its domains (21).…”

Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study

“…Therefore, we propose that TRP3 interacts with the micelles via conformational selection, i.e., the bound conformation is already present in the free ensemble and the equilibrium between conformations is re-established upon binding (52)(53)(54)(55)(56).…”