Direct Detection of Structurally Resolved Dynamics in a Multiconformation Receptor−Ligand Complex

Abstract

Structure-based drug design relies on static protein structures despite significant evidence for the need to include protein dynamics as a serious consideration. In practice, dynamic motions are neglected because they are not understood well enough to model – a situation resulting from a lack of explicit experimental examples of dynamic receptor-ligand complexes. Here, we report high-resolution details of pronounced ~1 ms timescale motions of a receptor-small molecule complex using a combination of NMR and X-ray crystallography. Large conformational dynamics in Escherichia coli dihydrofolate reductase are driven by internal switching motions of the drug-like, nanomolar-affinity inhibitor. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments and NOEs revealed the crystal structure to contain critical elements of the high energy protein-ligand conformation. The availability of accurate, structurally resolved dynamics in a protein-ligand complex should serve as a valuable benchmark for modeling dynamics in other receptor-ligand complexes and prediction of binding affinities.

Structural basis for negative cooperativity within agonist-bound TR:RXR heterodimers

“…The presence of strong (3× SD) peaks in the jF o j − jF c j coefficient electron density maps (Fig. 1C) confirms that the observed disordered density is not a crystallographic artifact and is analogous to previous reports of local or global dynamics within proteins (15) and protein•ligand (16) structures that manifest as either high individual atomic temperature factors (B factors) or discontinuous electron density (17). Finally, by occupancy refinement of only T3 (occupancy = 0.70) and 9c (occupancy = 0.99), we were able to remove the negative electron density on Author contributions: E.J.F.…”

Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α

“…We also demonstrated that modifying the ligand alters its preference for two different binding orientations, which are associated with different protein conformers and associated activity profiles 5 . This identified ligand dynamics as a novel mechanism to titrate the activity profile of an allosteric signaling system, and has since been verified by NMR in two other allosteric signaling proteins, PPARγ 6 and dihydrofolate reductase 7 , suggesting that it is a general tenet of ligand-protein allostery.…”

Evidence for dynamics in proteins as a mechanism for ligand dissociation

“…aValues taken from the literature 23 .bValue taken from the literature 24 .cPreviously published values 12 .dValues calculated from K i and k on , as described in the text.ePreviously published values 13 .fValues reported as apparent K i or k off values, since compounds 2 , 3 , 4 , and 6 are racemic mixtures.gSites were split into two groups. The best fit for the slower group is given, despite the observation that many sites possess high χ 2 ratios.…”