How Much NMR Data Is Required To Determine a Protein–Ligand Complex Structure?

Abstract

Here we present an NMR-based approach to solving protein-ligand structures. The procedure is guided by biophysical, biochemical, or knowledge-based data. The structures are mainly derived from ligand-induced chemical-shift perturbations (CSP) induced in the resonances of the protein and ligand-detected saturated transfer difference signals between ligands and selectively labeled proteins (SOS-NMR). Accuracy, as judged by comparison with X-ray results, depends on the nature and completeness of the experimental data. An experimental protocol is proposed that starts with calculations that make use of readily available chemical-shift perturbations as experimental constraints. If necessary, more sophisticated experimental results have to be added to improve the accuracy of the protein-ligand complex structure. The criteria for evaluation and selection of meaningful complex structures are discussed. These are exemplified for three complexes, and we show that the approach bridges the gap between theoretical docking approaches and complex NMR schemes for determining protein-ligand complexes; especially for relatively weak binders that do not lead to intermolecular NOEs.

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

“…In recent decades, various methods have been developed in order to derive protein-ligand complex structures faster than with the classical NMR structure calculation protocol, but these methods mostly rely on a preliminary docking step rather than on experimentally driven calculations. Moreover, sometimes partial resonance assignments of the receptor are required [39][40][41][42][43][44][45]47,49,72]. A complex structure calculation method that is based on defined and accurate NOEs [78][79][80] but also bypasses the long and tedious protein assignment step was missing.…”

“…In cases involving weak binders, NMR spectroscopy is currently the best method to provide high resolution structural data. Recently, attempts to derive structures and/or dynamics of protein-ligand complexes by NMR more efficiently, when compared to the traditional structure calculation protocol, have been proposed including the use of ambiguous restraints [38,39] (such as ambiguous NOEs), chemical shift perturbations [40][41][42][43][44], or saturation transfer experiments [45,46] in combination with computational methods such as docking and scoring [47][48][49]. Here, we describe the advantages and disadvantages of NMR 2 over some of the most commonly used techniques to quickly determine complex structures by NMR.…”

“…Finally, the CSP-based methods also use a docking scoring protocol that relies on force fields or scoring function. The most popular program used in NMR is CSP-HADDOCK [40,47,60], which can make use of a large set of additional experimental restraints such as residual dipolar couplings or pseudocontact shifts [41,61,62]. Other docking programs are BiGGER [63], AutoDockFilter [64], SAMPLEX [65], and LIGDOCK [47].…”

“…Example methods include SOS-NMR [45,47], NOE matching [49], INPHARMA [48,66,67], CORCEMA [46,68,69], or NMR 2 [32,33]. Except for NMR 2 , these methods require a docking step prior to the experimentally based scoring of the found poses and eventually perform an experimentally based refinement step.…”

NMR Studies of DOXP Reductoisomerase and its Inhibitor Complex

“…In favourable cases, the conformation of the complex can be predicted and can be verified experimentally by a combination of molecular dynamics and the incorporation of ambiguous NMR restraints. [29][30][31] Therefore, we performed an NMR spectroscopic analysis of DXR in complex with NADPH, Mg 2 + and fosmidomycin or FR900098.…”