FastLane Protein-ligand Complex Structure Analysis Services by X-ray Crystallography and NMR spectroscopy

Protein-Ligand Complex Structure: 1D- and 2D-NMR Analysis Services

Despite its widespread use, X-ray crystallography has several shortcomings, including difficulties in obtaining reproducible, stable crystals of new drug targets (e.g., proteins with flexible regions), crystals of complexes with low-affinity ligands (Kd > 10⁻⁶ M), and in establishing soaking systems (e.g., for crystallographic fragment screening). Additionally, the protein may be trapped in a non-ideal conformation for ligand binding during crystal soaking. In such cases, solution NMR spectroscopy can serve as an alternative to X-ray crystallography for obtaining structural information at the level of individual amino acids on ligand-binding sites, binding affinities, and ligand orientations during optimization of lead compounds.

With NMR spectroscopy, ligand complexes with affinities in the µM to mM range can be analysed, making the method suitable for studying the binding of small-molecule ligands, peptides, and proteins. The ligand binding site can be thoroughly analyzed using one-dimensional (1D) or two-dimensional (2D) NMR spectroscopy. The choice between the two methods depends on the availability of isotope-labeled protein and peak assignments. For 1D experiments, ligand-detection NMR experiments, combined with competition experiments using a known binder, can effectively identify a compound’s binding site. For 2D experiments, the binding site of a compound can be precisely identified at an atomic resolution if an assignment is available. However, even without an assignment, it is entirely feasible to identify the binding site if a known binder is available. Contact us for a detailed discussion of the method and its potential application to your project.