Speaker
Description
X-ray crystallography has become an essential technique for obtaining primary structural information on protein-ligand interactions, guiding the design of new drugs. However, determining the precise binding mode of ligands to proteins can be challenging, especially when ligands adopt multiple orientations or exhibit low occupancy in binding sites due to weak affinity—conditions common during the early stages of research. These challenges are further compounded by uncertainties in the protein structure model, often caused by flexibility, conformational changes, and insufficient resolution. One way to address these limitations is by exploiting additional information from anomalous difference Fourier maps, which are used in X-ray crystallography to visualize the location of anomalous scatterers. Many biologically active ligands contain elements that produce a measurable anomalous signal, enabling researchers to pinpoint the location of these scatterers and accurately determine the ligand's binding orientation. However, detecting lighter elements at standard beamlines has been challenging due to air absorption of X-rays and other technical limitations.
The long-wavelength beamline I23 at Diamond Light Source, optimized for data collection at wavelengths up to 5.5 Å, is well-suited for identifying light elements such as chlorine, sulfur, and phosphorus. Operating in a vacuum environment, the beamline eliminates scattering, resulting in a minimal background signal on the detector. This significantly improves the signal-to-noise ratio and enhances the quality of anomalous difference Fourier maps.
Recent studies on I23 have clearly demonstrated the unique advantages of long-wavelength crystallographic experiments. In one study, anomalous signals were used to unambiguously identify multiple binding orientations of small sulfur- and chlorine-containing fragments bound to the SARS-CoV-2 nsp1 protein [1]. In another, the anomalous signal from a sulfur atom enabled precise determination of the location and binding mode of the drug riluzole in a voltage-gated sodium channel membrane protein [2]. A subsequent study further exploited the long-wavelength capabilities of I23, using the anomalous signal from chlorine to definitively locate a volatile anaesthetic bound to a voltage-gated sodium channel [3]. This information proved essential for elucidating the molecular basis of the anaesthetic’s mechanism of action. These examples highlight the effectiveness of long-wavelength measurements in confidently fitting fragments into challenging electron density maps.
References
1. S. Ma et al., High confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulphur and halogen atoms, Acta Cryst. D, 80, 2024, 451-463.
2. D. Hollingworth et al., Structural basis for rescue of hyperexcitable cells by the ALS drug riluzole. Nature Communications, 15, 2024, 8426.
3. D. Hollingworth at al., Volatile anaesthetics modulate voltage-gated sodium channel function at a site directly linked to channel gating, Nature Communications, 2026 (in print).