<i>In situ</i> crystal data-collection and ligand-screening system at SPring-8

Okumura, Hideo; Sakai, Naoki; Murakami, Hideo; Mizuno, Nobuhiro; Nakamura, Yuki; Ueno, Go; Masunaga, Takuya; Kawamura, Takashi; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

doi:10.1107/s2053230x22005283

Cited by 9 publications

(1 citation statement)

References 42 publications

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“…A simple approach to determine room temperature crystal structures is to measure data directly from crystals within suitable crystallisation plates. The first dedicated beamline to do this was the versatile macromolecular crystallography in situ (VMXi) beamline at Diamond Light Source ( Sanchez-Weatherby et al, 2019 ), with several additional instruments now in operation worldwide ( Okumura et al, 2022 ). Alternative approaches involve measuring data from crystals between sheets of low background material such as mylar ( Broecker et al, 2018 ).…”

Section: X-ray Structure Determination At Room Temperaturementioning

confidence: 99%

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

Hough

Prischi

Worrall

2023

Front. Mol. Biosci.

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The interaction between macromolecular proteins and small molecule ligands is an essential component of cellular function. Such ligands may include enzyme substrates, molecules involved in cellular signalling or pharmaceutical drugs. Together with biophysical techniques used to assess the thermodynamic and kinetic properties of ligand binding to proteins, methodology to determine high-resolution structures that enable atomic level interactions between protein and ligand(s) to be directly visualised is required. Whilst such structural approaches are well established with high throughput X-ray crystallography routinely used in the pharmaceutical sector, they provide only a static view of the complex. Recent advances in X-ray structural biology methods offer several new possibilities that can examine protein-ligand complexes at ambient temperature rather than under cryogenic conditions, enable transient binding sites and interactions to be characterised using time-resolved approaches and combine spectroscopic measurements from the same crystal that the structures themselves are determined. This Perspective reviews several recent developments in these areas and discusses new possibilities for applications of these advanced methodologies to transform our understanding of protein-ligand interactions.

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Section: X-ray Structure Determination At Room Temperaturementioning

confidence: 99%

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

Hough

Prischi

Worrall

2023

Front. Mol. Biosci.

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Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods

Thompson

2023

Methods in Enzymology

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Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments

Szalai,

Bajusz,

Börzsei

et al. 2024

J. Chem. Inf. Model.

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Rational drug design focuses on the explanation and prediction of complex formation between therapeutic targets and small-molecule ligands. As a third and often overlooked interacting partner, water molecules play a critical role in the thermodynamics of protein−ligand binding, impacting both the entropy and enthalpy components of the binding free energy and by extension, on-target affinity and bioactivity. The community has realized the importance of binding site waters, as evidenced by the number of computational tools to predict the structure and thermodynamics of their networks. However, quantitative experimental characterization of relevant protein−ligand−water systems, and consequently the validation of these modeling methods, remains challenging. Here, we investigated the impact of solvent exchange from light (H 2 O) to heavy water (D 2 O) to provide complete thermodynamic profiling of these ternary systems. Utilizing the solvent isotope effects, we gain a deeper understanding of the energetic contributions of various components. Specifically, we conducted isothermal titration calorimetry experiments on trypsin with a series of psubstituted benzamidines, as well as carbonic anhydrase II (CAII) with a series of aromatic sulfonamides. Significant differences in binding enthalpies found between light vs heavy water indicate a substantial role of the binding site water network in protein−ligand binding. Next, we challenged two conceptually distinct modeling methods, the grid-based WaterFLAP and the molecular dynamicsbased MobyWat, by predicting and scoring relevant water networks. The predicted water positions accurately reproduce those in available high-resolution X-ray and neutron diffraction structures of the relevant protein−ligand complexes. Estimated energetic contributions of the identified water networks were corroborated by the experimental thermodynamics data. Besides providing a direct validation for the predictive power of these methods, our findings confirmed the importance of considering binding site water networks in computational ligand design.

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In situ crystal data-collection and ligand-screening system at SPring-8

Cited by 9 publications

References 42 publications

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods

Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments

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