Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions

Gajdoš, Lukáš; Blakeley, Matthew P.; Kumar, Atul; Wimmerová, Michaela; Haertlein, Michael; Forsyth, V. Trevor; Devos, Juliette M.

doi:10.1016/j.str.2021.03.003

Cited by 9 publications

(6 citation statements)

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“…A high-resolution crystal structure of LecB has been obtained previously 14 , but the role of the two calcium ions in the high-affinity binding of fucose remains unclear and further structural analyses are required. Neutron macromolecular crystallography is the technique of choice for determining the positions of hydrogen atoms and the protonation states of active groups 18 – 21 that are involved in the catalytic activity of enzymes or the binding of a ligand to a macromolecule 22 – 25 . Moreover, neutrons do not cause any radiation damage to the biological sample so the structure determination and data collection can be performed at room temperature (RT), giving a more accurate view of local flexibility and water mobility at biologically relevant temperatures 26 , 27 .…”

Section: Introductionmentioning

confidence: 99%

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

et al. 2022

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The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.

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Section: Introductionmentioning

confidence: 99%

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

et al. 2022

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“…Studying the effect of glycerol at the atomic level requires structural data of the highest quality, which are rarely available. Recently, Gajdos and coworkers reported that glycerol causes alternative loop conformations between repeats in the structure of the lectin PLL from Photorhabdus laumondii (Gajdos et al, 2021). Another notable example is human carbonic anhydrase II.…”

Section: Discussionmentioning

confidence: 99%

Structural insights into the effects of glycerol on ligand binding to cytochrome P450

Bukhdruker

Varaksa

Orekhov

et al. 2023

Acta Cryst Sect D Struct Biol

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New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124–CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124–CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural–functional studies and impede rational drug-design campaigns.

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“…I am grateful to the University of Manchester Department of Chemistry for continued support. As a further measure of the growth and importance of the theme of neutron protein crystallography in general and its use to determine lectin saccharide structures in full detail, and at a temperature relevant to their structure and function, I note that the Eleventh Erwin Felix Lewy Bertaut Prize of the European Neutron Scattering Association (ENSA) and the European Crystallographic Association (ECA) was awarded to Dr Luka ´s ˇGajdos in 2022 for his PhD research at the Institut Laue-Langevin Grenoble as reported in Gajdos et al (2021Gajdos et al ( , 2022.…”

Section: Acknowledgementsmentioning

confidence: 99%

“…protonation states of acidic residues in the carbohydratebinding site of LecB from the human pathogen P. aeruginosa (Gajdos et al, 2021(Gajdos et al, , 2022. The neutron crystal structures included apo and monosaccharide-bound forms; for an example of the fine details that can be seen in the nuclear density map, see Fig.…”

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confidence: 99%

Relating protein crystal structure to ligand-binding thermodynamics

Helliwell¹

2022

Acta Cryst Sect F

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An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.

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Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions

Cited by 9 publications

References 64 publications

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

Structural insights into the effects of glycerol on ligand binding to cytochrome P450

Relating protein crystal structure to ligand-binding thermodynamics

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