Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.
Bacterial Adhesion
/ genetics
Binding Sites
Calcium
/ metabolism
Cloning, Molecular
Cross Infection
/ microbiology
Crystallography, X-Ray
Deuterium
/ chemistry
Escherichia coli
/ genetics
Fucose
/ chemistry
Gene Expression
Genetic Vectors
/ chemistry
Humans
Hydrogen Bonding
Lectins
/ chemistry
Ligands
Neutrons
Protein Binding
Pseudomonas Infections
/ microbiology
Pseudomonas aeruginosa
/ chemistry
Recombinant Proteins
/ chemistry
Water
/ metabolism
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
11 01 2022
11 01 2022
Historique:
received:
24
09
2021
accepted:
15
12
2021
entrez:
12
1
2022
pubmed:
13
1
2022
medline:
9
2
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 35017516
doi: 10.1038/s41467-021-27871-8
pii: 10.1038/s41467-021-27871-8
pmc: PMC8752737
doi:
Substances chimiques
LecB protein, Pseudomonas aeruginosa
0
Lectins
0
Ligands
0
Recombinant Proteins
0
Water
059QF0KO0R
Fucose
28RYY2IV3F
Deuterium
AR09D82C7G
Calcium
SY7Q814VUP
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
194Informations de copyright
© 2022. The Author(s).
Références
Jurado-Martín, I., Sainz-Mejías, M. & McClean, S. Pseudomonas aeruginosa: an audacious pathogen with an adaptable arsenal of virulence factors. Int. J. Mol. Sci. 22, 1–37 (2021).
doi: 10.3390/ijms22063128
Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318–327 (2018).
pubmed: 29276051
doi: 10.1016/S1473-3099(17)30753-3
Chen, C. P., Song, S. C., Gilboa-Garber, N., Chang, K. S. S. & Wu, A. M. Studies on the binding site of the galactose-specific agglutinin PA-IL from Pseudomonas aeruginosa. Glycobiology 8, 7–16 (1998).
pubmed: 9451010
doi: 10.1093/glycob/8.1.7
Garber, N., Guempel, U., Gilboa-Garber, N. & Royle, R. J. Specificity of the fucose-binding lectin of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 48, 331–334 (1987).
doi: 10.1111/j.1574-6968.1987.tb02619.x
Funken, H. et al. Specific association of lectin LecB with the surface of Pseudomonas aeruginosa: role of outer membrane protein OprF. PLoS ONE 7, 46857 (2012).
doi: 10.1371/journal.pone.0046857
Passos da Silva, D. et al. The Pseudomonas aeruginosa lectin LecB binds to the exopolysaccharide Psl and stabilizes the biofilm matrix. Nat. Commun. 10, 2183 (2019).
pubmed: 31097723
pmcid: 6522473
doi: 10.1038/s41467-019-10201-4
Chemani, C. et al. Role of LecA and LecB lectins in Pseudomonas aeruginosa-induced lung injury and effect of carbohydrate ligands. Infect. Immun. 77, 2065–2075 (2009).
pubmed: 19237519
pmcid: 2681743
doi: 10.1128/IAI.01204-08
Imberty, A., Wimmerová, M., Mitchell, E. P. & Gilboa-Garber, N. Structures of the lectins from Pseudomonas aeruginosa: Insights into the molecular basis for host glycan recognition. Microbes Infect. 6, 221–228 (2004).
pubmed: 15049333
doi: 10.1016/j.micinf.2003.10.016
Tielker, D. et al. Pseudomonas aeruginosa lectin LecB is located in the outer membrane and is involved in biofilm formation. Microbiology 151, 1313–1323 (2005).
pubmed: 15870442
doi: 10.1099/mic.0.27701-0
Boukerb, A. M. et al. Antiadhesive properties of glycoclusters against Pseudomonas aeruginosa lung infection. J. Med. Chem. 57, 10275–10289 (2014).
pubmed: 25419855
doi: 10.1021/jm500038p
Cott, C. et al. Pseudomonas aeruginosa lectin LecB inhibits tissue repair processes by triggering β-catenin degradation. Biochim. Biophys. Acta Mol. Cell Res. 1863, 1106–1118 (2016).
doi: 10.1016/j.bbamcr.2016.02.004
Thuenauer, R. et al. The Pseudomonas aeruginosa lectin LecB causes integrin internalization and inhibits epithelial wound healing. MBio 11, e03260-19 (2020).
Mitchell, E. et al. Structural basis for oligosaccharide-mediated adhesion of Pseudomonas aeruginosa in the lungs of cystic fibrosis patients. Nat. Struct. Biol. 9, 918–921 (2002).
pubmed: 12415289
doi: 10.1038/nsb865
Mitchell, E. P. et al. High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL: 1.0 Å resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches. Proteins Struct. Funct. Bioinforma. 58, 735–746 (2004).
doi: 10.1002/prot.20330
Meiers, J., Siebs, E., Zahorska, E. & Titz, A. Lectin antagonists in infection, immunity, and inflammation. Curr. Opin. Chem. Biol. 53, 51–67 (2019).
pubmed: 31470348
doi: 10.1016/j.cbpa.2019.07.005
Sommer, R. et al. Glycomimetic, orally bioavailable LecB inhibitors block biofilm formation of Pseudomonas aeruginosa. J. Am. Chem. Soc. 140, 2537–2545 (2018).
pubmed: 29272578
doi: 10.1021/jacs.7b11133
Johansson, E. M. V. et al. Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB. Chem. Biol. 15, 1249–1257 (2008).
pubmed: 19101469
doi: 10.1016/j.chembiol.2008.10.009
Ahmed, H. U. et al. The determination of protonation states in proteins. Acta Crystallogr. D. Biol. Crystallogr. 63, 906–922 (2007).
pubmed: 17642517
doi: 10.1107/S0907444907029976
Blakeley, M. P. & Podjarny, A. D. Neutron macromolecular crystallography. Emerg. Top. Life Sci. 2, 39–55 (2018).
pubmed: 33525781
doi: 10.1042/ETLS20170083
Helliwell, J. R. Fundamentals of neutron crystallography in structural biology. Methods Enzymol. 634, 1–19 (2020).
pubmed: 32093828
doi: 10.1016/bs.mie.2020.01.006
Gajdos, L. et al. Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Structure 29, 1003–1013 (2021).
pubmed: 33765407
doi: 10.1016/j.str.2021.03.003
Azadmanesh, J., Lutz, W. E., Coates, L., Weiss, K. L. & Borgstahl, G. E. O. Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. Nat. Commun. 121, 1–12 (2021).
Kwon, H. et al. Direct visualization of a Fe(IV)–OH intermediate in a heme enzyme. Nat. Commun. 7, 13445 (2016).
Yee, A. W. et al. A molecular mechanism for transthyretin amyloidogenesis. Nat. Commun. 10, 925 (2019).
Dajnowicz, S. et al. Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme. Nat. Commun. 81, 1–9 (2017).
Fraser, J. S. et al. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc. Natl Acad. Sci. USA 108, 16247 LP–16216252 (2011).
doi: 10.1073/pnas.1111325108
Bradford, S. Y. C. et al. Temperature artifacts in protein structures bias ligand-binding predictions. Chem. Sci. 12, 11275–11293 (2021).
pubmed: 34667539
pmcid: 8447925
doi: 10.1039/D1SC02751D
Haertlein, M. et al. Biomolecular deuteration for neutron structural biology and dynamics. Methods Enzymol. 566, 113–157 (2016).
pubmed: 26791978
doi: 10.1016/bs.mie.2015.11.001
Gajdos, L. et al. Production of perdeuterated fucose from glyco-engineered bacteria. Glycobiology 31, 151–158 (2021).
pubmed: 32601663
doi: 10.1093/glycob/cwaa059
Emsley, J. Very strong hydrogen bonding. Chem. Soc. Rev. 9, 91–124 (1980).
doi: 10.1039/cs9800900091
Hibbert, F. & Emsley, J. Hydrogen bonding and chemical reactivity. Adv. Phys. Org. Chem. 26, 255–379 (1990).
Cleland, W. W. Low-barrier hydrogen bonds and low fractionation factor bases in enzymic reactions. Biochemistry 31, 317–319 (2002).
doi: 10.1021/bi00117a001
Kemp, M. T., Lewandowski, E. M. & Chen, Y. Low barrier hydrogen bonds in protein structure and function. Biochimica et. Biophysica Acta Proteins Proteom. 1869, 140557 (2021).
doi: 10.1016/j.bbapap.2020.140557
Elias, M. et al. The molecular basis of phosphate discrimination in arsenate-rich environments. Nature 491, 134–137 (2012).
pubmed: 23034649
doi: 10.1038/nature11517
Cleland, W. W. & Kreevoy, M. M. Low-barrier hydrogen bonds and enzymic catalysis. Science 264, 1887–1890 (1994).
pubmed: 8009219
doi: 10.1126/science.8009219
Loris, R., Tielker, D., Jaeger, K. E. & Wyns, L. Structural basis of carbohydrate recognition by the lectin LecB from Pseudomonas aeruginosa. J. Mol. Biol. 331, 861–870 (2003).
pubmed: 12909014
doi: 10.1016/S0022-2836(03)00754-X
Dam, T. K. & Brewer, C. F. Thermodynamic studies of lectin−carbohydrate interactions by isothermal titration calorimetry. Chem. Rev. 102, 387–429 (2002).
pubmed: 11841248
doi: 10.1021/cr000401x
Pokorná, M. et al. Unusual entropy-driven affinity of chromobacterium violaceum lectin CV-IIL toward fucose and mannose†,‡. Biochemistry 45, 7501–7510 (2006).
pubmed: 16768446
doi: 10.1021/bi060214e
Huang, G. Y. et al. Neutron diffraction reveals hydrogen bonds criticalfor cGMP-selective activation: insights for cGMP-dependent proteinkinase agonist design. Biochemistry 53, 6725 (2014).
pubmed: 25271401
doi: 10.1021/bi501012v
Blakeley, M. P. et al. Neutron macromolecular crystallography with LADI-III. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 1198–1205 (2010).
doi: 10.1107/S0907444910019797
Campbell, J. W., Hao, Q., Harding, M. M., Nguti, N. D. & Wilkinson, C. LAUEGEN version 6.0 and INTLDM. J. Appl. Crystallogr. 31, 496–502 (1998).
doi: 10.1107/S0021889897016683
Arzt, S., Campbell, J. W., Harding, M. M., Hao, Q. & Helliwell, J. R. LSCALE—the new normalization, scaling and absorption correction program in the Daresbury Laue software suite. J. Appl. Crystallogr. 32, 554–562 (1999).
doi: 10.1107/S0021889898015350
Evans, P. Scaling and assessment of data quality. Acta Crystallograph. D. Biol. Crystallogrph. 62, 72–82 (2006).
doi: 10.1107/S0907444905036693
Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. iMOSFLM: A new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr. Sect. D. Biol. Crystallogr. 67, 271–281 (2011).
doi: 10.1107/S0907444910048675
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. Sect. D. Biol. Crystallogr. 69, 1204–1214 (2013).
doi: 10.1107/S0907444913000061
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D: Biol. Crystallogr. 67, 235–242 (2011).
doi: 10.1107/S0907444910045749
Kabsch, W. et al. XDS. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 125–132 (2010).
doi: 10.1107/S0907444909047337
Adams, P. D. et al. PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. Sect. D. Biol. Crystallogr. 68, 352–367 (2012).
doi: 10.1107/S0907444912001308
Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr. Sect. D. Biol. Crystallogr. 65, 1074–1080 (2009).
doi: 10.1107/S0907444909029436
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
doi: 10.1002/pro.3330