High affinity fucose binding of <i>Pseudomonas aeruginosa</i> lectin PA‐IIL: 1.0 Å resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches

Mitchell, Edward P.; Sabin, C.; Šnajdrová, Lenka; Pokorná, Martina; Perret, Stéphanie; Gautier, Catherine; Hofr, Ctirad; Gilboa‐Garber, Nechama; Koča, Jaroslav; Wimmerová, Michaela; Imberty, Anne

doi:10.1002/prot.20330

Cited by 110 publications

(129 citation statements)

References 50 publications

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“…Water molecules and ligands were removed from the PDB files, with the exception of one water molecule (HOH 935) in 1Z4X, which is present in both ligand-free and sialyllactose-bound hemagglutinin-neuraminidase structures. For 2JDH, the two calcium ions in the fucose binding site were kept, and the partial charges for the calcium ions were assigned to 1.5 as suggested by previous studies (38). AutoDock4.2 (39) was used as the docking engine, with the grid files generated by Autogrid4.2 using default parameters and centered on the cocrystallized ligands.…”

Section: Methodsmentioning

confidence: 99%

Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate

Hansman

Shahzad‐ul‐Hussan

McLellan

et al. 2012

J Virol

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Human noroviruses bind with their capsid-protruding domains to histo-blood-group antigens (HBGAs), an interaction thought to direct their entry into cells. Although human noroviruses are the major cause of gastroenteritis outbreaks, development of antivirals has been lacking, mainly because human noroviruses cannot be cultivated. Here we use X-ray crystallography and saturation transfer difference nuclear magnetic resonance (STD NMR) to analyze the interaction of citrate with genogroup II (GII) noroviruses. Crystals of citrate in complex with the protruding domain from norovirus GII.10 Vietnam026 diffracted to 1.4 Å and showed a single citrate bound at the site of HBGA interaction. The citrate interaction was coordinated with a set of capsid interactions almost identical to that involved in recognizing the terminal HBGA fucose, the saccharide which forms the primary conserved interaction between HBGAs and GII noroviruses. Citrate and a water molecule formed a ring-like structure that mimicked the pyranoside ring of fucose. STD NMR showed the protruding domain to have weak affinity for citrate (460 M). This affinity, however, was similar to the affinities of the protruding domain for fucose (460 M) and H type 2 trisaccharide (390 M), an HBGA shown previously to be specifically recognized by human noroviruses. Importantly, competition STD NMR showed that citrate could compete with HBGA for norovirus binding. Together, the results suggest that citrate and other glycomimetics have the potential to block human noroviruses from binding to HBGAs.H uman noroviruses, family Caliciviridae, are the dominant cause of outbreaks of gastroenteritis. Many aspects of human norovirus replication, however, remain unclear, mainly because these viruses cannot be grown in cell culture. Transmission predominately occurs through ingestion of contaminated foods, airborne transmission, and person-to-person contact. Medical treatment usually involves orally administered fluids and electrolyte replacement therapy. Currently, there is no effective vaccine.Human noroviruses can be divided into 2 main genogroups (GI and GII), which can be further subdivided into at least 25 different genotypes (GI.1 to -8 and GII.1 to -17) (26, 57). The norovirus genome has three open reading frames (ORFs) that encode nonstructural, capsid, and small structural proteins, respectively. The capsid of human norovirus is composed of two domains, shell and protruding (P) domains. The shell forms a scaffold around the RNA, and the dimeric P domain contains determinants for both antigenicity and receptor binding (25,43,51). The P domain is further subdivided into P1 and P2 subdomains, where the P1 subdomain interacts with the shell domain and is buried under the outermost P2 subdomain.Human noroviruses bind to histo-blood group antigens (HBGAs), with recognition occurring in the P domain. HBGAs are complex carbohydrates present on mucosal epithelial cells or free antigens in blood, saliva, and other fluids (32). X-ray crystal structures of norovirus P domains in com...

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Section: Methodsmentioning

confidence: 99%

Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate

Hansman

Shahzad‐ul‐Hussan

McLellan

et al. 2012

J Virol

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“…A formal charge on Ca ++ equal to 1.8 and 2.0 gave results in good agreement with experiment. The value of 1.8 was chosen as a compromise, because Ca ++ surrounded by several negatively charged oxygen atoms adopts a smaller charge in reality (about 1.5, see Mitchell et al, 2005).…”

Section: Engineering Of the Pa-iil Lectin To Understand Its Sugar Prementioning

confidence: 99%

In Silico Engineering of Proteins That Recognize Small Molecules

Mishra¹,

Demo²,

Koča³

et al. 2012

Protein Engineering

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“…Fucose-binding lectins are widespread among microorganisms, animals and plants, including Pseudomonas aeruginosa lectin (PA-IIL), Anguilla anguilla agglutinin (AAA), Morone saxatilis agglutinin (MsaFBP32), Dicentrarchus labrax agglutinin, Chromobacterium violaceum lectin (CV-IIL), Ralstonia solanacearum lectin (RS-IIL), Ulex europaeus agglutinin (UEA-I) and Lotus tetragonolobus agglutinin (LTA) (Bianchet et al, 2002;Mitchell et al, 2005;Vandonselaar & Delbaere, 1994;Konami et al, 1990;Zinger-Yosovich et al, 2006;Odom & Vasta, 2006;Cammarata et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin fromLotus tetragonolobusseeds

Moreno

Martil

Cavada³

et al. 2006

Acta Cryst Sect F

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The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. A complete structural data set was collected at 2.00 Å resolution using a synchrotron-radiation source. LTA crystals were found to be monoclinic, belonging to space group P2 1 , with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 Å , = = 90, = 92 . Molecular replacement yielded a solution with a correlation coefficient and R factor of 34.4 and 51.6%, respectively. Preliminary analysis of the molecular-replacement solution indicates a new quaternary association in the LTA structure. Crystallographic refinement is under way.

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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

Cited by 110 publications

References 50 publications

Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate

Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate

In Silico Engineering of Proteins That Recognize Small Molecules

Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin fromLotus tetragonolobusseeds

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