Czech Infrastructure for Integrative Structural Biology – CIISB

A gateway to realm of structural data for biochemists, biophysicists, molecular biologist, and all scientists whose research benefits from accurate structure determination of biological macromolecules, assemblies, and complex molecular machineries at atomic resolution.

Open access to 10 high-end core facilities and assisted expertise in NMR, X-ray crystallography and crystallization, cryo-electron microscopy and tomography, biophysical characterization of biomolecular interaction, nanobiotechnology, proteomics and structural mass spectrometry.

A distributed infrastructure constituted by Core Facilities of CEITEC (Central European Institute of Technology), located in Brno, and BIOCEV (Biotechnology and Biomedicine Centre), located in Vestec near Prague, Central Bohemia.

Czech national centre of European Research Infrastructure Consortium INSTRUCT ERIC.

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Research highlights

Nat. Commun. 2018

Chemistry – A European Journal 2018

Interaction of TBEV virions with Fab fragments of neutralizing antibody 19/1786. a Cryo-EM micrograph of TBEV virions incubated with Fab fragments of 19/1786. Scale bar represents 100 nm. b Electron-density map of Fab-covered TBEV virion. c Molecular surface of TBEV virion covered with Fab 19/1786 fragments low-pass filtered to 7 Å resolution. E-proteins are shown in red, green, and blue. Fab fragments are shown in magenta (heavy chain) and pink (light chain). Scale bars in band c represent 10 nm. d Footprints of Fab 19/1786 on TBEV surface. e The Fab 19/1786 binds to the domain III at an angle of 135° relative to the axis of the E-protein ectodomain.

Pavel Plevka Research group

Significance

Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. Here, Pavel Plevka and his coworkers present cryo-EM structures of the native TBEV virion and its complex with Fab fragments of neutralizing antibody 19/1786. Flavivirus genome delivery depends on membrane fusion that is triggered at low pH. The virion structure indicates that the repulsive interactions of histidine side chains, which become protonated at low pH, may contribute to the disruption of heterotetramers of the TBEV envelope and membrane proteins and induce detachment of the envelope protein ectodomains from the virus membrane. The Fab fragments bind to 120 out of the 180 envelope glycoproteins of the TBEV virion. Unlike most of the previously studied flavivirus-neutralizing antibodies, the Fab fragments do not lock the E-proteins in the native-like arrangement, but interfere with the process of virus-induced membrane fusion. 

Fuzik, T. et al. Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody. Nature Communications 9, 11, doi:10.1038/s41467-018-02882-0 (2018). doi:10.1038/s41467-018-02882-0

 

Structure of PHL complex with propargyl a-l-fucoside. (A) PHL monomer (chain A) overall architecture with propargyl a-l-fucoside shown as magenta sticks. Individual binding sites are labelled in black (front plane) or grey (back plane) (B) Side view of PHL dimer with chain B shown in grey and without ligands. (C) Individual PHL fucose‐type binding sites with Compound 5 (magenta) bound. Amino acids responsible in ligand binding are highlighted and labelled. (D) PHL galactose‐type binding site with propargyl a-l-fucoside (magenta) bound and PHL galactose‐type binding site with d‐Gal (yellow) bound (PDB ID 5MXH). Colour code for panels C/D: amino acids involved in ligand‐binding through H‐bond=cyan, CH–π interaction=orange, or water bridge=grey.

Michalea Wimmerova Research Group

 Significance

Photorhabdus asymbiotica is a gram‐negative bacterium that is not only as effective an insect pathogen as other members of the genus, but it also causes serious diseases in humans. The recently identified lectin PHL from P. asymbiotica verifiably modulates an immune response of humans and insects, which supports the idea that the lectin might play an important role in the host–pathogen interaction. Dimeric PHL contains up to seven l‐fucose‐specific binding sites per monomer, and in order to target multiple binding sites of PHL, α‐l‐fucoside‐containing di‐, tri‐ and tetravalent glycoclusters were synthesized. The interaction between fucoside derivates and PHL was investigated by several biophysical and biological methods, ITC and SPR measurements, hemagglutination inhibition assay, and an investigation of bacterial aggregation properties were carried out. Details of the interaction between PHL and propargyl α‐l‐fucoside as a monomer unit were revealed using X‐ray crystallography. Besides this, the interaction with multivalent compounds was studied by NMR techniques. The newly synthesized multivalent fucoclusters proved to be up to several orders of magnitude better ligands than the natural ligand, l‐fucose.

 

Jancarikova, G. et al. Synthesis of a-l-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL). Chemistry-A European Journal, 24, 4055-4068, doi.org/10.1002/chem.201705853

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