Kateřina Hofbauerová

Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

BackgroundFungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined.ResultsThe complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation.ConclusionWhereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected enzyme stability in acidic conditions. Dimerization and N-glycosylation are the enzymes strategy for catalytic subunit stabilization. The disulfide bridge that connects Cys448 with Cys483 stabilizes a hinge region in a flexible loop close to the active site, which is an exclusive feature of the fungal enzymes, neither present in bacterial nor mammalian structures. This loop may play the role of a substrate binding site lid, anchored by a disulphide bridge that prevents the substrate binding site from being influenced by the flexible motion of the loop.

Study of chaperone-like activity of human haptoglobin: conformational changes under heat shock conditions and localization of interaction sites.

Abstract With respect to the mechanism of chaperonelike activity, we examined the behavior of haptoglobin under heat shock conditions. Secondary structure changes during heat treatment were followed by circular dichroism, Raman and infrared spectroscopy. A model of the haptoglobin tetramer, based on its sequence homology with serine proteases and the CCP modules, has been proposed. Sequence regions responsible for the chaperonelike activity were not fully identical with the region that takes part in formation of the hemoglobinhaptoglobin complex. We can postulate the presence of at least two different chaperonebinding sites on each haptoglobin heavy chain.

Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemical stability display prolonged circulation and remain intact in the blood of mice

We investigated the soluble forms of the earliest activation antigen of human leukocyte CD69. This receptor is expressed at the cell surface as a type II homodimeric membrane protein. However, the elements necessary to prepare the soluble recombinant CD69 suitable for structural studies are a matter of controversy. We describe the physical, biochemical and in vivo characteristics of a highly stable soluble form of CD69 obtained by bacterial expression of an appropriate extracellular segment of this protein. Our construct has been derived from one used for CD69 crystallization by further optimization with regard to protein stability, solubility and easy crystallization under conditions promoting ligand binding. The resulting protein is stable at acidic pH and at temperatures of up to 65 °C, as revealed by long‐term stability tests and thermal denaturation experiments. Protein NMR and crystallography confirmed the expected protein fold, and revealed additional details of the protein characteristics in solution. The soluble CD69 refolded in a form of noncovalent dimers, as revealed by gel filtration, sedimentation velocity measurements, NMR and dynamic light scattering. The soluble CD69 proved to be remarkably stable in vivo when injected into the bloodstream of experimental mice. More than 70% of the most stable CD69 proteins is preserved intact in the blood 24 h after injection, whereas the less stable CD69 variants are rapidly taken up by the liver.

Structural analysis of natural killer cell receptor protein 1 (NKR- P1) extracellular domains suggests a conserved long loop region involved in ligand specificity

Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat NKR-P1A and NKR-P1B, mouse NKR-P1A, NKR-P1C, NKR-P1F, and NKR-P1G, and human NKR-P1 receptors. Experimental data on secondary structure, tertiary interactions, and thermal transitions are acquired for four of the proteins using Raman and infrared spectroscopy. The experimental and modeling results are in agreement with respect to the overall structures of the NKR-P1 receptor domains, while suggesting functionally significant local differences among species and isoforms. Two sequence regions that are conserved in all analyzed NKR-P1 receptors do not correspond to conserved structural elements as might be expected, but are represented by loop regions, one of which is arranged differently in the constructed models. This region displays high flexibility but is anchored by conserved sequences, suggesting that its position relative to the rest of the domain might be variable. This loop may contribute to ligand-binding specificity via a coupled conformational transition.

Phe475 and Glu446 but not Ser445 participate in ATP-binding to the α-subunit of Na+/K+-ATPase

Abstract The ATP-binding site of Na + /K + -ATPase is localized on the large cytoplasmic loop of the α-subunit between transmembrane helices H 4 and H 5 . Site-directed mutagenesis was performed to identify residues involved in ATP binding. On the basis of our recently developed model of this loop, Ser 445 , Glu 446 , and Phe 475 were proposed to be close to the binding pocket. Replacement of Phe 475 with Trp and Glu 446 with Gln profoundly reduced the binding of ATP, whereas the substitution of Ser 445 with Ala did not affect ATP binding. Fluorescence measurements of the fluorescent analog TNP-ATP, however, indicated that Ser 445 is close to the binding site, although it does not participate in binding.

Molecular architecture of mouse activating NKR-P1 receptors

Receptors belonging to NKR-P1 family and their specific Clr ligands form an alternative missing self recognition system critical in immunity against tumors and viruses, elimination of tumor cells subjected to genotoxic stress, activation of T cell dependent immune response, and hypertension. The three-dimensional structure of the extracellular domain of the mouse natural killer (NK) cell receptor mNKR-P1Aex has been determined by X-ray diffraction. The core of the C-type lectin domain (CTLD) is homologous to the other CTLD receptors whereas one quarter of the domain forms an extended loop interacting tightly with a neighboring loop in the crystal. This domain swapping mechanism results in a compact interaction interface. A second dimerization interface resembles the known arrangement of other CTLD NK receptors. A functional dimeric form of the receptor is suggested, with the loop, evolutionarily conserved within this family, proposed to participate in interactions with ligands.

RETRACTED: Carboxylated calixarenes bind strongly to CD69 and protect CD69+ killer cells from suicidal cell death induced by tumor cell surface ligands

We have recently identified a new class of high affinity ligands for CD69 leukocyte membrane receptor, carboxylated calixarenes. Of the three compounds investigated here, thiacalix[4]arene had the highest affinity for CD69 in direct binding assays, and proved to be the most specific inhibitor of CD69 identified so far in receptor precipitation and cellular activation experiments. Carboxylated calixarenes also proved effective at protection of CD69(high) lymphocytes from apoptosis triggered by a multivalent ligand or antibody. Thus, carboxylated calixarenes set a new paradigm for noncarbohydrate ligands for CD69 making them attractive for protection of killer cells in combined animal tumor therapies.

Glycosylation Protects Proteins against Free Radicals Generated from Toxic Xenobiotics

Free radicals generated during peroxidase-catalyzed oxidation of two xenobiotics, carcinogenic Sudan I and an anticancer agent ellipticine, easily attack unmodified proteins but not glycoproteins. A significant inverse correlation between the extent of glycosylation of proteins and the degree of binding of Sudan I or ellipticine radicals to these proteins was observed, whereby the protection only occurs if oligosaccharides are covalently bound to the proteins. No influence of any other variables was found and further confirmed by experiments with proteins containing identical polypeptide chains differing only by the absence (ribonuclease A) or the presence (ribonuclease B) of a single oligosaccharide. The free radicals that are subject of this study did not react with the oligosaccharides because higher levels of the corresponding dimers, reaction products of the radicals, were found in presence of highly glycosylated proteins. The results indicate that carbohydrates protect polypeptides against modification by free radicals derived from toxic xenobiotics and provide passive shielding of the protein moiety.

Synthetic N-Acetyl-d-glucosamine Based Fully Branched Tetrasaccharide, a Mimetic of the Endogenous Ligand for CD69, Activates CD69+ Killer Lymphocytes upon Dimerization via a Hydrophilic Flexible Linker

On the basis of the highly branched ovomucoid-type undecasaccharide that had been shown previously to be an endogenous ligand for CD69 leukocyte receptor, a systematic investigation of smaller oligosaccharide mimetics was performed based on linear and branched N-acetyl-d-hexosamine homooligomers prepared synthetically using hitherto unexplored reaction schemes. The systematic structure-activity studies revealed the tetrasaccharide GlcNAcbeta1-3(GlcNAcbeta1-4)(GlcNAcbeta1-6)GlcNAc (compound 52) and its alpha-benzyl derivative 49 as the best ligand for CD69 with IC(50) as high as 10(-9) M. This compound thus approaches the affinity of the classical high-affinity neoglycoprotein ligand GlcNAc(23)BSA. Compound 68, GlcNAc tetrasaccharide 52 dimerized through a hydrophilic flexible linker, turned out to be effective in activating CD69(+) lymphocytes. It also proved efficient in enhancing natural killing in vitro, decreasing the growth of tumors in vivo, and activating the CD69(+) tumor infiltrating lymphocytes examined ex vivo. This compound is thus a candidate for carbohydrate-based immunomodulators with promising antitumor potential.

Cooperation between subunits is essential for high-affinity binding of N-acetyl-D-hexosamines to dimeric soluble and dimeric cellular forms of human CD69.

CD69 is an earliest lymphocyte activation antigen and a universal leukocyte triggering molecule expressed at sites of active immune response. The binding of GlcNAc to the dimeric human CD69 was followed by equilibrium dialysis, fluorescence titration, and NMR. Clear cooperation was observed in the high-affinity binding (K(d) = 4.0 x 10(-7) M) of the carbohydrate to two subunits of the dimeric CD69 (Hill coefficient 1.94). A control monosaccharide ManNAc was not bound by human CD69, and both monosaccharides had no effects on the structure of the receptor. However, a monomeric CD69 obtained by mutating Q93 and R134 at the dimer interface exhibited a much lower affinity for GlcNAc (K(d) = 1.3 x 10(-5) M) and no cooperativity (Hill coefficient 1.07). Perturbation of the dimer interface resulted in a severe impairment of the signaling ability of cellular CD69 when cross-linked with an antibody or with a bivalent high-affinity N-acetylhexosamine dimer-based ligand. The availability of stable preparations of soluble CD69 receptor with well-documented ligand binding properties will be beneficial for immunological experiments evaluating the role of this antigen in the complex environment of the immune system. Moreover, such preparations in combination with efficient ligand mimetics able to both activate CD69(+) lymphocytes and to block undesired hyperactivation caused by other cellular ligands will also become indispensable tools in explaining the exact role of the CD69 antigen in the interaction between the tumor cell and the effector natural killer lymphocyte.