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SUMMARY: The plant immune system perceives a diversity of carbohydrate ligands from plant and microbial cell walls through the extracellular ectodomains (ECDs) of pattern recognition receptors (PRRs), which activate pattern‐triggered immunity (PTI). Among these ligands are oligosaccharides derived from mixed‐linked β‐1,3/β‐1,4‐glucans (MLGs; e.g. β‐1,4‐D‐(Glc)2‐β‐1,3‐D‐Glc, MLG43) and cellulose (e.g. β‐1,4‐D‐(Glc)3, CEL3). The mechanisms behind carbohydrate perception in plants are poorly characterized except for fungal chitin oligosaccharides (e.g. β‐1,4‐d‐(GlcNAc)6, CHI6), which involve several receptor kinase proteins (RKs) with LysM‐ECDs. Here, we describe the isolation and characterization of Arabidopsis thaliana mutants impaired in glycan perception (igp) that are defective in PTI activation mediated by MLG43 and CEL3, but not by CHI6. igp1–igp4 are altered in three RKs – AT1G56145 (IGP1), AT1G56130 (IGP2/IGP3) and AT1G56140 (IGP4) – with leucine‐rich‐repeat (LRR) and malectin (MAL) domains in their ECDs. igp1 harbors point mutation E906K and igp2 and igp3 harbor point mutation G773E in their kinase domains, whereas igp4 is a T‐DNA insertional loss‐of‐function mutant. Notably, isothermal titration calorimetry (ITC) assays with purified ECD‐RKs of IGP1 and IGP3 showed that IGP1 binds with high affinity to CEL3 (with dissociation constant KD = 1.19 ± 0.03 μm) and cellopentaose (KD = 1.40 ± 0.01 μM), but not to MLG43, supporting its function as a plant PRR for cellulose‐derived oligosaccharides. Our data suggest that these LRR‐MAL RKs are components of a recognition mechanism for both cellulose‐ and MLG‐derived oligosaccharide perception and downstream PTI activation in Arabidopsis. Significance Statement: The mechanisms of perception of newly described cell‐wall derived oligosaccharides that trigger plant immunity are poorly characterized. Here we described three Arabidopsis thaliana receptor kinases (RK) with Leucine Rich Repeat (LRR) and Malectin (MAL) domains in their ectodomains (ECDs), which are components of a novel mechanism of both cellulose and mixed‐linked β‐glucan (MLGs)‐derived oligosaccharides perception and downstream immune activation. One of these RKs binds cellulose oligosaccharides indicating that is a plant pattern recognition receptor (PRR). [ABSTRACT FROM AUTHOR]

Two different polyglycine-rich fragments were selected as representatives of major ampullate gland spidroins (MaSp) 1 and 2 types, and their behavior in a water-saturated environment was simulated within the framework of molecular dynamics (MD). The selected fragments are found in the sequences of the proteins MaSp1a and MaSp2.2a of Argiope aurantia with respective lengths of 36 amino acids (MaSp1a) and 50 amino acids (MaSp2.2s). The simulation took the fully extended β-pleated conformation as reference, and MD was used to determine the equilibrium configuration in the absence of external forces. Subsequently, MD were employed to calculate the variation in the distance between the ends of the fragments when subjected to an increasing force. Both fragments show an elastomeric behavior that can be modeled as a freely jointed chain with links of comparable length, and a larger number of links in the spidroin 2 fragment. It is found, however, that the maximum recovery force recorded from the spidroin 2 peptide (Fmax ≈ 400 pN) is found to be significantly larger than that of the spidroin 1 (Fmax ≈ 250 pN). The increase in the recovery force of the spidroin 2 polyglycine-rich fragment may be correlated with the larger values observed in the strain at breaking of major ampullate silk fibers spun by Araneoidea species, which contain spidroin 2 proteins, compared to the material produced by spider species that lack these spidroins (RTA-clade). [ABSTRACT FROM AUTHOR]

The ion complexes NO3(super -)(HNO3)(sub n), n = 1-3, is studied by using ab initio calculations at the B3YLP/aug-cc-pVTZ level of theory. The calculations have shown small differences of energy in the variation of the two nitrate groups from planarity to an almost perpendicular form for n = 1 and in all the cases, binding energies close to that of covalent compounds are estimated.

Background: Previously, the protective farm effect was imitated using the whey protein beta‐lactoglobulin (BLG) that is spiked with iron‐flavonoid complexes. Here, we formulated for clinical translation a lozenge as food for special medical purposes (FSMP) using catechin‐iron complexes as ligands for BLG. The lozenge was tested in vitro and in a therapeutical BALB/c mice model. Methods: Binding of iron‐catechin into BLG was confirmed by spectroscopy and docking calculations. Serum IgE binding of children allergic or tolerating milk was assessed to loaded (holo‐) versus empty (apo‐) BLG and for human mast cell degranulation. BLG and Bet v 1 double‐sensitized mice were orally treated with the holoBLG or placebo lozenge, and immunologically analysed after systemic allergen challenge. Human PBMCs of pollen allergic subjects were flow cytometrically assessed after stimulation with apoBLG or holoBLG using catechin‐iron complexes as ligands. Results: One major IgE and T cell epitope were masked by catechin‐iron complexes, which impaired IgE binding of milk‐allergic children and degranulation of mast cells. In mice, only supplementation with the holoBLG lozenge reduced clinical reactivity to BLG and Bet v 1, promoted Tregs, and suppressed antigen presentation. In allergic subjects, stimulation of PBMCs with holoBLG led to a significant increase of intracellular iron in circulating CD14+ cells with significantly lower expression of HLADR and CD86 compared to their stimulation with apoBLG. Conclusion: The FSMP lozenge targeted antigen presenting cells and dampened immune activation in human immune cells and allergic mice in an antigen‐non‐specific manner, thereby conferring immune resilience against allergic symptoms. The whey protein beta‐lactoglobulin BLG binding to micronutrients such as iron‐catechin complexes (holoBLG) was recognized less by IgE antibodies of children allergic to milk, leading to reduced mast cell degranulation. BLG also facilitated catechin‐dependent activation of the anti‐inflammatory arylhydrocarbon receptor. In mice, oral application of a holoBLG‐based lozenge which also contained zinc and vitamin A, improved the allergic symptoms of double‐sensitized mice independent of the allergens they were challenged with. Double‐sensitized mice supplemented with the holoBLG lozenge also had reduced levels of allergen‐specific antibodies and a lower frequency of activated antigen presenting cells. [ABSTRACT FROM AUTHOR]

Background: Growing up on a cattle farm and consuming raw cow's milk protects against asthma and allergies. We expect a cattle‐specific protein as active component in this farm effect. Methods: Dust was collected from cattle and poultry stables and from mattresses of households. Urine was obtained from cattle, and ambient aerosols were sampled. Samples were analysed for BLG by SDS PAGE/immunoblot and mass spectrometry, and for association with metals by SEC‐ICP‐MS. PBMC of healthy donors were incubated with BLG +/− zinc, and proliferation and cytokines determined. BALB/c mice were pre‐treated intranasally with stable dust extract containing BLG or depleted of BLG, and subsequent allergy response after sensitization was evaluated on antibody and symptom level. Results: A major protein in dust from cattle farms and ambient air was identified as BLG. Urine from female and male cattle is a major source of BLG. In dust samples, BLG was associated with zinc. In vitro, zinc‐BLG provoked significantly lower proliferation of CD4+ and CD8+ cells while inducing significantly higher levels of IFN‐γ and IL‐6 than the apo‐BLG devoid of zinc. In vivo, pre‐treatment of mice with dust extract containing BLG resulted in lower allergy symptom scores to BLG and unrelated Bet v 1 than pre‐treatment with extract depleted of BLG. These in vitro and in vivo effects were independent of endotoxin. Conclusion: The lipocalin BLG is found in large amounts in cattle urine, accumulates in bovine dust samples and is aerosolized around farms. Its association with zinc favorably shapes the human cellular immune response towards Th1‐cytokines in vitro. BLG together with zinc in stable dust protects mice from allergic sensitization. BLG with its associated ligands may in an innate manner contribute to the allergy‐protective farm effect. [ABSTRACT FROM AUTHOR]

Based on our I in silico i structural analyses, the IgE-specific effects may be due to epitope masking by the VD3 ligand of two previously described IgE-binding B-cell epitope regions in the molecular surface of Bet v 1 (Figure 1C). Keywords: Bet v 1; birch pollen allergy; immunomodulation; lipocalin-like; vitamin D EN Bet v 1 birch pollen allergy immunomodulation lipocalin-like vitamin D 3801 3804 4 12/01/21 20211201 NES 211201 Abbreviations ANS 1-anilino-8-naphthalene sulfonate BCA bicinchoninic acid BP birch pollen E aff affinity energy FCS foetal calf serum IL interleukin K D binding constant kDa kilodalton MFI mean fluorescence intensity OD optical density PBMCs peripheral blood mononuclear cells PDB protein data bank RA retinoic acid RFUs relative fluorescence units VD3 Vitamin D3 VDRE vitamin D response element ACKNOWLEDGEMENTS We thank Bart R. Blokhuis for excellent technical assistance. [Extracted from the article]

Virus infections affect plant developmental traits but this aspect of the interaction has not been extensively studied so far. Two strains of Turnip mosaic virus differentially affect Arabidopsis development, especially flower stalk elongation, which allowed phenotypical, cellular, and molecular characterization of the viral determinant, the P3 protein. Transiently expressed wild‐type green fluorescent protein‐tagged P3 proteins of both strains and selected mutants of them revealed important differences in their behaviour as endoplasmic reticulum (ER)‐associated peripheral proteins flowing along the reticulum, forming punctate accumulations. Three‐dimensional (3D) model structures of all expressed P3 proteins were computationally constructed through I‐TASSER protein structure predictions, which were used to compute protein surfaces and map electrostatic potentials to characterize the effect of amino acid changes on features related to protein interactions and to phenotypical and subcellular results. The amino acid at position 279 was the main determinant affecting stalk development. It also determined the speed of ER‐flow of the expressed proteins and their final location. A marked change in the protein surface electrostatic potential correlated with changes in subcellular location. One single amino acid in the P3 viral protein determines all the analysed differential characteristics between strains differentially affecting flower stalk development. A model proposing a role of the protein in the intracellular movement of the viral replication complex, in association with the viral 6K2 protein, is proposed. The type of association between both viral proteins could differ between the strains. [ABSTRACT FROM AUTHOR]

Retinoic acid-loading of the major birch pollen allergen Bet v 1 may improve specific allergen immunotherapy: In silico, in vitro and in vivo data in BALB/c mice Even if this was not due to altered endolysosomal stability of Bet v 1a due to RA binding (Figure S3), it seemed so far like RA-loading transforms the hyperallergen Bet v 1a to a hypoallergen with improved tolerogenic capacity of potential implications for allergen immunotherapy. Mice were first made allergic against the major birch pollen allergen Bet v 1a and subsequently treated intranasally with either the I apo i -Bet v 1a, or with the RA-loaded I holo i -Bet v 1a, or as a control with RA alone. [Extracted from the article]

Background: Despite all the efforts made up to now, the reasons that facilitate a protein becoming an allergen have not been elucidated yet. Alt a 1 protein is the major fungal allergen responsible for chronic asthma, but little is known about its immunological activity. Our main purpose was to investigate the ligand‐dependent interactions of Alt a 1 in the human airway epithelium. Methods: Alt a 1 with and without its ligand (holo‐ and apo‐ forms) was incubated with the pulmonary epithelial monolayer model, Calu‐3 cells. Allergen transport and cytokine production were measured. Pull‐down and immunofluorescence assays were employed to identify the receptor of Alt a 1 using the epithelial cell model and mouse tissues. Receptor‐allergen‐ligand interactions were analyzed by computational modeling. Results: The holo‐form could activate human monocytes, PBMCs, and polarized airway epithelial (Calu‐3) cell lines. The allergen was also transported through the monolayer, without any alteration of the epithelial integrity (TEER). Alt a 1 also induced the production of proinflammatory IL8 and specific epithelial cytokines (IL33 and IL25) by Calu‐3 cells. The interaction between epithelial cells and holo‐Alt a 1 was found to be mediated by the SLC22A17 receptor, and its recognition of Alt a 1 was explained in structural terms. Conclusions: Our findings identified the Alt a 1 ligand as a central player in the interaction of the allergen with airway mucosa, shedding light into its potential role in the immunological response, while unveiling its potential as a new target for therapy intervention. [ABSTRACT FROM AUTHOR]

A study is conducted on short strong hydrogen bond (SSHB) complexes that focuses on the changes of NMR proton chemical shifts accompanying the H-transfer from the donor to the acceptor in the systems formed by 4-methylimidazole and acetate and 4-methylimidazolium cation and acetate. The goals intended in the selection of these hydrogen bond (HB) systems as well as the theoretical methodology used are presented.

Abstract Biological production and oxidation of hydrogen is mediated by hydrogenases, key enzymes for these energy-relevant reactions. Synthesis of [NiFe] hydrogenases involves a complex series of biochemical reactions to assemble protein subunits and metallic cofactors required for enzyme function. A final step in this biosynthetic pathway is the processing of a C-terminal tail (CTT) from its large subunit, thus allowing proper insertion of nickel in the unique NiFe(CN) 2 CO cofactor present in these enzymes. In silico modelling and Molecular Dynamics (MD) analyses of processed vs. unprocessed forms of Rhizobium leguminosarum bv. viciae (Rlv) hydrogenase large subunit HupL showed that its CTT (residues 582-596) is an intrinsically disordered region (IDR) that likely provides the required flexibility to the protein for the final steps of proteolytic maturation. Prediction of pKa values of ionizable side chains in both forms of the enzyme's large subunit also revealed that the presence of the CTT strongly modify the protonation state of some key residues around the active site. Furthermore, MD simulations and mutant analyses revealed that two glutamate residues (E27 in the N-terminal region and E589 inside the CTT) likely contribute to the process of nickel incorporation into the enzyme. Computational analysis also revealed structural details on the interaction of Rlv hydrogenase LSU with the endoprotease HupD responsible for the removal of CTT. Highlights • C-terminal tails of NiFe hydrogenases are Intrinsically Disordered Region (IDRs). • IDRs might provide flexibility for interaction with protease and other accessory proteins. • Modelling of [NiFe] hydrogenase unprocessed form reveals changes in the environment of key residues following processing. • Molecular dynamics and mutant analyses indicate that residues E27 and E589 are relevant for nickel incorporation. [ABSTRACT FROM AUTHOR]

Saposins are small proteins implicated in trafficking and loading of lipids onto Cluster of Differentiation 1 (CD1) receptor proteins that in turn present lipid antigens to T cells and a variety of T-cell receptors, thus playing a crucial role in innate and adaptive immune responses in humans. Despite their low sequence identity, the four types of human saposins share a similar folding pattern consisting of four helices linked by three conserved disulfide bridges. However, their lipid-binding abilities as well as their activities in extracting, transporting and loading onto CD1 molecules a variety of sphingo- and phospholipids in biological membranes display two striking characteristics: a strong pH-dependence and a structural change between a compact, closed conformation and an open conformation. In this work, we present a comparative computational study of structural, electrostatic, and dynamic features of human saposins based upon their available experimental structures. By means of structural alignments, surface analyses, calculation of pH-dependent protonation states, Poisson-Boltzmann electrostatic potentials, and molecular dynamics simulations at three pH values representative of biological media where saposins fulfill their function, our results shed light into their intrinsic features. The similarities and differences in this class of proteins depend on tiny variations of local structural details that allow saposins to be key players in triggering responses in the human immune system. [ABSTRACT FROM AUTHOR]

Fungal cell walls, which are essential for environmental adaptation and host colonization by the fungus, have been evolutionarily selected by plants and animals as a source of microbe-associated molecular patterns ( MAMPs) that, upon recognition by host pattern recognition receptors ( PRRs), trigger immune responses conferring disease resistance. Chito-oligosaccharides [β-1,4- N-acetylglucosamine oligomers, (Glc NAc) n] are the only glycosidic structures from fungal walls that have been well-demonstrated to function as MAMPs in plants. Perception of (Glc NAc)4-8 by Arabidopsis involves CERK1, LYK4 and LYK5, three of the eight members of the LysM PRR family. We found that a glucan-enriched wall fraction from the pathogenic fungus Plectosphaerella cucumerina which was devoid of Glc NAc activated immune responses in Arabidopsis wild-type plants but not in the cerk1 mutant. Using this differential response, we identified the non-branched 1,3-β- d-(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3-β- d-(Glc)6 was impaired in cerk1 but not in mutants defective in either each of the LysM PRR family members or in the PRR-co-receptor BAK1. Transcriptomic analyses of Arabidopsis plants treated with 1,3-β- d-(Glc)6 further demonstrated that this fungal MAMP triggers the expression of immunity-associated genes. In silico docking analyses with molecular mechanics and solvation energy calculations corroborated that CERK1 can bind 1,3-β- d-(Glc)6 at effective concentrations similar to those of (Glc NAc)4. These data support that plants, like animals, have selected as MAMPs the linear 1,3-β- d-glucans present in the walls of fungi and oomycetes. Our data also suggest that CERK1 functions as an immune co-receptor for linear 1,3-β- d-glucans in a similar way to its proposed function in the recognition of fungal chito-oligosaccharides and bacterial peptidoglycan MAMPs. [ABSTRACT FROM AUTHOR]

The viability of viral-derived nanoparticles (virions and VLPs) aimed to nanobiotechnological functionalizations of the coat protein (CP) of turnip mosaic virus has been studied by means of advanced computational methodologies that include molecular dynamics. The study has allowed to model the structure of the complete CP and its functionalization with three different peptides and obtain essential structural features such as order/disorder, interactions, and electrostatic potentials of their constituent domains. The results provide for the first time a dynamic view of a complete potyvirus CP, since experimental available structures so far obtained lack N- and C-terminal segments. The relevance of disorder in the most distal N-terminal subdomain, and the interaction of the less distal N-terminal subdomain with the highly ordered CP core, stand out as crucial characteristic for a viable CP. Preserving them proved of outmost importance to obtain viable potyviral CPs presenting peptides at their N-terminus. [ABSTRACT FROM AUTHOR]

Atmospheric iodine chemistry plays a key role in tropospheric ozone catalytic destruction, new particle formation, and as one of the possible sinks of gaseous polar elemental mercury. Moreover, it has been recently proposed that reaction of ozone with iodide on the sea surface could be the major contributor to the chemical loss of atmospheric ozone. However, the mechanism of the reaction between aqueous iodide and ozone is not well known. The aim of this paper is to improve the understanding of such a mechanism. In this paper, an ab initio study of the reaction of aqueous iodide and ozone is presented, evaluating thermodynamic data of the different reactions proposed in previous experimental studies. In addition, the structures, energetics and possible evolution of the key IOOO− intermediate are discussed for the first time. [ABSTRACT FROM AUTHOR]

In the search for factors that make a protein allergenic (an issue that remains so far elusive) some common features of allergens such as small size, high stability and lipid binding are recognized in spite of their structural diversity. Other relevant but still poorly understood feature is their capability to form homodimers. We investigated by means of Molecular Dynamics (MD) calculations the stability in solution of several dimers of three major allergens from Alternaria mold, birch pollen, and peach fruit known to play essential roles in allergic disease. By running 20 ns MD simulations we found essential properties on solution that provide information of interest on their dimerization, stability of their epitopes and dynamical features of ligand binding cavities. Our results show that three essential allergen proteins display a distinct behavior on their trends to form homodimers in solution. [ABSTRACT FROM AUTHOR]

[NiFe] hydrogenases are key enzymes for the energy and redox metabolisms of different microorganisms. Synthesis of these metalloenzymes involves a complex series of biochemical reactions catalyzed by a plethora of accessory proteins, many of them required to synthesize and insert the unique NiFe(CN)2CO cofactor. HypC is an accessory protein conserved in all [NiFe] hydrogenase systems and involved in the synthesis and transfer of the Fe(CN)2CO cofactor precursor. Hydrogenase accessory proteins from bacteria-synthesizing hydrogenase in the presence of oxygen include HupK, a scaffolding protein with a moderate sequence similarity to the hydrogenase large subunit and proposed to participate as an intermediate chaperone in the synthesis of the NiFe cofactor. The endosymbiotic bacterium Rhizobium leguminosarum contains a single hydrogenase system that can be expressed under two different physiological conditions: free-living microaerobic cells (~12 µm O2) and bacteroids from legume nodules (~0-100 µm O2). We have used bioinformatic tools to model HupK structure and interaction of this protein with HypC. Site-directed mutagenesis at positions predicted as critical by the structural analysis have allowed the identification of HupK and HypC residues relevant for the maturation of hydrogenase. Mutant proteins altered in some of these residues show a different phenotype depending on the physiological condition tested. Modeling of HypC also predicts the existence of a stable HypC dimer whose presence was also demonstrated by immunoblot analysis. This study widens our understanding on the mechanisms for metalloenzyme biosynthesis in the presence of oxygen. [ABSTRACT FROM AUTHOR]

The mechanisms of allergic sensitization to milk are still elusive. The major allergen Bos d 5 belongs to the lipocalin-family and thus is able to transport numerous ligands. In this study we investigated its ability to bind to iron-siderophore complexes and tested the immune-modulatory properties of Bos d 5 in either forms. Structural and in silico docking analysis of Bos d 5 revealed that Bos d 5 is able to bind to iron via catechol-based flavonoids (quercetin, myricetin, luteolin) that act as siderophores as confirmed by spectral-analysis and iron staining. Calculated dissociation constants of docking analyses were below 1 µM by virtual addition of iron. When incubated with human peripheral blood mononuclear cells (PBMCs), only the apo-form of Bos d 5 led to an increase of CD4+positive cells and significantly elevated IL13 and IFNγ-levels. In contrast, holo-Bos d 5 decreased numbers of CD4 expressing cells and induced apoptosis. Taken together, our data give evidence that Bos d 5 is capable of binding iron via siderophores. Moreover, our data support for the first time the notion that the form of application (apo- or holo-form) is decisive for the subsequent immune response. The apo-form promotes Th2 cells and inflammation, whereas the holo-form appears to be immunosuppressive. [ABSTRACT FROM AUTHOR]

Highlights: [•] Alt a 1 could be detected in the pulp of fruits, without fungus development. [•] Alt 1 can bind to members of PR5 family. [•] Alt a 1 partially inhibits enzymatic activity of PR5. [•] Patients with chronic asthma could suffer from symptoms eating contaminated fruit. [Copyright &y& Elsevier]

The physical, biochemical, and immunological characteristics of plant allergens have been widely studied, but no definite conclusion has been reached about what actually makes a protein an allergen. In this sense, N-glycosylation is an exclusive characteristic of plant allergens not present in mammals and it could be implied in allergenic sensitization. With this aim, we evaluated and compared the allergenic activity of the protein fraction and the N-glycan fraction of the thaumatin-like protein and the main kiwi allergen, Act d 2. The natural allergen, Act d 2, was deglycosylated by trifluoromethanesulfonic acid treatment; the N-glycan fraction was obtained by extended treatment with proteinase K. N-glycan- and protein- fractions were recognized by specific IgE of kiwi-allergic patients. By contrast, the sugar moiety showed a reduced capacity to activate basophils and T cells, but not dendritic cells derived from patients' monocytes. Related to this, the production of cytokines such as IL6 and IL10 was increased by the incubation of dendritic cells with sugar moiety. Thus, the sugar moiety plays a significant role in sensitization, inducing the activation of antigen-presenting cells, but it is the protein fraction that is responsible for the allergic reactions. [ABSTRACT FROM AUTHOR]