Machine learning milestones in computational chemistry are overshadowed by their unaccountability and the overwhelming zoo of tools for each specific task. A promising path to tackle these problems ...is using machine learning to reproduce physical magnitudes as a basis to derive many other properties. By using a model of the electron density consisting of an analytical expansion on a linear set of isotropic and anisotropic functions, we implemented in this work a message-passing neural network able to reproduce electron density in molecules with just a 2.5% absolute error in complex cases. We also adapted our methodology to describe electron density in large biomolecules (proteins) and to obtain atomic charges, interaction energies, and DFT energies. We show that electron density learning is a new promising avenue with a variety of forthcoming applications.
We present an analytical model representation of the electron density ρ(r) in molecules in the form of expansions of a few functions (exponentials and a Gaussian) per atom. Based on a former ...analytical model of ρ(r) in atoms, we devised its molecular implementation by introducing the anisotropy inherent in the electron distribution of atoms in molecules by means of proper anisotropic functions. The resulting model named A2MD (anisotropic analytical model of density) takes an analytical form highly suitable for obtaining the electron density in large biomolecules as its computational cost scales linearly with the number of atoms. To obtain the parameters of the model, we first devised a fitting procedure to reference electron densities obtained in ab initio correlated quantum calculations. Second, in order to skip costly ab initio calculations, we also developed a machine learning (ML)-based predictor that used neural networks trained on broad molecular datasets to determine the parameters of the model. The resulting ML methodology that we named A2MDnet (A2MD network-trained) was able to provide reliable electron densities as a basis to predict molecular features without requiring quantum calculations. The results presented together with the low computational scaling associated to the A2MD representation of ρ(r) suggest potential applications to obtain reliable electron densities and ρ(r)-based molecular properties in biomacromolecules.
An all-atom Molecular Dynamics (MD) study was applied to three viral nanoparticles (VLPs) of Turnip mosaic virus (TuMV), a potyvirus: the particles genetically functionalized with two peptides, VIP ...(human vasoactive intestinal peptide) and VEGFR (peptide derived from the human receptor 3 of the vascular endothelial growth factor), and the non-functionalized VLP. Previous experimental results showed that VIP-VLP was the only construct of the three that was not viable. VLPs subjected to our MD study were modeled by four complete turns of the particle involving 35 subunits of the coat protein (CP). The MD simulations showed differences in structures and interaction energies associated to the crucial contribution of the disordered N-terminal arms of CP to the global stability of the particle. These differences suggested an overall stability greater in VEGFR-VLP and smaller in VIP-VLP as compared to the unfunctionalized VLP. Our novel MD study of potyviral VLPs revealed essential clues about structure and interactions of these assembled protein particles and suggests that the computational prediction of the viability of VLPs can be a valuable contribution in the field of viral nanobiotechnology.
Summary 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 beta-1,4-N-acetylglucosamine oligomers, (GlcNAc)n are the only glycosidic structures from fungal walls that have been well-demonstrated to function as MAMPs in plants. Perception of (GlcNAc)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 GlcNAc 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-beta-d-(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3-beta-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-beta-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-beta-d-(Glc)6 at effective concentrations similar to those of (GlcNAc)4. These data support that plants, like animals, have selected as MAMPs the linear 1,3-beta-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-beta-d-glucans in a similar way to its proposed function in the recognition of fungal chito-oligosaccharides and bacterial peptidoglycan MAMPs. Significance statement Despite pioneering work and recently regained momentum, the plant-specific knowledge about the mechanisms of beta-glucan perception and its role in activation of plant defence clearly lags behind the animal field. This article demonstrates that Arabidopsis can perceive non-branched 1,3-beta-glucans of various degrees of polymerization and that this recognition is at least partially mediated by CERK1, but it does not involve BAK1, the co-receptor of other PRRs.
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).
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.
Beta-lactoglobulin (BLG) is a bovine lipocalin in milk with an innate defense function. The circumstances under which BLG is associated with tolerance of or allergy to milk are not understood.
Our ...aims were to assess the capacity of ligand-free apoBLG versus loaded BLG (holoBLG) to protect mice against allergy by using an iron-quercetin complex as an exemplary ligand and to study the molecular mechanisms of this protection.
Binding of iron-quercetin to BLG was modeled and confirmed by spectroscopy and docking calculations. Serum IgE binding to apoBLG and holoBLG in children allergic to milk and children tolerant of milk was assessed. Mice were intranasally treated with apoBLG versus holoBLG and analyzed immunologically after systemic challenge. Aryl hydrocarbon receptor (AhR) activation was evaluated with reporter cells and Cyp1A1 expression. Treated human PBMCs and human mast cells were assessed by fluorescence-activated cell sorting and degranulation, respectively.
Modeling predicted masking of major IgE and T-cell epitopes of BLG by ligand binding. In line with this modeling, IgE binding in children allergic to milk was reduced toward holoBLG, which also impaired degranulation of mast cells. In mice, only treatments with holoBLG prevented allergic sensitization and anaphylaxis, while sustaining regulatory T cells. BLG facilitated quercetin-dependent AhR activation and, downstream of AhR, lung Cyp1A1 expression. HoloBLG shuttled iron into monocytic cells and impaired their antigen presentation.
The cargo of holoBLG is decisive in preventing allergy in vivo. BLG without cargo acted as an allergen in vivo and further primed human mast cells for degranulation in an antigen-independent fashion. Our data provide a mechanistic explanation why the same proteins can act either as tolerogens or as allergens.
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Summary
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, (GlcNAc)n are the only glycosidic structures from fungal walls that have been well‐demonstrated to function as MAMPs in plants. Perception of (GlcNAc)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 GlcNAc 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 (GlcNAc)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.
Significance statement
Despite pioneering work and recently regained momentum, the plant‐specific knowledge about the mechanisms of β‐glucan perception and its role in activation of plant defence clearly lags behind the animal field. This article demonstrates that Arabidopsis can perceive non‐branched 1,3‐β‐glucans of various degrees of polymerization and that this recognition is at least partially mediated by CERK1, but it does not involve BAK1, the co‐receptor of other PRRs.
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.
The remarkable ability of tardigrades to withstand a wide range of physical and chemical extremes has attracted a considerable interest in these small invertebrates, with a particular focus on the ...protective roles of proteins expressed during such conditions. The discovery that a tardigrade-unique protein named Dsup (damage suppressor) protects DNA from damage produced by radiation and radicals, has raised expectations concerning its potential applications in biotechnology and medicine. We present in this paper what might be dubbed a "computational experiment" on the Dsup-DNA system. By means of molecular modelling, calculations of electrostatic potentials and electric fields, and all-atom molecular dynamics simulations, we obtained a dynamic picture of the Dsup-DNA interaction. Our results suggest that the protein is intrinsically disordered, which enables Dsup to adjust its structure to fit DNA shape. Strong electrostatic attractions and high protein flexibility drive the formation of a molecular aggregate in which Dsup shields DNA. While the precise mechanism of DNA protection conferred by Dsup remains to be elucidated, our study provides some molecular clues of their association that could be of interest for further investigation in this line.
![Non-branched [beta]-1,3-glu...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0960-7412/small "Non-branched [beta]-1,3-glucan oligosaccharides trigger immune responses in Arabidopsis")
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