Delineation of molecular interactions of plant growth promoting bacteria induced β-1,3-glucanases and guanosine triphosphate ligand for antifungal response in rice: a molecular dynamics approach

Background The plant growth is influenced by multiple interactions with biotic (microbial) and abiotic components in their surroundings. These microbial interactions have both positive and negative effects on plant. Plant growth promoting bacterial (PGPR) interaction could result in positive growth under normal as well as in stress conditions. Methods Here, we have screened two PGPR’s and determined their potential in induction of specific gene in host plant to overcome the adverse effect of biotic stress caused by Magnaporthe grisea, a fungal pathogen that cause blast in rice. We demonstrated the glucanase protein mode of action by performing comparative modeling and molecular docking of guanosine triphosphate (GTP) ligand with the protein. Besides, molecular dynamic simulations have been performed to understand the behavior of the glucanase-GTP complex. Results The results clearly showed that selected PGPR was better able to induce modification in host plant at morphological, biochemical, physiological and molecular level by activating the expression of β-1,3-glucanases gene in infected host plant. The docking results indicated that Tyr75, Arg256, Gly258, and Ser223 of glucanase formed four crucial hydrogen bonds with the GTP, while, only Val220 found to form hydrophobic contact with ligand. Conclusions The PGPR able to induce β-1,3-glucanases gene in host plant upon pathogenic interaction and β-1,3-glucanases form complex with GTP by hydrophilic interaction for induction of defense cascade for acquiring resistance against Magnaporthe grisea. Graphical abstract

Probing the Influence of Single-Site Mutations in the Central Cross-β Region of Amyloid β (1–40) Peptides

Amyloid β (Aβ) is a peptide known to form amyloid fibrils in the brain of patients suffering from Alzheimer’s disease. A complete mechanistic understanding how Aβ peptides form neurotoxic assemblies and how they kill neurons has not yet been achieved. Previous analysis of various Aβ40 mutants could reveal the significant importance of the hydrophobic contact between the residues Phe19 and Leu34 for cell toxicity. For some mutations at Phe19, toxicity was completely abolished. In the current study, we assessed if perturbations introduced by mutations in the direct proximity of the Phe19/Leu34 contact would have similar relevance for the fibrillation kinetics, structure, dynamics and toxicity of the Aβ assemblies. To this end, we rationally modified positions Phe20 or Gly33. A small library of Aβ40 peptides with Phe20 mutated to Lys, Tyr or the non-proteinogenic cyclohexylalanine (Cha) or Gly33 mutated to Ala was synthesized. We used electron microscopy, circular dichroism, X-ray diffraction, solid-state NMR spectroscopy, ThT fluorescence and MTT cell toxicity assays to comprehensively investigate the physicochemical properties of the Aβ fibrils formed by the modified peptides as well as toxicity to a neuronal cell line. Single mutations of either Phe20 or Gly33 led to relatively drastic alterations in the Aβ fibrillation kinetics but left the global, as well as the local structure, of the fibrils largely unchanged. Furthermore, the introduced perturbations caused a severe decrease or loss of cell toxicity compared to wildtype Aβ40. We suggest that perturbations at position Phe20 and Gly33 affect the fibrillation pathway of Aβ40 and, thereby, influence the especially toxic oligomeric species manifesting so that the region around the Phe19/Leu34 hydrophobic contact provides a promising site for the design of small molecules interfering with the Aβ fibrillation pathway.

Peptide backbone modifications of amyloid β (1–40) impact fibrillation behavior and neuronal toxicity

Fibril formation of amyloid β (Aβ) peptides is one of the key molecular events connected to Alzheimer’s disease. The pathway of formation and mechanism of action of Aβ aggregates in biological systems is still object of very active research. To this end, systematic modifications of the Phe19–Leu34 hydrophobic contact, which has been reported in almost all structural studies of Aβ40 fibrils, helps understanding Aβ folding pathways and the underlying free energy landscape of the amyloid formation process. In our approach, a series of Aβ40 peptide variants with two types of backbone modifications, namely incorporation of (i) a methylene or an ethylene spacer group and (ii) a N-methylation at the amide functional group, of the amino acids at positions 19 or 34 was applied. These mutations are expected to challenge the inter-β-strand side chain contacts as well as intermolecular backbone β-sheet hydrogen bridges. Using a multitude of biophysical methods, it is shown that these backbone modifications lead, in most of the cases, to alterations in the fibril formation kinetics, a higher local structural heterogeneity, and a somewhat modified fibril morphology without generally impairing the fibril formation capacity of the peptides. The toxicological profile found for the variants depend on the type and extent of the modification.

Transparent Self-Cleaning Coatings Based on Colorless Polyimide/Silica Sol Nanocomposite

We herein report transparent self-cleaning coatings based on polyimide-fluorinated silica sol (PIFSS) nanocomposite. Polyamic acid-silica sol (PASS) suspensions were synthesized by adding four different amounts of a silica sol suspension to each end-capped polyamic acid solution. The PASS suspensions were spin-coated on glass slides, thermally imidized and treated with triethoxy-1H,1H,2H,2H-perfluorodecylsilane (TEFDS) to prepare PIFSS coatings. The PIFSS coatings showed high resistance to separation from glass substrates and thermal stability. Furthermore, the PIFSS coatings on the glass substrate could be cleanly removed using polar aprotic solvents and repeated coating was possible. As the amount of silica sol particles in the PIFSS coating was increased, the hydrophobic contact angle increased. Among them, PIFSS-10 and PIFSS-15 coatings showed nearly superhydrophobic contact angles (144° and 148°, respectively) and good self-cleaning property. It was confirmed by SEM and AFM studies that their hydrophobic and self-cleaning properties are due to uniform particle distribution and relatively high surface roughness. PIFSS-10 coating showed a high transmittance value (88%) at 550 nm and good self-cleaning property, therefore suitable as a transparent self-cleaning coating. The advantages of the coating are that the fabrication process is simple, and the substrate is reusable. The PIFSS coating is expected to be applied in solar cell panels, windows, lenses and safety goggles.

Diaminomaleonitrile derivatives as new potential antichagasic compounds: a study of structure–activity relationships

Background: Schiff bases are synthetically accessible compounds that have been used in medicinal chemistry. Methods & results: In this work, 27 Schiff bases derived from diaminomaleonitrile were synthesized in high yields (80–98%). Molecular docking studies suggested that the Schiff bases interact with the catalytic site of cruzain. The most active cruzain inhibitor, analog 13 (IC50 = 263 nM), was predicted to form an additional hydrophobic contact with Met68 in the binding site of the enzyme. A strong correlation between the IC50 values and ChemScore binding energies was observed (R = 0.99). Kernel-based 2D quantitative structure–activity relationship models for the whole dataset yielded sound correlation coefficients (R2 = 0.844; Q2 = 0.719). Conclusion: These novel and potent cruzain inhibitors are worthwhile starting points in further Chagas disease drug discovery programs.

Exchange Counterion in Polycationic Hydrogels: Tunability of Hydrophobicity, Water State, and Floating Capability for a Floating pH Device

Smart gel materials are capable of controlling and switching swelling, water state, and wettability properties triggered by external stimuli. In this study, we fabricated a series of polyelectrolyte hydrogels bearing a 3-trimethylammoniumpropyl pendant to a methacrylamide-based backbone and examined the switchability with hydrophobic-like counteranions. The exchange between the initial chloride and camphor sulfate (CaS), dodecyl sulfate (DS), and perfluorooctanoate (PFO) counterions was investigated. The kinetics of the exchange showed that the fast exchange (within 4 h) of PFO allowed for a favorable coordination for ion pairing, resulting in a decrease in hydration. The reversibility of the exchange to the Cl- ion was only enabled for the CaS ion due to its bulkiness, while the PFO and DS hydrogels were unable to exchange, even by using tetrabutylammonium chloride, which is a structurally similar reagent, due to aggregation or the coagulates in the collapsed state of the linear tails of the counterions. The hydrogels exhibited a modulable water state and water swelling. Moreover, the hydrogels containing DS and PFO, as counterions, showed surface hydrophobic (contact angle 90°) and high hydrophobic (110°) behavior, respectively. The Raman spectrometry fluorescence with a pyrene probe indicated an increase in strong hydrogen-bonded water molecules, water confinement, and hydrophobic domains in the PFO hydrogel. Moreover, the PFO-modified hydrogel demonstrated a free-floating ability on the water surface, with a strong water repellency, showing that it has the potential to be applied in a floating pH detection device to distinguish between volatile and nonvolatile bases in a controlled manner.

Use of Polycaprolactone Electrospun Nanofiber Mesh in a Face Mask

Electrospun nanofiber mesh has previously been used as an air filtration device. However, the qualification of polycaprolactone (PCL) nanofiber mesh cloth in face masks to protect individuals against airborne particles carrying microorganisms has yet to be investigated. The long-term goal of this study is to develop methods to use PCL nanofiber mesh to provide better protection against microorganisms. To achieve this goal, we observed the morphology, water droplet absorption, thermal (differential scanning calorimetry), mechanical, and airborne particle filtering capabilities, and also the microbial activities of a PCL cloth, to evaluate whether it is suitable to act as a filter in a face mask. We have produced a polycaprolactone (PCL) nanofiber cloth after electrospinning it onto a drum for 3 and 10 min, referred to hereafter as PCL-3 and PCL-10, respectively. Our study found that the middle protection layer (control) of the Henry Schein Earloop Procedure Mask contains pores (average diameter = 5.72 ± 0.62 µm) which are 48 times larger than the diameter of a microorganism an average diameter of ~120 nanometers. However, PCL-10 nanofiber membranes show pores with an average diameter of 1.42 ± 0.34 µm. Our contact angle measurement tests found that all the samples were very hydrophobic (contact angle values varied between 120 and 150 degrees). However, both PCL cloths’ contact angle values were lower compared to the control. The produced PCL cloths showed a lower water droplet absorption compared to the control. Thermal studies found that PCL is stable in extreme conditions and no plasticizing effect occurs due to the presence of a solvent. Mechanical tests showed that PCL-10 cloth had higher strength and modulus compared to the control and PCL-3 under tension loading conditions. A vacuum experiment found that the PCL-10 fiber cloth could withstand a negative pressure of 18 Psi without any signs of breakage, and the mask was able to capture airborne particles and microorganisms. The feasibility of immobilizing anti-bacterial nanoparticles with PCL during electrospinning creates the future potential of producing an anti-bacterial face mask using PCL.

Crystal structure of fungal tannase from Aspergillus niger

Tannases are serine esterases that were first discovered in fungi more than one and half centuries ago. They catalyze the hydrolysis of the gallolyl ester bonds in gallotannins to release gallic acid, which is an important intermediate in the chemical and pharmaceutical industries. Since their discovery, fungal tannases have found wide industrial applications, although there is scarce knowledge about these enzymes at the molecular level, including their catalytic and substrate-binding sites. While this lack of knowledge hinders engineering efforts to modify the enzymes, many tannases have been isolated from various fungal strains in a search for the desired enzymatic properties. Here, the first crystal structure of a fungal tannase, that from Aspergillus niger, is reported. The enzyme possesses a typical α/β-hydrolase-fold domain with a large inserted cap domain, which together form a bowl-shaped hemispherical shape with a surface concavity surrounded by N-linked glycans. Gallic acid is bound at the junction of the two domains within the concavity by forming two hydrogen-bonding networks with neighbouring residues. One is formed around the carboxyl group of the gallic acid and involves residues from the hydrolase-fold domain, including those from the catalytic triad, which consists of Ser206, His485 and Asp439. The other is formed around the three hydroxyl groups of the compound, with the involvement of residues mainly from the cap domain, including Gln238, Gln239, His242 and Ser441. Gallic acid is bound in a sandwich-like mode by forming a hydrophobic contact with Ile442. All of these residues are found to be highly conserved among fungal and yeast tannases.

Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins

Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

Molecular dynamics and free energy simulations have been carried out to elucidate the structural origin of differential protein–protein interactions between the common receptor protein angiotensin converting enzyme 2 (ACE2) and the receptor binding domains of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [A. E. Gorbalenyaet al.,Nat. Microbiol.5, 536–544 (2020)] that causes coronavirus disease 2019 (COVID-19) [P. Zhouet al.,Nature579, 270–273 (2020)] and the SARS coronavirus in the 2002–2003 (SARS-CoV) [T. Kuikenet al., Lancet 362, 263–270 (2003)] outbreak. Analysis of the dynamic trajectories reveals that the binding interface consists of a primarily hydrophobic region and a delicate hydrogen-bonding network in the 2019 novel coronavirus. A key mutation from a hydrophobic residue in the SARS-CoV sequence to Lys417 in SARS-CoV-2 creates a salt bridge across the central hydrophobic contact region, which along with polar residue mutations results in greater electrostatic complementarity than that of the SARS-CoV complex. Furthermore, both electrostatic effects and enhanced hydrophobic packing due to removal of four out of five proline residues in a short 12-residue loop lead to conformation shift toward a more tilted binding groove in the complex in comparison with the SARS-CoV complex. On the other hand, hydrophobic contacts in the complex of the SARS-CoV–neutralizing antibody 80R are disrupted in the SARS-CoV-2 homology complex model, which is attributed to failure of recognition of SARS-CoV-2 by 80R.