Journal: Nature computational science

Article Title: Binding affinity estimation from restrained umbrella sampling simulations.

doi: 10.1038/s43588-022-00389-9

Figure Lengend Snippet: Fig. 1 | Average grid PMF based on our alternative distance-based BEUS simulations. Average grid PMFs in terms of |x|, where x is the three-dimensional position vector of the ligand with respect to the center of the binding pocket. The x axis represents |x| and the y axis represents ΔF(|x|), which is an average over all ΔF(x) with the same |x|, that is, the ligand distance from the center of the binding pocket. The error bars represent the standard deviation obtained from all values of ΔF(x) at various grid points x with the same |x|. Representative images of heparin hexasaccharide bound to hFGF1 (|x| = 0 Å) and unbound (|x| = 30 Å) are shown above the grid PMF plot. We used n = 31 MD replicas to generate the data in all cases.

Article Snippet: We also define Ur(x) similar to UΩ(x) in relation (15) except for using r instead of Ω. Ur Ω (x) is also defined similar to UΩ(x) except for the additional restraint on r: Ur Ω (x) = −RT ln⟨e− 1 2 kΩ 2 RT ⟩rx = −RT ln ∫∞0 ∫ ππ 0 e − F(x,Ω,r)+ 12 k ′ r2+ 12 kΩ 2 RT dΩdr ∫∞0 ∫ ππ 0 e − (F(x,Ω,r)+ 12 k ′ r2) RT dΩdr (26) Finally, we have: ΔG (x) = ΔGΩ,r (x) − ΔUr (x) − ΔUrΩ (x) (27) In brief, if we choose to restrain both the orientation and RMSD, our absolute binding-free-energy estimate includes the following terms: ΔG∘ = −ΔGΩ,r (xB) + ΔUr (xB) + ΔUrΩ (xB) + ΔGV (28) Here we are using an approximation similar to that in relation (19): VP ≈ ∫ pocket e− ΔGΩ,r (x) RT dV (29) Using relations (20) and (28), we can generalize the stratification strategy to include three restraints on arbitrary collective variables α, β and γ: ΔG∘ = −ΔGα,β,γ (xB) + ΔUγ (xB) + ΔUγβ (xB) + ΔU β,γ α (xB) + ΔGV (30) where: ΔGV ≈ −RT ln∫ pocket e− ΔGα,β,γ(x) RT dV Å3 − ΔGB (31) Isothermal titration calorimetry of hFGF1 with heparin hexasaccharide ITC data were obtained using MicroCal iTC 200 (Malvern) with microcal origin software.

Techniques: Plasmid Preparation, Binding Assay, Standard Deviation

Journal: Journal of Experimental Botany

Article Title: Linear β-1,2-glucans trigger immune hallmarks and enhance disease resistance in plants

doi: 10.1093/jxb/erae368

Figure Lengend Snippet: β-1,2-Glucan (B2G3 and B2G6) oligosaccharides trigger reactive oxygen species (ROS) production in Arabidopsis seedlings. (A) ROS production in Arabidopsis (Col-0) seedlings measured as relative luminescence units (RLUs) over time after treatment with β-1,2-glucan oligosaccharides (trimer, B2G3 and hexamer, B2G6 at a concentration of 100 µM), β-1,2-glucan polysaccharide (0.1–0.5 mg ml –1 ), hexaacetyl-chitohexaose (Chi6, 100 µM), β- d -cellobiosyl-(1,3)-β- d -glucose (MLG43, 100 µM), α-1,3-glucan trisaccharide (A3G3, 100 µM), and water (mock), which was the negative control. (B) Total production of ROS measured as total RLUs over 120 min after the treatment with oligosaccharides. Statistically non-significant (n.s.) and significant differences according to one-tailed Student’s t -test (* P ≤0.05, *** P ≤0.001) compared with the mock treatment are shown. (C) ROS production using different concentrations of B2G3 (from 0.01 µM to 1 mM). Data represent the mean ±SE ( n =8) from one experiment out of three performed that produced similar results. (D) Dose–response curve in Arabidopsis seedlings. Total response measured as total RLUs over 120 min after elicitation with different concentrations of B2G3 (from 0.01 µM to 1 mM). The arrow indicates the estimated effective dose (EED; 50% of total signal); 64.83 µM in this case.

Article Snippet: The oligosaccharides α-1,3-glucan trisaccharide A3G3 [α-1,3-(glucose) 3 ], hexaacetyl-chitohexaose Chi6 [β-1,4-( N -acetylglucosamine) 6 ], MLG43 [β-1,3, β-1,4-(glucose) 3 ], β-1,2-glucan trisaccharide B2G3 [β-1,2-(glucose) 3 ], β-1,2-glucan hexasaccharide B2G6 [β-1,2-(glucose) 6 ], and β-1,2-glucan polysaccharide [β-1,2-(glucose) n ] were acquired from Megazyme (Wicklow, Ireland).

Techniques: Concentration Assay, Negative Control, One-tailed Test, Produced

Journal: Journal of Experimental Botany

Article Title: Linear β-1,2-glucans trigger immune hallmarks and enhance disease resistance in plants

doi: 10.1093/jxb/erae368

Figure Lengend Snippet: Pattern-triggered immunity hallmark activation by B2G3 and B2G6 in Arabidopsis. Mitogen-activated protein kinase (MAPK) phosphorylation in seedlings determined by western blot using phospho-p44/42 MAPK antibody for phosphorylated MAPK moieties at different time points (5, 15, 30, and 60 min) after treatment with (A) B2G3 (100 µM) and (B) B2G6 (100 µM). NT indicates the non-treated sample, which was the negative control, and MLG43 (100 µM) was used as the positive control. Arrowheads indicate the position of phosphorylated MPK6 (top), MPK3 (middle), and MPK4/11 (bottom). Ponceau S red-stained membranes show equal protein loading. Quantitative RT–PCR analysis of the relative expression levels of immune-related genes (C) CYP81F2 and (D) WRKY53 normalized to the expression of the UBC21 gene at 30 min in treated and non-treated Arabidopsis seedlings ( n =6). NT and distilled water (mock) were used as negative controls, and Chi6 and MLG43 were used as positive controls. All treatments were performed at 100 µM. Data are presented as box plots, with the centre line showing the median, the box limits showing the 25th and 75th percentiles, and the whiskers showing the full range of data. All the data displayed belong to one of the three independent experiments carried out, which gave similar results. Statistically significant differences according to one-tailed Student’s t -test (*** P ≤0.001) compared with the mock treatment are shown.

Article Snippet: The oligosaccharides α-1,3-glucan trisaccharide A3G3 [α-1,3-(glucose) 3 ], hexaacetyl-chitohexaose Chi6 [β-1,4-( N -acetylglucosamine) 6 ], MLG43 [β-1,3, β-1,4-(glucose) 3 ], β-1,2-glucan trisaccharide B2G3 [β-1,2-(glucose) 3 ], β-1,2-glucan hexasaccharide B2G6 [β-1,2-(glucose) 6 ], and β-1,2-glucan polysaccharide [β-1,2-(glucose) n ] were acquired from Megazyme (Wicklow, Ireland).

Techniques: Activation Assay, Western Blot, Negative Control, Positive Control, Staining, Quantitative RT-PCR, Expressing, One-tailed Test

Journal: Journal of Experimental Botany

Article Title: Linear β-1,2-glucans trigger immune hallmarks and enhance disease resistance in plants

doi: 10.1093/jxb/erae368

Figure Lengend Snippet: B2G3 induces an immune response in maize and wheat and protects against fungal diseases. (A) Reactive oxygen species (ROS) production in maize plants measured as relative luminescence units (RLUs) over time after treatment with A3G3, Chi6, B2G3, and B2G6 (all at 100 µM). Distilled water (mock) was used as negative control. Data represent the mean ±SE ( n =8). (B) Total ROS production in maize plants measured as total RLUs over 120 min after treatment with the oligosaccharides. (C) Quantification of Colletotrichum graminicola genomic DNA per maize leaf area (cm 2 ). Genomic DNA was quantified at 4 dpi by quantitative PCR using C. graminicola- specific primers for histone 3 (Cg H3 ) ( n =4–5). The experiment was performed in plants treated with distilled water (mock), MLG43 (1 mM and 0.5 ml per plant) (positive control), and B2G3 (1 mM and 0.5 ml per plant). (D) ROS production in wheat plants measured as RLUs over time after treatment with the peptide flg22 (1 µM) and two concentrations of B2G3 (100 µM and 400 µM). Distilled water (mock) was used as negative control. Data represent the mean ±SE ( n =8). (E) Total ROS production in wheat plants measured as total RLUs over 60 min after treatment with flg22 (1 µM) and B2G3 (100 µM and 400 µM). (F) Lesion area (%) caused by Zymoseptoria tritici infection in wheat plants after treatment with distilled water (mock) and B2G3 (500 µM and 0.78 ml per plant) ( n =16) at 12 dpi. Statistically non-significant (n.s.) and significant differences according to one-tailed Student’s t -test (* P ≤ 0.05, ** P ≤0.01, *** P ≤0.001) compared with the mock treatment are indicated.

Article Snippet: The oligosaccharides α-1,3-glucan trisaccharide A3G3 [α-1,3-(glucose) 3 ], hexaacetyl-chitohexaose Chi6 [β-1,4-( N -acetylglucosamine) 6 ], MLG43 [β-1,3, β-1,4-(glucose) 3 ], β-1,2-glucan trisaccharide B2G3 [β-1,2-(glucose) 3 ], β-1,2-glucan hexasaccharide B2G6 [β-1,2-(glucose) 6 ], and β-1,2-glucan polysaccharide [β-1,2-(glucose) n ] were acquired from Megazyme (Wicklow, Ireland).

Techniques: Negative Control, Real-time Polymerase Chain Reaction, Positive Control, Infection, One-tailed Test

Journal: Chemmedchem

Article Title: Tumor‐Associated Carbohydrate Antigen 19–9 (CA 19–9), a Promising Target for Antibody‐Based Detection, Diagnosis, and Immunotherapy of Cancer

doi: 10.1002/cmdc.202400491

Figure Lengend Snippet: Chemical synthesis pathways of CA 19–9. Syntheses of a) protected CA 19–9 tetrasaccharide 2 ; b) pentenyl CA 19–9 hexasaccharide 9 ; c) CA 19–9 tetrasaccharide 13 with an amino propyl linker at the reducing end; and d) a second synthesis of CA 19–9 tetrasaccharide 13 .

Article Snippet: The second reported chemical synthesis of CA 19–9 as pentenyl glycoside of CA 19–9 hexasaccharide 9 was by the Optimer Pharmaceuticals to facilitate their vaccine studies.

Techniques: