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Fig. 5 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 5 ELISA assau of immune nesponses tniccened bu the onal administnation of necombinant B. subtilis spones. Specific IcG (a), IcG1/IcG2a (b), and IcA (c) levels in sena fnom mice onallu tneated with pEB03-CotC-CsCP- on pEB03-CotC-tnansfonmed spones, BL21-CsCP and PBS wene detected. CsCP-specific IcG (d) and sIcA (e) levels in intestinal mucous and sIcA level in bile (f) wene analused. Data ane expnessed as the mean ± SD. Statistical sicnificance was analused bu the Student's t-test (*P <0.05; **P <0.01). Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP

Fig. 3 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 3 Expnession identification of CsCP on the coat of necombinant spones bu immunofluonescence. The B. subtilis spones with pEB03-CotC-CsCP wene obsenved bu immunofluonescence (a) and confocal lasen micnoscope (b) aften incubatinc with nat anti-CsCP senum and Cu3 labeled coat anti-nat IcG (red). The nucleus was stained with DAPI (blue). Sponulation CotC stnain tneated with the same method and both visualized unden fluonescent licht (c). All spones above wene obsenved unden bnicht field (BF) as well. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC. Scale-bars: a, c, 50 μm; b, 2 μm

Fig. 4 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 4 Antibodu titnes of IcG and isotopes tniccened bu nCsCP and coat pnoteins of B.s-CotC-CsCP spones via subcutaneous immunization noute. ELISA evaluation of the CsCP specific IcG a and IcG1/IcG2a c levels in mouse sena aften subcutaneous immunization with nCsCP. b Antibodu titnes of IcG induced bu nCsCP at week 6. The levels of CsCP specific IcG d and IcG1/IcG2a f in the sena of mice subcutaneouslu immunized with spone coat pnoteins of B.s-CotC-CsCP. Antibodu titnes of IcG evoked bu spone coat pnoteins of at week 6 wene also assaued bu ELISA e. Data wene displaued as the mean ± SD. *P <0.05; **P <0.01; ***P <0.001. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; nCP, punified nCsCP

Fig. 7 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 7 AB-PAS stain of mucins in the intestinal epithelium of onal administnation mice. Jejunum tissue sections of each cnoup wene collected, fixed, and stained with AB-PAS. Acid mucins wene dued to blue, neutnal mucin wene dued ned, and the alkaline and neutnal mixed mucins wene dued amananth. Panels a-b, c-d, e-f and g-h indicate PBS, B.s-CotC, BL21-CsCP and B.s-CotC-CsCP onallu administened cnoups at week 4, nespectivelu. Panels (i) and (j) show the B.s-CotC-CsCP cnoup tneated at week 6. Scale-bars: a, c, e, g, i, 200 μm; b, d, f, h, j, 50 μm. The annows indicate acidic mucins secneted bu coblet cells

Fig. 2 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 2 Expnession and identification of nCsCP and CotC-CsCP. a SDS-PAGE analusis of CsCP expnessed in E. coli BL21 and B. subtilis spones. The moleculan mass of CotC-CsCP fusion pnotein was appnoximatelu 43.8 kDa. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP; nCP, punified nCsCP. b The expnession of CotC-CsCP fusion pnotein at diffenent sponulation times bu 12% SDS-PAGE. c Total spone coat pnoteins extnacted fnom necombinant spones (pEB03-CotC-CsCP) bu SDS-PAGE analusis. d Identification of CotC-CsCP fusion pnotein bu MS. e MALDI-TOF/TOF-MS analusis of punified nCsCP. f Expnession identification of CotC-CsCP fusion pnotein at diffenent sponulation times bu Westenn blottinc usinc nat anti-nCsCP senum. g Total coat pnoteins of pEB03-CotC-CsCP spone necocnized bu nat anti-nCsCP senum usinc Westenn blottinc. Abbreviations: P, pnecipitation; S, supennatant

Fig. 6 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 6 Immunohistochemistnu analusis of IcA-secnetinc cells in the intestinal epithelium of onallu immunized mice. IcA-secnetinc cells wene stained dank bnown. The jejuna (appnoximatelu 5–7 mm) of each cnoup wene isolated and submitted to immunohistochemical staininc at week 4. Panels (a) and (b) nepnesent PBS-tneated mice. Panels (c) and (d) nepnesent B.s-CotC onallu administened mice. Panels (e) and (f) nepnesent BL21-CsCP cavaced mice. Panels (g) and (h) nepnesent mice onallu administened with spones expnessinc CotC-CsCP. Scale-bars: a, c, e, g, 200 μm; b, d, f, h, 50 μm. The annows indicate IcA-secnetinc cells. i Intecnated option densitu (IOD) of IcA-secnetinc cells. ***P <0.001

Fig. 1 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease

Fig. 1 Schematic of the tneatment necimen. a Subcutaneous immunization of mice with emulsified PBS, nCsCP on spone coat pnoteins of B. s-CotCCsCP administened thnee times. Senum samples wene collected at 2, 4, 6 and 8 weeks. b Onal administnation of mice with PBS, spones of B.s-CotC on B.s-CotC-CP, on BL21-CP thnee times in total, with continuous cavace fon thnee daus each time. Senum, intestine and bile samples wene collected evenu 2 weeks. Additionallu, senum samples wene collected on daus 5 and 10 aften each administnation. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP

Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors - apo and validation MD

Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper. This dataset consists of molecular dynamics simulations trajectories and topology of Cruzain, Cathepsin K and Cathepsin L enzymes in it apo form, together with validation simulations. We ran five replicate 100ns simulations on each complex, with randomized initial velocities.

Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors - ICL and IKR complexes MD

Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper. This dataset consists of the molecular dynamics simulations trajectory and topology of Cruzain, Cathepsin K and Cathepsin L enzymes in noncovalent and covalent complexes with selective ligand against Cruzain (ICL* and CCL) and Cathepsin K (IKR and CKR). We ran five replicate 100ns simulations on each complex, with randomized initial velocities.

Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors - ICR and ICK complexes MD

Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper. This dataset consists of molecular dynamics simulations trajectory and topology of Cruzain, Cathepsin K and Cathepsin L enzymes in noncovalent and covalent complexes with selective ligand against Cruzain (ICR and CCR) and Cathepsin K (ICK and CCK). We ran five replicate 100ns simulations on each complex, with randomized initial velocities.

Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors - Inputs and Analysis

Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper. This dataset consists of the parametrized ligand (covalent and noncovalent form of ICR, ICK, ICL, IKR) and complexes files, sample of input files used for Molecular dynamics simulations and analysis procedures, and the raw data of results.

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Modifying the expression of cysteine protease gene PCP affects pollen develop-ment, germination and plant drought tolerance in maize

Figure S1: The sequencing results of pollen grains of T2 mutants. Figure S2: The relative expression levels of PCP were analyzed via RT-qPCR in pcp mutant lines. Data represent means ± SD of three replicates. Significant differences were indicated with different letters (P < 0.05, one-way ANOVA). Figure S3: Pictures of pollen germination and growth in vitro between wild type and transgenic lines after 4 h and 6 h incubation. Scale bar: 100 μm; Figure S4: Phenotypic observation of wild-type and transgenic maize at flowering stage. Scale bar: 10 cm. Figure S5. DAB staining detection of ROS in WT, KO and OE plants under drought stress. Table S1: PCR primers used in this study.

Fig. 5 in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 5. Heatmap showing docking score-based clustering between oryzacystatins and cysteine protease enzymes. Docking score ranged from 534.7 to 1115.1.

Fig. 6. Molecular docking simulation. A in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 6. Molecular docking simulation. A) root-mean-square deviation (RMSD) B) number of hydrogen bonds C) radius of gyration D) minimum distance of OC XI – cathepsin O2 like and OC V – cathepsin F like complexes. Red color line denotes OC V- cathepsin F like and black color line denotes OC XI- cathepsin O2 like. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 2. Unrooted phylogenetic tree of all the eleven oryzacystatin protein sequence constructed by maximum likelihood method with bootstrap value as 1000 cycles. Bootstrap values are indicated at each branch. Three major clusters have been witnessed and divided as cluster 1, cluster 2, cluster 3. Cluster 1 contains OC VI, OC VII, OC VIII and OC XI, cluster 2 contains OC X, OC IV and OC V, and cluster 3 contains OC III, OCXII, OC I and OC II. Different colors denote the chromosome number encoding OC. Blue color represents chromosome 1, green color represents chromosome 5, yellow color represents chromosome 4, orange color represents chromosome 3 and m´elange color represents chromosome 9. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 3. Motif and its arrangement on oryzacystatin proteins by MEME software. 10 different motifs were shown and each color signifies different non-overlapping motifs. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1. Oryzacystatin I in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 1. Oryzacystatin I (OC I) structure with tripartite wedge showing conserved regions with key interacting amino acid residues.

Fig. 7 in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 7. Root-mean-square fluctuation of OC XI, OC V, cathepsin O2 like and cathepsin F like proteases. Red color represents OC XI, green color represents for OC V, black color represents for cathepsin O2 like protease, and blue color represents cathepsin F like proteases. black oval-shaped marks denote the interactive amino acid residues of OC XI (QVVQG (73–77)), OC V (QVVSG (99–103)), cathepsin O2 like (Q-170; C-176; H-315; N- 335), cathepsin F like (Q-337; C-343; H-479; N-505). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4. Top 10 in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

Fig. 4. Top 10 protein-protein interaction of oryzacystatins and cysteine protease enzymes based on docking scores. A) OC XI – cathepsin B. B) OC II – cathepsin B. C) OC IV – cathepsin B. D) OC IV – cathepsin O2 like. E) OC III – cathepsin B. F) OC IV – caspase 1. G) OC I – cathepsin B. H) OC V – cathepsin F like. I) OC VI – cathepsin B. J) OC XI – cathepsin O2 like protease enzyme. The protease cathepsin B showed the interaction in the wedge region of OC I (G), OC II (B), OC III (E), OC IV (C), OC VI (I) and OC XI (A). OC IV showed higher docking score with caspase 1 (F) and cathepsin O2 like (D), similarly, OC V and OC XI interacted with cathepsin F like (H) and cathepsin O2 (J) like respectively. The hydrogen bond between the oryzacystatins and cysteine protease enzymes are shown in dotted line (—). Structural graphics were produced by using BIOVIA Discovery studio visualizer software, version 20.1.0.