Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental

Silk fibroin-based scaffolds for tissue engineering

Silk fibroin is an important natural fibrous protein with excellent prospects for tissue engineering applications. With profound studies in recent years, its potential in tissue repair has been developed. A growing body of literature has investigated various fabricating methods of silk fibroin and their application in tissue repair. The purpose of this paper is to trace the latest developments of SF-based scaffolds for tissue engineering. In this review, we first presented the primary and secondary structures of silk fibroin. The processing methods of SF scaffolds were then summarized. Lastly, we examined the contribution of new studies applying SF as scaffolds in tissue regeneration applications. Overall, this review showed the latest progress in the fabrication and utilization of silk fibroin-based scaffolds.

Biomolecular characterization of Antheraea mylitta cocoonase: A secreted protease

Cocoonase is a protease secreted during the emergence of silk moths. In the present study cocoonase of Antheraea mylitta was collected, purified and secondary structure was determined using circular dichroism (CD) spectroscopy which revealed the presence of α-helix 4.3%, β-sheet 55%, turn 8% and random coil 32.7%. The thermal stability of cocoonase was studied using CD spectroscopy while the thermal property was observed using Differential Scanning Calorimetry (DSC). Furthermore, MALDI-TOF peptide mass fingerprinting (PMF) was performed for similar protein identification using the MASCOT server. Using casein as the substrate, the kinetic constants Km and Vmax were 13 × 103 mg/ml and 15.09 × 10-2 μg/mg.s1 respectively. The specific activity of cocoonase was observed to be maximum at temperature 40 °C, pH-8.0. The effect of heavy metals Hg2+, Cd2+, Co2+, Pb2+ showed inhibitory activity at higher concentrations, while few metals like Mn2+, Fe3+ enhanced the activity while the effect of Ca2+ was not much on the activity. Soybean trypsin inhibitor and PMSF showed an inhibitory effect on the activity of cocoonase. Additionally, antioxidant scavenging and fibrinolytic properties were also observed. Furthermore, the imperative information generated through the present study will serve to explore cocoonase for its prospective pharmaceutical applications.

A novel method for silkworm cocoons self-degumming and its effect on silk fibers

INTRODUCTION

Conventional hot-alkaline cocoon degumming techniques greatly weaken the physicochemical and mechanical properties of silk fibroin fiber, thus affecting the quality of silk fabric. Moreover, it causes massive energy waste and serious environmental pollution.

OBJECTIVE

This study aims to establish a novel cocoon self-degumming method by genetic modification of silkworm varieties and silk fibers.

METHODS

The self-degummed cocoon material was generated by specifically overexpressing trypsinogen protein in the sericin layer of silk thread; the effect of cocoon self-degumming method was evaluated by the degumming rate of sericin protein, the cleanliness and equivalent diameter of silk fibroin fiber; the basic characteristics of silk fibroin fiber degummed by cocoon self-degumming method and conventional hot-alkaline degumming technique were determined by electron microscopy, Fourier infrared spectroscopy, X-ray diffraction and tensile tests; the composition and biological activity of degummed sericin protein was respectively analyzed by liquid chromatograph-mass spectrometry and cytological experiments.

RESULTS

The genetically engineered self-degumming cocoon containing trypsinogen protein was successfully created, and the content of trypsinogen protein in silk was 47.14 ± 0.90 mg/g. The sericin protein in the self-degumming cocoon was removed out in water or 1 mM Tris-HCl buffer (pH = 8.0). Compared to alkaline-degummed silk fibroin, self-degummed silk fibroin had better cleanliness, thicker equivalent diameter, more complete silk structure and better mechanical property. In addition, sericin protein degummed from self-degumming cocoons significantly promoted cell proliferation and caused no obvious cytotoxicity.

CONCLUSION

Compared to conventional hot-alkaline degumming technique, the cocoon self-degumming method by genetically overexpressing trypsinogen protein in sericin layer of silk thread can self-degummed in a mild degumming condition, and gain silk fiber with better quality and more biologically active sericin protein products. This strategy can not only reduce the environmental impact, but also generate greater economic value, which will accelerate its application in the silk and pharmaceutical industries.

Biomimetic polymer fibers-function by design

Biomimicry applies the fundamental principles of natural materials, processes, and structures to technological applications. This review presents the two strategies of biomimicry-bottom-up and top-down approaches, using biomimetic polymer fibers and suitable spinning techniques as examples. The bottom-up biomimicry approach helps to acquire fundamental knowledge on biological systems, which can then be leveraged for technological advancements. Within this context, we discuss the spinning of silk and collagen fibers due to their unique natural mechanical properties. To achieve successful biomimicry, it is imperative to carefully adjust the spinning solution and processing parameters. On the other hand, top-down biomimicry aims to solve technological problems by seeking solutions from natural role models. This approach will be illustrated using examples such as spider webs, animal hair, and tissue structures. To contextualize biomimicking approaches in practical applications, this review will give an overview of biomimetic filter technologies, textiles, and tissue engineering.

Protein-protein docking and molecular dynamics studies of sericin and cocoonase of silkworm: an insight for cocoon softening

Cocoonase is known to digest the sericin protein that encapsulates the silkworm cocoon's fibroin protein. Silk fibroin and sericin are two types of proteins that make up silk, and accounts for around 20-30% of the overall cocoon weight. The aim of the study was to see the protein-protein interaction (PPI) and molecular dynamic study of sericin, cocoonase and protein-protein docked complex of silkworm by computational approaches. Here motif analysis, phylogenetic analysis, principal component analysis, root-mean-square deviation (RMSD), root mean square fluctuation, radius of gyration, structural and functional study of cocoonase and sericin as well as molecular docking study were carried out. The 33 amino acid residues of cocoonase shows interaction with 38 aa residues of sericin involving 4 disulphide bonds, 22 hydrogen bonds and 319 non-bonded contacts. The confirmational stability and flexibility of both the proteins as well as protein-protein complex were achieved at 70 ns of MD simulation study. RMSD-based data indicated that cocoonase is more stable than sericin and complex, and complex has a greater fluctuation with more compact (higher Rg) value than cocoonase and sericin, inferring higher conformational stability and flexibility of protein-protein complex than cocoonase and sericin. This study provides a new dimension for PPI study by computational approaches.Communicated by Ramaswamy H. Sarma.

Evaluating the role of trypsin in silk degumming: An in silico approach

The trypsin being universal enzyme forming family of proteases catalyzes the hydrolysis of proteins into amino acids and regenerates the serine hydroxyl an active site. The trypsin enzyme from D. saccharalis, uses sericin as its preferred substrate. Presence of catalytic triad (serine, aspartic acid and histidine) at the substrate binding site of this enzyme is very important for the catalytic activity. In the current study, the interacting mechanism between the substrate sericin protein and enzyme trypsin protein were explored by integrating various computational approaches including physico-chemical properties, biophysical properties, dynamics, gene ontology, molecular docking, protein - protein interactions, binding free energy calculation and structural motifs were studied. The evolutionary study performed by MEGA X showed that trypsin protein sequence (ALE15212.1) is closely related to cocoonase protein sequence (ADG26770.1) from Antheraea pernyi. 3-D models of trypsin and sericin proteins were predicted using I-TASSER and further validated by PROCHECK, and ProSAweb softwares. The predicted trypsin structure model was assigned E.C. no. 3.4.21.4 which refers hydrolytic mechanism. Gene Ontology predicted by QuickGO showed that trypsin has serine hydrolase activity (GO: 00017171), and part of proteolysis (GO: 0006508) as well as protein metabolic process (GO:0019538) actvity. Molecular docking studies between trypsin and sericin proteins were conducted by the HADDOCK 2.4 having best docked protein complex with Z-score - 1.9. 2D and 3D protein-protein interaction was performed with LIGPLOT⁺ and HAWKDOCK, PDBsum, respectively. The amino acid residues interacting across proteins interface are sericin_chain A representing "Ser133, Tyr214, Thr188, Thr243, Ser225, Ser151, Ser156, His294, Arg293, Gly296″ and trypsin_chain B "Lys120, Tyr246, Asn119, Glu239, Ser62, Tyr194, Ile197, Ser171, Tyr169, Gly170″. Based on our results trypsin shows similarity with cocoonase and presumably trypsin can be used as an alternative source in cocoon degumming.

In silico structural and functional characterization of Antheraea mylitta cocoonase

Background

Cocoonase is a serine protease present in sericigenous insects and majorly involved in dissolving of sericin protein allowing moth to escape. Cocoon structure is made up of sericin protein which holds fibroin filaments together. Cocoonase enzyme hydrolyzes sericin protein without harming the fibroin. However, until date, no detailed characterization of cocoonase enzyme and its presence in wild silk moth Antheraea mylitta has been carried out. Therefore, current study aimed for detailed characterization of amplified cocoonase enzyme, secondary and tertiary structure prediction, sequence and structural alignment, phylogenetic analysis, and computational validation. Several computational tools such as ProtParam, Iterative Threading Assembly Refinement (I-TASSER), PROCHECK, SAVES v6.0, TM-align, Molecular Evolutionary Genetics Analysis (MEGA) X, and Figtree were employed for characterization of cocoonase protein.

Results

The present study elucidates about the isolation of RNA, cDNA preparation, PCR amplification, and in silico characterization of cocoonase from Antheraea mylitta. Here, total RNA was isolated from head region of A. mylitta, and gene-specific primers were designed using Primer3 followed by PCR-based amplification and sequencing. The newly constructed 377-bp length sequence of cocoonase was subjected to in silico characterization. In silico study of A. mylitta cocoonase showed 26% similarity to A. pernyi strain Qing-6 cocoonase using Blastp and belongs to member of chymotrypsin-like serine protease superfamily. From phylogenetic study, it was found that A. mylitta cocoonase sequence is closely related to A. pernyi cocoonase sequence.

Conclusions

The present study revealed about the detailed in silico characterization of cocoonase gene and encoded protein obtained from A. mylitta head region. The results obtained infer the presence of cocoonase enzyme in the wild silkworm A. mylitta and can be used for cocoon degumming which will be a valuable and cost-effective strategy in silk industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00367-8.

Exploring the toxic interactions between Bisphenol A and glutathione peroxidase 6 from Arabidopsis thaliana

As primary industrial raw material, the widespread usage of bisphenol A (BPA) has resulted in sustained release and accumulation in the environment. Besides its endocrine-disrupting character, BPA was reported to generate excessive reactive oxygen species (ROS). However, the potential toxic mechanisms of the BPA-induced oxidative damage to plants were poorly understood. In this study, glutathione peroxidase 6 from Arabidopsis thaliana (AtGPX6) was regarded as biomarker to investigate the toxic effects of BPA on plants by multi-spectroscopic techniques and molecular docking method. Firstly, BPA effectively quenched the intrinsic fluorescence of AtGPX6 via static quenching mechanism, and a single binding site of AtGPX6 towards BPA was presumed. Moreover, the binding force was mainly driven by van der Waals forces and hydrogen bonding based on the negative values of ΔH⁰ and ΔS⁰, which was consistent with the molecular docking result. In addition, the conformational changes of AtGPX6 accompanied with the enhancement of the hydrophilicity around the tryptophan residues upon the combination with BPA, were evaluated through the combination of the fluorescence, UV-visible absorption and Circular dichroism (CD) spectroscopy. Finally, the inhibitory impact on the development of Arabidopsis seedling roots was observed under BPA exposure. Therefore, the exploration of the molecular mechanism of AtGPX6 with BPA would provide valuable assessments on the toxic effects of BPA on plants.

Effects of trypsin-induced limited hydrolysis on the structural, functional, and bioactive properties of sericin

The effects of trypsin-induced hydrolysis on the structural, functional, and antioxidant properties of sericin were studied. The structural properties of sericin and its hydrolysates were characterized by using SDS-PAGE, SEC-HPLC, surface hydrophobicity, and circular dichroism. Antioxidative properties were evaluated based on quenching capacity against hydroxyl, DPPH, and ABTS, and metal (Fe²⁺, Cu²⁺) chelating activity. The enzymatic hydrolysis raised the flexibility, changed emulsifying and foaming properties, and improved the solubility and antioxidant activity of sericin. Meanwhile, the hydrolysis led to a decline in gelation capacity, oil holding capacity, and water holding capacity. Sericin and its hydrolysates exhibited excellent function with regard to oil holding, emulsifying, and foaming. Sericin and its hydrolysates had clear effects on the growth of both Enterococcus faecalis and Lactobacillus bulgaricus strains.

Sericin was hydrolyzed to a limited extent using trypsin, then the physicochemical, prebiotic, and antioxidative properties of the obtained hydrolysates were investigated.