Supramolecular Organization of Inulinases from Aspergillus awamori, Aspergillus ficuum and Kluyveromyces marxianus: A Comparative Aspect

Holyavka, M. G.; Makin, S. M.; Kondratyev, Maxim S.; Abdullatypov, Azat; Kovaleva, T. A.; Artyukhov, V. G.

doi:10.1134/s0006350918060155

Cited by 3 publications

(4 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The structure preparation of ficin (PDB ID: 4YYW, accessed on 20 December 2022) for docking was performed according to the standard scheme for Autodock Vina ( accessed on 20 December 2022), described as follows: atoms and atom coordinates of solvent, buffer, and ligands were removed from the input PDB file. The center of the molecule and box parameters were set manually, ensuring that the protease molecule is completely inside the computational space domain [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization

et al. 2023

View full text Add to dashboard Cite

The present work is devoted to research on the interaction between carboxymethyl cellulose sodium salt and its derivatives (graft copolymer of carboxymethyl cellulose sodium salt and N,N-dimethyl aminoethyl methacrylate) with cysteine protease (ficin). The interaction was studied by FTIR and by flexible molecular docking, which have shown the conjugates’ formation with both matrices. The proteolytic activity assay performed with azocasein demonstrated that the specific activities of all immobilized ficin samples are higher in comparison with those of the native enzyme. This is due to the modulation of the conformation of ficin globule and of the enzyme active site by weak physical interactions involving catalytically valuable amino acids. The results obtained can extend the practical use of ficin in biomedicine and biotechnology.

show abstract

Section: Methodsmentioning

confidence: 99%

Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization

et al. 2023

View full text Add to dashboard Cite

show abstract

“…The preparation of the structure of the cysteine proteases for docking [ 19 ] and the process of modeling interactions were carried out as described by Holyavka et al [ 32 , 33 ]. The PDB IDs for enzyme input files were the following: 1W0Q for bromelain, 4YYW for ficin, and 9PAP for papain.…”

Section: Methodsmentioning

confidence: 99%

“…This problem can be solved by immobilizing the enzyme on an inert or antibacterial matrix [ 13 , 14 , 15 , 16 , 17 , 18 ]. Immobilization increases the rigidity of the tertiary structure of the enzyme molecules, thereby stabilizing it and increasing the half-life [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Novel Immobilized Biocatalysts Based on Cysteine Proteases Bound to 2-(4-Acetamido-2-sulfanilamide) Chitosan and Research on Their Structural Features

et al. 2022

View full text Add to dashboard Cite

Briefly, 2-(4-Acetamido-2-sulfanilamide) chitosan, which is a chitosan water-soluble derivative, with molecular weights of 200, 350, and 600 kDa, was successfully synthesized. The immobilization of ficin, papain, and bromelain was carried out by complexation with these polymers. The interaction mechanism of 2-(4-acetamido-2-sulfanilamide) chitosan with bromelain, ficin, and papain was studied using FTIR spectroscopy. It was found that the hydroxy, thionyl, and amino groups of 2-(4-acetamido-2-sulfanilamide) chitosan were involved in the complexation process. Molecular docking research showed that all amino acid residues of the active site of papain formed hydrogen bonds with the immobilization matrix, while only two catalytically valuable amino acid residues took part in the H-bond formation for bromelain and ficin. The spectral and in silico data were in good agreement with the catalytic activity evaluation data. Immobilized papain was more active compared to the other immobilized proteases. Moreover, the total and specific proteolytic activity of papain immobilized on the carrier with a molecular weight of 350 kDa were higher compared to the native one due to the hyperactivation. The optimal ratio of protein content (mg × g −1 of carrier), total activity (U × mL−1 of solution), and specific activity (U × mg−1 of protein) was determined for the enzymes immobilized on 2-(4-acetamido-2-sulfanilamide) chitosan with a molecular weight of 350 kDa.

show abstract

“…With the advancements in bioinformatics and computational biology, the identification of interaction mechanisms between enzymes and immobilization matrices, as well as their effects on enzyme structure, has become more accessible. Molecular docking methods have made it possible to unveil the interaction mechanisms down to the specific amino acid residue and the characteristic type of interaction [34][35][36][37]. However, due to the imperfections of simulation algorithms and the absence of a complete macromolecule model, in silico results should be validated with experimental data.…”

Section: Introductionmentioning

confidence: 99%

Complexation of Bromelain, Ficin, and Papain with the Graft Copolymer of Carboxymethyl Cellulose Sodium Salt and N-Vinylimidazole Enhances Enzyme Proteolytic Activity

Сорокин

Goncharova

Lavlinskaya

et al. 2023

IJMS

View full text Add to dashboard Cite

This study investigates the features of interactions between cysteine proteases (bromelain, ficin, and papain) and a graft copolymer of carboxymethyl cellulose sodium salt with N-vinylimidazole. The objective is to understand the influence of this interactions on the proteolytic activity and stability of the enzymes. The enzymes were immobilized through complexation with the carrier. The interaction mechanism was examined using Fourier-transform infrared spectroscopy and flexible molecular docking simulations. The findings reveal that the enzymes interact with the functional groups of the carrier via amino acid residues, resulting in the formation of secondary structure elements and enzyme’s active sites. These interactions induce modulation of active site of the enzymes, leading to an enhancement in their proteolytic activity. Furthermore, the immobilized enzymes demonstrate superior stability compared to their native counterparts. Notably, during a 21-day incubation period, no protein release from the conjugates was observed. These results suggest that the complexation of the enzymes with the graft copolymer has the potential to improve their performance as biocatalysts, with applications in various fields such as biomedicine, pharmaceutics, and biotechnology.

show abstract

Supramolecular Organization of Inulinases from Aspergillus awamori, Aspergillus ficuum and Kluyveromyces marxianus: A Comparative Aspect

Cited by 3 publications

References 19 publications

Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization

Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization

Novel Immobilized Biocatalysts Based on Cysteine Proteases Bound to 2-(4-Acetamido-2-sulfanilamide) Chitosan and Research on Their Structural Features

Complexation of Bromelain, Ficin, and Papain with the Graft Copolymer of Carboxymethyl Cellulose Sodium Salt and N-Vinylimidazole Enhances Enzyme Proteolytic Activity

Contact Info

Product

Resources

About