Effect of N-terminal modification on the mode of action between the Xyn11A and Xylotetraose

Ngenyoung, Apichet; Muhammad, Auwal; Rattanarojpong, Triwit; Sutthibutpong, Thana; Khunrae, Pongsak

doi:10.1016/j.ijbiomac.2020.12.154

Cited by 5 publications

(2 citation statements)

References 31 publications

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“…Protein concentration was determined using the NanoDrop™ Lite Spectrophotometer. The chimeric EiCh protein (2 mg/ml) and whole‐cell lysates from E. ictaluri strains 2234 and 2083 (positive controls) and A. veronii, E. faecium and 2 mg/ml each of the Xyn11A xylanase (Ngenyoung et al., 2021) and green fluorescent protein (EGFP) (negative controls) were 2‐fold serially diluted until 1:32 dilution. Each dilution of the proteins and bacteria (2 µl per each blot) was blotted on nitrocellulose membrane, and the membrane was blocked overnight with 5% Bovine serum albumin (BSA) (Sigma‐Aldrich, Inc.).…”

Section: Methodsmentioning

confidence: 99%

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Machimbirike

Pornputtapong

Senapin

et al. 2021

Journal of Fish Diseases

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Edwardsiella ictaluri infects several fish species and protection of the all the susceptible fish hosts from the pathogen using a monovalent vaccine is impossible because the species is composed of host-based genotypes that are genetic, serological and antigenic heterogenous. Here, immunoinformatic approach was employed to design a cross-immunogenic chimeric EiCh protein containing multi-epitopes. The chimeric EiCh protein is composed of 11 B-cell epitopes and 7 major histocompatibility complex class II epitopes identified from E. ictaluri immunogenic proteins previously reported.The 49.32 kDa recombinant EiCh protein was expressed in vitro in Escherichia coli BL-21 (DE3) after which inclusion bodies were successfully solubilized and refolded.Ab initio protein modelling revealed secondary and tertiary structures. Secondary structure was confirmed by circular dichroism spectroscopy. Antigenicity of the chimeric EiCh protein was exhibited by strong reactivity with serum from striped catfish and Nile tilapia experimentally infected with E. ictaluri. Furthermore, immunogenicity of the chimeric EiCh protein was investigated in vivo in Nile tilapia juveniles and it was found that the protein could strongly induce production of specific antibodies conferring agglutination activity and partially protected Nile tilapia juveniles with a relative survival percentage (RPS) of 42%. This study explored immunoinformatics as reverse vaccinology approach in vaccine design for aquaculture to manage E. ictaluri infections.

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Section: Methodsmentioning

confidence: 99%

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Machimbirike

Pornputtapong

Senapin

et al. 2021

Journal of Fish Diseases

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“…Atomistic MD simulations were used to understand the mechanisms underlying these efficiency losses. The MD trajectory analysis suggested that the mutation-induced binding pocket tilting resulted in an additional hydrophobic contact between the reducing end of xylooligosaccharides and Trp128 (Ngenyoung et al, 2021).…”

Section: Cellulases and Hemicellulasesmentioning

confidence: 99%

Revisiting Theoretical Tools and Approaches for the Valorization of Recalcitrant Lignocellulosic Biomass to Value-Added Chemicals

et al. 2022

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Biorefinery processes for converting lignocellulosic biomass to fuels and chemicals proceed via an integrated series of steps. Biomass is first pretreated and deconstructed using chemical catalysts and/or enzymes to liberate sugar monomers and lignin fragments. Deconstruction is followed by a conversion step in which engineered host organisms assimilate the released sugar monomers and lignin fragments, and produce value-added fuels and chemicals. Over the past couple of decades, a significant amount of work has been done to develop innovative biomass deconstruction and conversion processes that efficiently solubilize biomass, separate lignin from the biomass, maximize yields of bioavailable sugars and lignin fragments and convert the majority of these carbon sources into fuels, commodity chemicals, and materials. Herein, we advocate that advanced in silico approaches provide a theoretical framework for developing efficient processes for lignocellulosic biomass valorization and maximizing yields of sugars and lignin fragments during deconstruction and fuel and chemical titers during conversion. This manuscript surveys the latest developments in lignocellulosic biomass valorization with special attention given to highlighting computational approaches used in process optimization for lignocellulose pretreatment; enzyme engineering for enhanced saccharification and delignification; and prediction of the genome modification necessary for desired pathway fine-tuning to upgrade products from biomass deconstruction into value-added products. Physics-based modeling approaches such as density functional theory calculations and molecular dynamics simulations have been most impactful in studies aimed at exploring the molecular level details of solvent-biomass interactions, reaction mechanisms occurring in biomass-solvent systems, and the catalytic mechanisms and engineering of enzymes involved in biomass degradation. More recently, with ever increasing amounts of data from, for example, advanced mutli-omics experiments, machine learning approaches have begun to make important contributions in synthetic biology and optimization of metabolic pathways for production of biofuels and chemicals.

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Investigation into the effects of CbXyn10C and Xyn11A on xylooligosaccharide profiles produced from sugarcane bagasse and rice straw and their impact on probiotic growth

Gufe

Ngenyoung

Rattanarojpong

et al. 2022

Bioresource Technology

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Effect of N-terminal modification on the mode of action between the Xyn11A and Xylotetraose

Cited by 5 publications

References 31 publications

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Revisiting Theoretical Tools and Approaches for the Valorization of Recalcitrant Lignocellulosic Biomass to Value-Added Chemicals

Investigation into the effects of CbXyn10C and Xyn11A on xylooligosaccharide profiles produced from sugarcane bagasse and rice straw and their impact on probiotic growth

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