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Efficient degradation of azo dyes by an engineered myoglobin with a modified heme active site showing high peroxidase activity

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Process Biochemistry 2025年 156卷 153-163页

作者： Jing-Jing Liu Bin-Bin Jiang Ya-Han Zhu Shu-Qin Gao Ying-Wu Lin School of Chemistry and Chemical Engineering University of South China Hengyang 421001 China Laboratory of Protein Structure and Function University of South China Hengyang 421001 China

Azo dyes, widely used in global textiles, persist in wastewater causing significant ecological and health risks, necessitating efficient degradation to protect ecosystems and public health. The development of artificial metalloenzymes has provided advanced biotechnological solutions to address this challenge. This study presents a highly efficient artificial metalloenzyme, F43Y/H64D myoglobin (F43Y/H64D Mb), engineered from sperm whale myoglobin with a modified heme active site by replacement of Phe43 with Tyr and His64 with Asp, respectively, for azo dye degradation. The engineered enzyme achieved degradation efficiencies of approximately 93 %, 93 %, and 90 % for Acid Orange 7, Methyl Orange, and Acid Blue 92, respectively, within 10 seconds. Its overall catalytic efficiency was found to be approximately 3.6 times higher than that of horseradish peroxidase, a widely used natural enzyme. HPLC and ESI-MS analyses proposed degradation pathways, and bacterial toxicity tests confirmed reduced toxicity post-degradation. Furthermore, F43Y/H64D Mb exhibited excellent performance in natural aquatic environments, surpassing many recently reported results in efficiency, reaction speed, and operational simplicity. These findings highlight the feasibility of F43Y/H64D Mb for efficient azo dye decolorization and degradation in wastewater, offering a novel enzymatic tool for sustainable environmental remediation.

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Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling

Results in Chemistry

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Results in Chemistry 2025年 16卷

作者： Mfeka, Mbalenhle Onisuru, Olalekan Pandian, Ramesh Sayed, Yasien Khoza, Thandeka Achilonu, Ikechukwu Department of Biochemistry School of Life Sciences College of Agriculture Engineering & Science University of KwaZulu-Natal Pietermaritzburg 3209 South Africa Protein Structure-Function and Research Laboratory School of Molecular and Cell Biology Faculty of Science University of the Witwatersrand Braamfontein Johannesburg 2000 South Africa

Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schistosome drug target, a careful selection of crystal structure space groups used for CADD is emphasized in this study. Sb28GST was successfully overexpressed and purified to grow protein crystals with a resolution of 2.4 Å in an orthorhombic space group system. High-throughput virtual screening (HTVS) of a flavonoid compound was performed on monoclinic 8ALS and orthorhombic 8BHZ Sb28GST to identify potential ligands. The results showed a diverse selection of hit compounds with apigenin 7-O-(2G-rhamnosyl)gentiobioside (apigenin) being the common ligand. However, quercetin-3-O-Beta-D-Glucose-7-O-Beta-D-Gentiobioside (quercetin) showed the highest affinity to 8ALS with a Glide gscore of −15.66 kcal/mol. Also, 500-ns molecular dynamics simulations (MDS) of the 8ALS-Sb28GST and 8BHZ-Sb28GST apo systems, as well as their corresponding apigenin and quercetin complexes, show two distinct trajectories which reveal significant differences in their dynamic behaviour and also showed varying interactions. This highlights the need for collective assessment of protein polymorphs to comprehensively understand protein dynamics. The inhibitory potency of apigenin and quercetin via a GSH-CDNB conjugation assay confirmed that they significantly reduced the specific enzyme activity of Sb28GST with both ligands having half-maximal inhibitory concentration (IC₅₀) of 0.13 mM. Extrinsic fluorescence studies and thermal shift assay indicated that these compounds bind to the hydrophobic H-site and allosteric L-site at the dimer interface and have a minimal effect on the protein's thermal stability. © 2025 The Authors

关键词： Binding Empirical, ligand High-throughput virtual screening Molecular dynamics simulations Polymorphs Schistosoma bovis

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Steric Effect Modulating the structures of Trinuclear Zinc Carboxylate Frameworks

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Chinese Journal of Structural Chemistry 2016年第9期35卷 1413-1419页

作者：孙允凯谢睿王小峰文格波林英武 School of Chemistry and Chemical Engineering University of South China Laboratory of Protein Structure and Function University of South China

By the reaction of different aromatic dicarboxylic acid with zinc nitrate, three metal-carboxylate frameworks, [Zn3（BDC）3（EtOH）2]（1）, [Zn3（BDC）3（py）2]·2DMF（2）, and [Zn3（NH2-BDC）3（H2O）2]·5DMF（3） which are constructed on the same linear trinuclear Zn3（RCOO）6 secondary building units, have been synthesized and characterized by X-ray diffraction analyses. Structural analyses showed that there are terephthalic acids as ligand linkers to form the hxl topological layer structures for 1 and 2. The introduction of the rigid aromatic ring pyridine in 2 as the terminal co-ligand of Zn3-SBU to instead of the flexible ethanol in 1, will form the layer-pillared supramolecular systems with 2-D crisscross channels, through its π-π stacking interactions. Owing to the steric hindrance of amino groups, 3 was assembled into a three-dimensional porous structure with pcu topology derived from the 2-amino-terephthalic acid as linkers to connect the Zn3-SBUs through a head-to-tail type.

关键词： zinc（Ⅱ） metal-carboxylate framework steric effect crystal structure

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Uranyl-cytochrome b_5 interaction regulated by surface mutations and cytochrome c

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Nuclear Science and Techniques 2015年第5期26卷 44-47页

作者：孙美慧杜可杰聂长明文格波林英武 School of Chemistry and Chemical Engineering University of South China Laboratory of Protein Structure and Function University of South China

Understanding uranium-protein interaction is important for revealing the mechanism of uranyl ion(UO2+2)toxicity. In this study, we investigated the interaction between UO2+2and a quadruple mutant of cytochrome b5(E44/48/56A/D60 A cyt b5, namely 4A cyt b5) by spectroscopic approaches. The four mutated negativelycharged surface residues of cyt b5 have been considered to be the interactive sites with cytochrome c(cyt c).Also, we studied the interaction between UO2+2and the protein-protein complex of 4A cyt b5-cyt c. The results were compared to the interaction between UO2+2and cyt b5, and the interaction between cyt c and cyt b5-cyt c complex, from previous studies. It was found that the interaction of UO2+2-cyt b5, i.e., uranyl ion binding to cyt b5 surface at Glu37 and Glu43 as previously proposed by molecular modeling, is regulated by both surface mutations of cyt b5 and its interacting protein partner cyt c. These provide valuable information on metal-protein-protein interactions and clues for understanding the mechanism of uranyl toxicity.

关键词：蛋白质相互作用细胞色素b5 细胞色素C 铀酰离子突变体表面蛋白质复合物毒性机理

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Rational design of functional metalloenzymes in myoglobin for green biocatalysis

Rational design of functional metalloenzymes in myoglobin fo...

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作者： Ying-Wu Lin School of Chemistry and Chemical Engineering University of South China Laboratory of Protein Structure and Function University of South China

Design of functional metalloenzymes have addressed much attention in the last decade. Myoglobin(Mb) is an ideal model protein for heme protein design, and we have rationally designed some functional enzymes in Mb by using several strategies, such as by using post-translational modifications, design of a metal-binding site and an intramolecular disulfide bond, and introduction of non-native cofactors, etc. The designed artificial metalloenzymes include artificial nitrite reductase, hydrolase, dye-decolorizing peroxidases(DyP s) and dehaloperoxidases(DHPs), with the catalytic efficiency close to or even exceeding those of native enzymes. Moreover, we have solved the X-ray crystal structure of some artificial enzymes, which provides valuable insights into the structure and function relationship, as well as potential applications for green biocatalysis.

关键词： Metalloenzymes protein design biocatalysis DyP DHP

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Rational design of functional metalloenzymes in myoglobin for green biocatalysis

Rational design of functional metalloenzymes in myoglobin fo...

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中国化学会第六届全国生物物理化学会议（NCBPC-6）

作者：林英武 School of Chemistry and Chemical Engineering University of South China Laboratory of Protein Structure and Function University of South China

Design of functional metalloenzymes have addressed much attention in the last decade. Myoglobin（Mb） is an ideal model protein for heme protein design, and we have rationally designed some functional enzymes in Mb by using several strategies, such as by using post-translational modifications, design of a metal-binding site and an intramolecular disulfide bond, and introduction of non-native cofactors, etc. The designed artificial metalloenzymes include artificial nitrite reductase, hydrolase, dye-decolorizing peroxidases（DyPs） and dehaloperoxidases（DHPs）, with the catalytic efficiency close to or even exceeding those of native enzymes. Moreover, we have solved the X-ray crystal structure of some artificial enzymes, which provides valuable insights into the structure and function relationship, as well as potential applications for green biocatalysis.

关键词： Metalloenzymes protein design biocatalysis DyP DHP

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Rational Design of an Artificial Hydrolytic Nuclease by Introduction of A Sodium Copper Chlorophyllin in L29e Myoglobin

SSRN

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SSRN 2022年

作者： Dong, Yao Chen, Yu-Mei Kong, Xiang-Jun Gao, Shu-Qin Lang, Jia-Jia Lin, Ying-Wu Du, Ke-Jie School of Chemistry and Chemical Engineering Laboratory of Protein Structure and Function Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang421001 China

Heme proteins have recently emerged as promising artificial metalloenzymes for catalyzing diverse reactions. In this report, L29E Mb, a single mutant of myoglobin, was reconstituted with a sodium copper cholorophyllin to form a new green artificial enzyme (CuCP-L29E Mb), which was characterized by spectroscopic techniques (UV-vis and EPR). The CuCP-L29E Mb was found to exhibit hydrolytic DNA cleavage activity that was not depending on O 2 . In addition, Mg 2+ ion could effectively promote the DNA cleavage activity of CuCP-L29E Mb. CuCP-WT Mb, wild-type myoglobin reconstituted with CuCP, did not show DNA cleavage activity under the same conditions. These results suggested the ligand Glu29 of protein is a critical residue for the nuclease activity. © 2022, The Authors. All rights reserved.

关键词： Enzymes

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Oncoprotein LAMTOR5-mediated CHOP silence via DNA hypermethylation and miR-182/miR-769 in promotion of liver cancer growth

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中国药理学报（英文版） 2024年第12期45卷 2625-2645页

作者： Xue Wang Qian-qian Li Yan-xin Tang Ye Li Lu Zhang Fei-fei Xu Xue-li Fu Kai Ye Jia-qi Ma Shi-man Guo Fang-yuan Ma Zhi-yu Liu Xu-he Shi Xian-meng Li Hui-min Sun Yue Wu Wei-ying Zhang Li-hong Ye State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein SciencesDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesNankai UniversityTianjin 300071China State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein SciencesDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesNankai UniversityTianjin 300071China Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Biomedical Engineering Tianjin 300192China State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein SciencesDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesNankai UniversityTianjin 300071China Institute of Radiation Medicine Peking Union Medical College & Chinese Academy of Medical SciencesTianjin 300192China State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein SciencesDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesNankai UniversityTianjin 300071China Center for Cell Structure and Function Shandong Provincial Key Laboratory of Animal Resistance BiologyCollaborative Innovation Center of Cell Biology in Universities of ShandongCollege of Life SciencesShandong Normal UniversityJinan 250014China

C/EBP homologous protein(CHOP)triggers the death of multiple cancers via endoplasmic reticulum(ER)***,the function and regulatory mechanism of CHOP in liver cancer remain *** have reported that late endosomal/lysosomal adapter,mitogen-activated protein kinase and mTOR activator 5(LAMTOR5)suppresses apoptosis in various ***,we show that the transcriptional and posttranscriptional inactivation of CHOP mediated by LAMTOR5 accelerates liver cancer *** bioinformatic analysis revealed that the expression of CHOP was low in liver cancer tissues and that its increased expression predicted a good *** CHOP contributed to destruction of LAMTOR5-induced apoptotic suppression and ***,LAMTOR5-recruited DNA methyltransferase 1(DNMT1)to the CpG3 region(-559/-429)of the CHOP promoter and potentiated its hypermethylation to block its interaction with general transcription factor Ⅱi(TFⅡ-Ⅰ),resulting in its ***,LAMTOR5-enhanced miR-182/miR-769 reduced CHOP expression by targeting its 3'***,lenvatinib,a first-line targeted therapy for liver cancer,could target the LAMTOR5/CHOP axis to prevent liver cancer ***,LAMTOR5-mediated silencing of CHOP via the regulation of ER stress-related apoptosis promotes liver cancer growth,providing a theoretical basis for the use of lenvatinib for the treatment of liver cancer.

关键词： liver cancer CHOP LAMTOR5 lenvatinib DNA methylation miR-182/miR-769

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Novel Copper Complexes with Tridentate Ligand: Synthesis, Crystal structure, DNA Binding and Anticancer Studies

SSRN

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SSRN 2023年

作者： Chen, Yu-Mei Liu, Yu-Can Wang, Jin-Quan Ou, Guang-Chuan Wang, Xiao-Feng Gao, Shu-Qin Lin, Ying-Wu Du, Ke-Jie School of Chemistry and Chemical Engineering Laboratory of Protein Structure and Function Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang421001 China School of Biosciences & Biopharmaceutics Guangdong Pharmaceutical University Guangzhou510000 China Department of Biology and Chemistry Hunan University of Science and Engineering Yongzhou425199 China

Metal complexes, particularly copper (II) complexes, are often used as anticancer drugs due to their ability to generate reactive oxygen species (ROS) in cells. Four copper (II) complexes were designed based on ligands for triplet pyridine derivatives (complexes 1-4), and their structures were determined using X-ray single crystal analysis. The interaction of these complexes with calf thymus DNA (CT-DNA) was investigated using various techniques, including UV-vis absorption, viscosity measurements, and circular dichroism spectral measurements. The results indicated that complexes 1-4 strongly interact with DNA through partial intercalation. Further investigation using agarose gel electrophoresis showed that all four complexes can cleave pBR322 DNA in the presence of ascorbic acid as a reducing agent, and the DNA cleavage mechanism is through the generation of singlet oxygen (1O2). In vitro anticancer activity of these complexes was evaluated using A549, MDA-MB-231, HeLa, and HepG2 cells. The calculated IC50 values indicated significant efficacy against cancer cells. Additionally, AO/EB staining assays revealed that these complexes induced cell apoptosis in HeLa cell line. © 2023, The Authors. All rights reserved.

关键词： DNA

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Variation in Polyamine Content among 12 Pollinated Wheat Genotypes under Drought Stress Condition

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Open Journal of Geology 2017年第8期7卷 1094-1109页

作者： Mahdi Seyedsalehi Parisa Sharifi Ombretta Paladino Gassan Hodaifa Elba C. Villegas Randa M. Osman Department of Environmental Engineering Science and Research Branch Islamic Azad University Tehran Iran Department of Agronomy Faculty of Agriculture Urmia University Urmia Iran Department of Civil Chemical and Environmental Engineering Università di Genova Genoa Italy Department of Molecular Biology and Biochemical Engineering Chemical Engineering Area University of Pablo de Olavide Seville Spain Laboratory of Function-Structure and Protein Engineering Center for Research on Biotechnology Autonomous University of Morelos State (UAEM) Cuernavaca Mexico Department of Chemical Engineering and Pilot Plant National Research Centre Cairo Egypt

The present work aims to study the drought stress effects on polyamine content and its relationship with growth and development in seeds, during cell division (from the beginning and until 17 days after pollination) and grain filling (until reaching the physiological maturity) stages. Factorial experiment based on Randomized Complete Block (RCB) design was carried out with three replications. Two factors of the experiment were considered: the level of irrigation (irrigation without and with drought stress during cell division stage and with drought stress during grain filling stage) and the level of wheat genotype (drought-resistant, semi-resistant and sensitive genotypes). As control treatment, soil moisture content of the field was considered. For drought-stress treatment, the 50% of the soil moisture content in control treatment was established. According to the experimental results, Putrescine content value is higher in control treatment which develops seeds of drought-resistant genotypes than that are registered for semi-resistant and sensitive genotypes. Both drought stress treatments induced significant rises in putrescine amount in the different genotypes of the study. The rises of putrescine content in sensitive and semi-resistant genotypes, however, were higher than in resistant ones, and the highest rise in putrescine content appeared in manning semi-resistant genotype during the stage of grain filling (27 days after pollination). Exerting drought stress in both stages of cell division and grain filling led to significant increase in spermine and spermidine contents of developing seeds of entire genotypes of the study. The highest spermidine content during grain filling stage occurred in sensitive genotypes of Shark and Tevee’s, and the lowest occurred in semi-resistant genotype of Sabalan. The highest spermine content during cell division stage, though, happened in semi-resistant genotype of manning. In fact, spermine and spermidine act as analogous to p

关键词： Polyamines Drought Wheat Randomized Complete Block (RCB)

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