Article
Biochemistry & Molecular Biology
Huabiao Miao, Yu Ma, Yuanyuan Zhe, Xianghua Tang, Qian Wu, Zunxi Huang, Nanyu Han
Summary: This study investigated the effect of inserting the C2 submodule from hyperthermophilic CBM9_1-2 on the thermostability of xylanase CDBFV. The results showed that the insertion of the C2 submodule significantly enhanced the thermostability of CDBFV, resulting in longer half-lives at the optimal temperature.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Lei Ma, Guangqi Li, Yunpeng Liu, Zhihong Li, Youzhi Miao, Qun Wan, Dongyang Liu, Ruifu Zhang
Summary: In this study, two non-catalytic amino acid mutations N179S and R246K were found to decrease substrate-binding ability and affinity of the thermophilic xylanase XynAF1. Interestingly, the N179S mutation increased catalytic efficiency, while R246K and N179S-R246K mutations led to decreased catalytic efficiency.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jelena Vucinic, Gleb Novikov, Cedric Y. Montanier, Claire Dumon, Thomas Schiex, Sophie Barbe
Summary: This study examines the structure and activity of two different xylanases, NpXyn11A and EvXyn11(TS), through molecular dynamics simulations to identify key stability regions for potential engineering improvements. The results suggest that regions like the thumb region and larger substrate binding cleft play a major role in the activity of NpXyn11A, while areas with higher flexibility contribute to the thermal stability differences between the two enzymes. By pinpointing critical molecular regions, this research offers promising targets for enhancing GH-11 xylanases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Guangqi Li, Xuan Zhou, Zhihong Li, Yunpeng Liu, Dongyang Liu, Youzhi Miao, Qun Wan, Ruifu Zhang
Summary: This study characterized and engineered a thermophilic GH10 family xylanase XynAF1 to improve its thermostability, resulting in a 6-fold increase in stability through rational design and saturation mutagenesis. The high-resolution X-ray crystallographic structure of XynAF1 revealed a rigid skeleton contributing to its hyperthermophilic characteristics. The study provides a promising biocatalyst for high-temperature biotechnological applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Samaila Boyi Ajeje, Yun Hu, Guojie Song, Sunday Bulus Peter, Richmond Godwin Afful, Fubao Sun, Mohammad Ali Asadollahi, Hamid Amiri, Ali Abdulkhani, Haiyan Sun
Summary: The conversion of lignocellulose into monosaccharides is crucial for biofuel production. Enzymatic degradation is efficient and can lead to the production of valuable industrial enzymes, but challenges remain in the commercial production of thermostable cellulases and xylanases. The review focuses on recent advancements in isolating, manufacturing, and enhancing the activity of these enzymes from thermophilic and hyperthermophilic microbes using genetic engineering for economic production.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Azucena Lopez-Lopez, Alejandro Santiago-Hernandez, Maribel Cayetano-Cruz, Yolanda Garcia-Huante, Jorge E. Campos, Ismael Bustos-Jaimes, Rodolfo Marsch-Moreno, Claudia Cano-Ramirez, Claudia G. Benitez-Cardoza, Maria Eugenia Hidalgo-Lara
Summary: The biomass-degrading thermophilic ascomycete fungus Thielavia terrestris Co3Bag1 produces TtCel7A, a bifunctional cellulase/xylanase GH7 family that shows excellent catalytic activity and potential for industrial applications.
Article
Green & Sustainable Science & Technology
Zhi-Yuan Bai, Shuai You, Fang Zhang, Zhi-Wei Dong, Yi-Fan Zhao, Hong-Jian Wen, Jun Wang
Summary: The study modified xylanase through rational design and used it with cellulase to synergistically degrade mulberry branches pretreated with seawater. The mutant S21Y/N318W showed improved thermostability and specific activity. Under the condition of seawater immersion pre-treatment, the highest yield of fermentable sugar and degree of synergy were achieved. This study provides an efficient method of biomass saccharification for biofuel production.
Article
Biotechnology & Applied Microbiology
Yawei Wang, Jing Wang, Zhongqiang Zhang, Jiangke Yang, Ossi Turunen, Hairong Xiong
Summary: This study investigates the characteristics of a hyperthermostable xylanase from Thermotoga maritima. Site-directed mutagenesis was performed to improve enzyme half-life, and error-prone PCR generated a mutant with improved stability and lower K-m. Additional mutations decreased thermostability and temperature optimum while increasing K-m. The study reveals the importance of active site hydrophobicity for high activity at extreme temperatures.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yunlei Yi, Shenyuan Xu, Andrey Kovalevsky, Xia Zhang, Dongyang Liu, Qun Wan
Summary: A GH11 family xylanase, Xyn11A, with high thermostability and catalytic activity was discovered, exhibiting optimal reaction temperature at 80 degrees C with activity of 2907.3 U/mg. Xyn11A has a compact structure with more H-bonds, and electrostatic interactions in specific regions contribute to its high thermostability and activity. Introduction of a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 degrees C with augmented activity.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Weijia Zhu, Liqin Qin, Youqiang Xu, Hongyun Lu, Qiuhua Wu, Weiwei Li, Chengnan Zhang, Xiuting Li
Summary: Three strategies were investigated to improve the thermostability of xylanase, including reducing surface entropy, constructing intramolecular disulfide bonds, and molecular cyclization. Molecular simulations showed that all mutants exhibited improved thermostability and catalytic efficiency compared to the wild-type enzyme.
Review
Food Science & Technology
Zhaolin Huang, Dawei Ni, Ziwei Chen, Yingying Zhu, Wenli Zhang, Wanmeng Mu
Summary: Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation, as a comprehensive technology, has been widely used for structure information analysis and enzyme modification. This review focuses on the progress and development of MD simulation, its application in various food enzymes for thermostability and catalytic improvement, and the limitations and prospects of MD simulation in food enzyme modification research.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Chemistry, Applied
Xiaofeng Ban, Xiaofang Xie, Caiming Li, Zhengbiao Gu, Yan Hong, Li Cheng, Bhalerao Kaustubh, Zhaofeng Li
Summary: This review focuses on the characteristics, distribution, configuration, and location of salt bridges in ?-amylases, both naturally present and introduced through mutagenesis, aiming to provide an overview of desirable salt bridges in the protein structure.
Article
Chemistry, Physical
Yiming Guo, Laura Alvigini, Mohammad Saifuddin, Ben Ashley, Milos Trajkovic, Lur Alonso-Cotchico, Andrea Mattevi, Marco W. Fraaije
Summary: This study presents a one-pot biocatalytic cascade reaction for the efficient synthesis of racemic syringaresinol, a valuable compound in nutraceutical and polymer chemistry. The process utilizes renewable lignocellulosic material and involves the engineering of enzymes to achieve high conversion and chemoselectivity. The study demonstrates the potential for the biocatalytic production of syringaresinol from renewable sources.
Article
Biochemistry & Molecular Biology
Gautam Anand, Meirav Leibman-Markus, Dorin Elkabetz, Maya Bar
Summary: Plants lack a circulating adaptive immune system, instead relying on a complex and efficient innate immune system based on defense mechanisms triggered by elicitors such as microbe-associated molecular patterns (MAMPs). The fungal MAMP protein Ethylene Inducing Xylanase (EIX) from Trichoderma is a useful tool for studying plant immunity, eliciting defense responses in tobacco and tomato. Xylanases like EIX, hydrolytic enzymes mainly synthesized by fungi, play a role in xylan breakdown and can effectively induce plant defense responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biotechnology & Applied Microbiology
Yunzi Hu, Anshu Priya, Chao Chen, Cuiyi Liang, Wen Wang, Qiong Wang, Carol Sze Ki Lin, Wei Qi
Summary: Lignocellulosic biorefinery, as a potential strategy for sustainable production, faces challenges of low degradation efficiency and high enzyme dosage. This article provides a comprehensive review on this subject by discussing recent advances in substrate modification techniques, enzyme synergism mechanisms, and structure-activity interaction. Newly developed modeling and multi-omic analysis techniques for commercial enzyme preparations are introduced, offering possible avenues for achieving economic viability of lignocellulose bioconversion.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2023)
Article
Plant Sciences
Ricardo M. F. da Costa, Rachael Simister, Luned A. Roberts, Emma Timms-Taravella, Arthur B. Cambler, Fiona M. K. Corke, Jiwan Han, Richard J. Ward, Marcos S. Buckeridge, Leonardo D. Gomez, Maurice Bosch
Article
Biochemistry & Molecular Biology
Gilvan Pessoa Furtado, Marcos Roberto Lourenzoni, Carlos Alessandro Fuzo, Raquel Fonseca-Maldonado, Maria-Eugenia Guazzaroni, Lucas Ferreira Ribeiro, Richard J. Ward
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2018)
Article
Biochemical Research Methods
Sibeli Carli, Lara Aparecida Buffoni de Campos Carneiro, Richard John Ward, Luana Parras Meleiro
PROTEIN EXPRESSION AND PURIFICATION
(2019)
Article
Microbiology
Jean Carlos Rodrigues Silva, Jose Carlos Santos Salgado, Ana Claudia Vici, Richard John Ward, Maria Lourdes Teixeira Moraes Polizeli, Luis Henrique Souza Guimaraes, Rosa Prazeres Melo Furriel, Joao Atilio Jorge
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Thiago Machado Pasin, Jose Carlos Santos Salgado, Ana Silvia de Almeida Scarcella, Tassio Brito de Oliveira, Rosymar Coutinho de Lucas, Mariana Cereia, Jose Cesar Rosa, Richard John Ward, Marcos Silveira Buckeridge, Maria de Lourdes Teixeira de Moraes Polizeli
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Lummy Maria Oliveira Monteiro, Ana Claudia Vici, Matheus Pinto Pinheiro, Paulo Ricardo Heinen, Arthur Henrique Cavalcante de Oliveira, Richard John Ward, Rolf Alexander Prade, Marcos S. Buckeridge, Maria de Lourdes Teixeira de Moraes Polizeli
SCIENTIFIC REPORTS
(2020)
Article
Plant Sciences
Thatiane R. Mota, Wagner R. de Souza, Dyoni M. Oliveira, Polyana K. Martins, Bruno L. Sampaio, Felipe Vinecky, Ana P. Ribeiro, Karoline E. Duarte, Thalyta F. Pacheco, Norberto de K. Monteiro, Raquel B. Campanha, Rogerio Marchiosi, Davi S. Vieira, Adilson K. Kobayashi, Patricia A. de O. Molinari, Osvaldo Ferrarese-Filho, Rowan A. C. Mitchell, Hugo B. C. Molinari, Wanderley D. dos Santos
Summary: The study identified a BAHD gene involved in p-coumaroylation of AX in the cell wall of Setaria viridis. Silenced lines with reduced levels of SvBAHD05 showed decreased ester-linked p-coumarate and improved biomass saccharification. This indicates the potential of targeting SvBAHD05 for enhancing biomass digestibility in biofuels, biorefineries, and animal feed.
Article
Biochemistry & Molecular Biology
P. Matheus Pinheiro, A. G. Renata Reis, Paul Dupree, J. Richard Ward
Summary: Efficient enzymatic mobilization of plant cell wall polymers is crucial for biofuel production. Novel multifunctional enzymes with improved activity against lignocellulose have been developed, demonstrating the importance of interdomain geometry in chimera design.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Sibeli Carli, Jose Carlos Santos Salgado, Luana Parras Meleiro, Richard John Ward
Summary: Pectinases are immobilized on ferromagnetic nanoparticles to overcome limitations in catalytic activity, stability, cost, and re-use compatibility. The immobilized pectinase shows improved thermostability and synergistic effects with commercial enzyme cocktails in releasing reducing sugars from orange wastes, suggesting potential applications in processing pectin-rich agroindustrial residues.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Applied
Gilvan Pessoa Furtado, Sibeli Carli, Luana Parras Meleiro, Jose Carlos Santos Salgado, Richard John Ward
Summary: A RtCBM11-BglS chimera was created and showed increased hydrolytic efficiency against purified barley beta-glucan, making it potentially useful for treatment of crude barley extracts in the brewing industry.
Article
Biotechnology & Applied Microbiology
Jessica M. Soares, Lara A. B. C. Carneiro, Matheus Q. Barreto, Richard J. Ward
Summary: The researchers successfully immobilized four enzymes required for xyloglucan degradation on functionalized nanoparticles and demonstrated their effectiveness in breaking down complex polysaccharides. The immobilized enzymes showed reduced catalytic activity but could be optimized for higher xyloglucan saccharification by adjusting their proportions.
BIOFUELS BIOPRODUCTS & BIOREFINING-BIOFPR
(2022)
Article
Biochemistry & Molecular Biology
Eduardo Augusto da Silva Diniz, Diana Pontes da Silva, Sarah de Sousa Ferreira, Matheus de Freitas Fernandes-Pedrosa, Davi Serradella Vieira
Summary: Snakebite envenoming-induced myotoxicity is a major problem in ophidic accidents, and current serum therapy is ineffective in neutralizing it. An alternative approach is to search for small molecule inhibitors that can target multiple venom components. This study investigates the inhibitory effect of Rosmarinic (RSM) and Chlorogenic (CHL) acids on the catalytic properties of snake venom Phospholipase A(2) (PLA(2)) from Bothrops brazili through experimental and computational approaches, providing important information for future inhibitor design.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Sergio Ruschi Bergamachi Silva, Jose Xavier de Lima Neto, Carlos Alessandro Fuzo, Umberto Laino Fulco, Davi Serradella Vieira
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Article
Engineering, Chemical
Elenira H. M. Mendonca, Nilton Cesar Avanci, Luis Henrique Romano, Daniel Lopes Branco, Alessandra Xavier de Padua, Richard John Ward, Alvaro de Baptista Neto, Marcos Roberto Lourenzoni
BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING
(2020)
Article
Chemistry, Multidisciplinary
Janine Araujo, Fabricio G. Menezes, Heloiza F. O. Silva, Davi S. Vieira, Sergio R. B. Silva, Adailton J. Bortoluzzi, Celso Sant'Anna, Mateus Eugenio, Jannyely M. Neri, Luiz H. S. Gasparotto
NEW JOURNAL OF CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
A. Prabakaran, Amit Alexander
Summary: The molecular interactions and mucoadhesive nature of chitosan-coated liposomes with mucin are crucial for the development of an effective drug delivery system. The positively charged SA-CH-LPs showed stronger interaction and better mucoadhesive properties compared to negatively charged SALPs, thereby improving drug retention in the nasal cavity and enhancing therapeutic efficacy.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Maryam Noei-Khesht Masjedi, Esmaeil Sadroddiny, Jafar Ai, Saeed Balalaie, Yazdan Asgari
Summary: This study discovered an effective strategy for cargo sorting within exosomes by incorporating an appropriate cleavage site, providing further insight into the potential of exosomes as nano-shuttles bearing therapeutic biomolecules.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Pei -Gee Yap, Chee-Yuen Gan
Summary: This study collected the sequences of 128 tyrosinase inhibitory peptides and analyzed their hydrophobicity/hydrophilicity properties and amino acid profiles. Molecular docking analysis was used to investigate the binding interactions between peptides and tyrosinase. The study found that hydrophobic and/or polar neutral properties facilitate or stabilize peptide binding with tyrosinase, and short peptides with cysteine and tyrosine tend to bind to the active site of tyrosinase. These findings provide detailed explanations for the relationship between peptide/amino acid structures and tyrosinase inhibition, as well as potential anti-melanogenesis mechanisms for peptide-based treatments against skin hyperpigmentation.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ye Yang, Hai-Lian Chen, Su Fang Wu, Wei Bao
Summary: The study found that CHMP4B and VPS4A play an important role in reversing GSDMD-mediated pyroptosis by facilitating cell membrane remodeling in endometrial carcinoma.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aya Al Othman, Dmitry Bagrov, Julian M. Rozenberg, Olga Glazova, Gleb Skryabin, Elena Tchevkina, Alexandre Mezentsev, Mikhail Durymanov
Summary: Arc protein is found in glutamatergic neurons of vertebrates and can be transferred between neurons in extracellular vesicles (EVs). In glioma cells, Arc protein is also present in EVs and can facilitate the transfer of mRNA, potentially contributing to tumor progression and affecting synaptic plasticity in cancer patients.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Nan Zhang, Meng-yu Shen, Qing-li Meng, Hao-ping Sun, Fang-yi Fan, Hai Yi, Yong-jian Yang
Summary: In this study, it was demonstrated for the first time that FAT1 inhibited AML proliferation by reducing autophagy level. FAT1 achieved this by decreasing the expression of ATG4B, which is related to autophagy. Mechanistically, FAT1 decreased the levels of phosphorylated and intranuclear smad2/3, thus decreasing the activity of the ATG4B gene promoter. It was also found that FAT1 competitively bound to TGF-beta R II, leading to reduced phosphorylation of TGF-beta R I and smad2/3. Knockdown of FAT1 promoted AML autophagy and proliferation in vivo.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Oleh Demianchuk, Myroslava Vatashchuk, Dmytro Gospodaryov, Viktoria Hurza, Marian Ivanochko, Vitalii Derkachov, Vladyslav Berezovskyi, Oleh Lushchak, Kenneth B. Storey, Maria Bayliak, Volodymyr I. Lushchak
Summary: This study investigated the effects of a high-fat high-fructose diet (HFFD) on the behavior, energy metabolism, and oxidative stress markers in the cerebral cortex of mice. The results showed that HFFD stimulated locomotion and defecation, while an AKG-supplemented diet had a tendency to promote anxiety-like behavior. Additionally, there were significant differences in glutathione-dependent detoxification and processes related to autophagy between the two diets.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Yusaku Chukai, Ginga Ito, Yasuo Miki, Koichi Wakabayashi, Ken Itoh, Eriko Sugano, Hiroshi Tomita, Tomokazu Fukuda, Taku Ozaki
Summary: The study found that mitochondrial calpain-5 plays an important role in the occurrence and development of ischemia-reperfusion injury and is expressed in the human and mouse brains. Targeting the expression or activity of mitochondrial calpain-5 may have significant implications for suppressing inflammation during I/R injuries such as cerebrovascular diseases.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aline Dias da Purificaca, Victor Debbas, Leonardo Yuji Tanaka, Gabriele Veronica de Mello Gabriel, Joao Wosniak Junior, Tiphany Coralie De Bessa, Sheila Garcia-Rosa, Francisco Rafael Martins Laurindo, Percillia Victoria Santos Oliveira
Summary: The ER transmembrane chaperones DNAJB12 and DNAJB14 play important roles in protein folding and ER stress response. They are regulated by thiol redox processes and are involved in ER protein reflux.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ekaterina O. Bryanskaya, Andrey Y. Vinokurov, Angelina I. Dolgikh, Andrey Dunaev, Plamena R. Angelova, Andrey Y. Abramov
Summary: FAD autofluorescence in cells can assess enzymatic activity, and its intensity variations may be related to different cell types and tissues. High levels of FAD autofluorescence can indicate cell pathology and potentially predict the occurrence of apoptosis and necrosis.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Rumei Luan, Manyu Luo, Dongyan Ding, Xin Su, Junling Yang
Summary: Zinc deficiency can worsen obesity-related lung damage, and Nrf2 activation is one of the important mechanisms of this protective effect. Regulating zinc homeostasis can contribute to the prevention and treatment of obesity-related lung injury.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)