Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biochemistry & Molecular Biology
Saurabh Rajendra Nirantar
Summary: Enzymes play a crucial role in biotransformations, however, they often need to be engineered for better performance in biotechnological applications. Researchers have developed a variety of wet-lab methods over the years to achieve this goal, which are examined in this review.
Article
Chemistry, Multidisciplinary
Guangcai Xu, Andreas Kunzendorf, Michele Crotti, Henriette J. Rozeboom, Andy-Mark W. H. Thunnissen, Gerrit J. Poelarends
Summary: This study used gene duplication and fusion strategy to evolve a promiscuous homohexameric enzyme into an efficient catalyst with high catalytic activity for enantioselective reactions. Through directed evolution and structural analysis, the asymmetric features of the protein were revealed, suggesting that this strategy may become an important technique in enzyme engineering.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemical Research Methods
Aitor Manteca, Alejandra Gadea, David Van Assche, Pauline Cossard, Melanie Gillard-Bocquet, Thomas Beneyton, C. Axel Innis, Jean-Christophe Baret
Summary: Optimizing the properties of biological molecules is crucial for various industrial and medical applications. Directed evolution is a powerful technique for modifying biomolecules by mimicking natural evolution. Droplet-based microfluidic systems offer a high-throughput solution for enhancing efficiency and overcoming screening limitations.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Fereniki Perperopoulou, Maria Fragoulaki, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Summary: This study involved DNA recombination of tau class GmGSTUs leading to the identification of a variant, GmGSTsf, with enhanced catalytic activity towards alachlor. A key mutation (Ile69Val) at the subunit interface was found to be responsible for the altered catalytic properties. The resulting optical biosensor showed a linear concentration range for alachlor from 30-300 μM. The research provides a method for generating novel enzymes for eco-efficient analytical technologies and highlights the use of protein symmetry for enzyme design.
Article
Biochemistry & Molecular Biology
Mohammed Hamed Alqarni, Ahmed Ibrahim Foudah, Magdy Mohamed Muharram, Aftab Alam, Nikolaos E. Labrou
Summary: The study found that myricetin can serve as a potential GST inhibitor, effectively inhibiting the activity of human glutathione transferase A1-1 and could be further developed as a natural, safe, and effective anti-cancer chemotherapy drug targeting GST.
Article
Biochemistry & Molecular Biology
Mohammed Hamed Alqarni, Ahmed Ibrahim Foudah, Magdy Mohamed Muharram, Nikolaos E. Labrou
Summary: This study investigated the interaction between dyes and hGSTA1-1, finding that PBMX-R displayed higher affinity and specifically inactivated the enzyme with negative cooperativity. It was also found to be a competitive inhibitor of glutathione and a mixed-type inhibitor of CDNB, suggesting it could be a useful probe for assessing the drugability of the enzyme in future drug-design efforts.
Article
Biochemistry & Molecular Biology
Oleksii Kupreienko, Fotini Pouliou, Konstantinos Konstandinidis, Irene Axarli, Eleni Douni, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Summary: Multidrug resistance poses a significant barrier to effective anticancer therapies. This study identified iprodione as a potential lead compound with high inhibitory potency against the isoenzyme GSTP1-1 from Mus musculus. The findings shed light on the inhibition mechanism of MmGSTP1-1 and provide a new compound for future drug development.
Article
Biochemistry & Molecular Biology
Panagiota Pantiora, Veronika Furlan, Dimitris Matiadis, Barbara Mavroidi, Fereniki Perperopoulou, Anastassios C. Papageorgiou, Marina Sagnou, Urban Bren, Maria Pelecanou, Nikolaos E. Labrou
Summary: This study investigated the inhibitory effects of two curcuminoids and eleven monocarbonyl curcumin analogues against human glutathione transferase P1-1 (hGSTP1-1). The results showed that Demethoxycurcumin (Curcumin II) and three monocarbonyl curcumin analogues exhibited the highest inhibitory activity, with IC50 values ranging between 5.45 and 37.72 μM. The most potent inhibitors functioned as non-competitive/mixed-type inhibitors. Structural analysis revealed that the strongest hGSTP1-1 inhibitor, DM96, formed hydrophobic interactions and hydrogen bonds with specific residues, contributing to its superior inhibitory activity. The study highlights the potential of DM96 as a strong hGSTP1-1 inhibitor and its relevance for cancer chemosensitization.
Article
Chemistry, Multidisciplinary
Yi Shuang Wang, Wan Zheng, Nan Jiang, Yun Xia Jin, Zi Kang Meng, Meng Xin Sun, Yu Liang Zong, Tong Xu, Jiapeng Zhu, Ren Xiang Tan
Summary: This study discovered a new class of enzymes called ChaP that can catalyze the deconstruction of intradiol-like o-quinones and release CO2. Experimental evidence showed that by mutating and replacing specific residues, the enzyme's reaction trajectory and regioselectivity can be altered. The results of this study highlight the catalytic versatility and enzymatic plasticity of VOC enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Tian Yang, Zhixia Ye, Michael D. Lynch
Summary: Enzyme evolution is important in biotechnology and synthetic biology but requires multiple rounds of screening to identify optimal mutant sequences. This is due to the scarcity of the fitness landscape caused by epistatic mutations. The approach proposed in this study incorporates diverse substrate analogues in the screening process to accurately identify epistatic mutant residues without testing the entire combinatorial search space.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Emily Radley, John Davidson, Jake Foster, Richard Obexer, Elizabeth L. Bell, Anthony P. Green
Summary: The development and implementation of engineered enzymes and biocatalytic technologies are crucial for achieving sustainable development goals and protecting the environment. By using directed evolution and other methods, engineered enzymes can improve the sustainability of processes such as carbon capture and utilization, bioremediation, plastic deconstruction, and renewable feedstock generation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Agriculture, Multidisciplinary
Li-Wei Meng, Meng-Ling Chen, Guo-Rui Yuan, Li-Sha Zheng, Wei Dou, Yu Peng, Shu-Xia Zhang, Jin-Jun Wang
Summary: The oriental fruit fly, Bactrocera dorsalis, is a damaging insect pest that has developed resistance to various chemical insecticides. This study identified several glutathione S-transferases (GSTs) in B. dorsalis and characterized their relationships with five insecticides. It was found that an antenna-abundant BdGSTd8 responded to four different classes of insecticides. Further analysis confirmed that BdGSTd8 is primarily located in the antenna and has the ability to enhance cell viability by interacting with specific insecticides. These findings enhance our understanding of GST characteristics in B. dorsalis and their role in detoxification.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Eric J. Ma, Elina Siirola, Charles Moore, Arkadij Kummer, Markus Stoeckli, Michael Faller, Caroline Bouquet, Fabian Eggimann, Mathieu Ligibel, Dan Huynh, Geoffrey Cutler, Luca Siegrist, Richard A. Lewis, Anne-Christine Acker, Ernst Freund, Elke Koch, Markus Vogel, Holger Schlingensiepen, Edward J. Oakeley, Radka Snajdrova
Summary: This study evaluated machine-directed evolution as an enzyme engineering strategy and found that within one cycle, it yielded a library of high-activity mutants with a significantly different activity distribution compared to traditional directed evolution. Structure-guided analysis suggested that linear additivity might provide a simple explanation for the effectiveness of machine-directed evolution in accessing chiral molecules.
Article
Biochemistry & Molecular Biology
Elisavet Ioannou, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Summary: This study created a library of mutant GSTF genes through DNA shuffling, and identified enzyme variants with improved characteristics through activity screening and characterization. The structural and functional analysis of these enzyme variants revealed their involvement in crop herbicide resistance mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Toxicology
Juliana Garcia, Vera Marisa Costa, Alexandra T. P. Carvalho, Ricardo Silvestre, Jose Alberto Duarte, Daniel F. A. R. Dourado, Marcelo D. Arbo, Teresa Baltazar, Ricardo Jorge Dinis-Oliveira, Paula Baptista, Maria de Lourdes Bastos, Felix Carvalho
ARCHIVES OF TOXICOLOGY
(2015)
Article
Genetics & Heredity
Fabienne C. Fiesel, Thomas R. Caulfield, Elisabeth L. Moussaud-Lamodiere, Kotaro Ogaki, Daniel F. A. R. Dourado, Samuel C. Flores, Owen A. Ross, Wolfdieter Springer
Meeting Abstract
Toxicology
J. Garcia, V. M. Costa, A. Carvalho, R. Silvestre, A. Duarte, D. Dourado, R. Oliveira, P. Baptista, M. L. Bastos, F. Carvalho
TOXICOLOGY LETTERS
(2015)
Article
Multidisciplinary Sciences
Ravi Kiran Koripella, Mikael Holm, Daniel Dourado, Chandra Sekhar Mandava, Samuel Flores, Suparna Sanyal
SCIENTIFIC REPORTS
(2015)
Article
Chemistry, Physical
Daniel F. A. R. Dourado, Stefan Pohle, Alexandra T. P. Carvalho, Dharmendra S. Dheeman, Jill M. Caswell, Timofey Skvortsov, Iain Miskelly, Rodney T. Brown, Derek J. Quinn, Christopher C. R. Allen, Leonid Kulakov, Meilan Huang, Thomas S. Moody
Article
Multidisciplinary Sciences
Daniel F. A. R. Dourado, Samuel Coulbourn Flores
SCIENTIFIC REPORTS
(2016)
Article
Chemistry, Physical
Alexandra T. P. Carvalho, Daniel F. A. R. Dourado, Timofey Skvortsov, Miguel de Abreu, Lyndsey J. Ferguson, Derek J. Quinn, Thomas S. Moody, Meilan Huang
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Biochemistry & Molecular Biology
Masoumeh Nosrati, Sara Solbak, Olle Nordesjo, Mikael Nissbeck, Daniel F. A. R. Dourado, Ken G. Andersson, Mohammad Reza Housaindokht, John Lofblom, Anders Virtanen, U. Helena Danielson, Samuel Coulbourn Flores
PROTEIN ENGINEERING DESIGN & SELECTION
(2017)
Article
Chemistry, Physical
Alexandra T. P. Carvalho, Daniel F. A. R. Dourado, Timofey Skvortsov, Miguel de Abreu, Lyndsey J. Ferguson, Derek J. Quinn, Thomas S. Moody, Meilan Huang
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2018)
Article
Chemistry, Medicinal
A. C. Pimenta, D. F. A. R. Dourado, J. M. Martins, A. Melo, M. N. Dias Soeiro Cordeiro, R. D. Almeida, G. Morra, I. S. Moreira
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2014)
Article
Biochemical Research Methods
Juliana Garcia, Alexandra T. P. Carvalho, Daniel F. A. R. Dourado, Paula Baptista, Maria de Lourdes Bastos, Felix Carvalho
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2014)
Article
Chemistry, Physical
Daniel F. A. R. Dourado, Pedro Alexandrino Fernandes, Bengt Mannervik, Maria Joao Ramos
JOURNAL OF PHYSICAL CHEMISTRY A
(2014)
Article
Biochemistry & Molecular Biology
Daniel F. A. R. Dourado, Samuel Coulbourn Flores
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2014)
Article
Chemistry, Multidisciplinary
Daniel F. A. R. Dourado, Marcel Swart, Alexandra T. P. Carvalho
CHEMISTRY-A EUROPEAN JOURNAL
(2018)
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)