Article
Chemistry, Multidisciplinary
Fabian B. H. Rehm, Tristan J. Tyler, Simon J. de Veer, David J. Craik, Thomas Durek
Summary: This study reports an engineered enzyme that accepts various nucleophile substrate mimetics, especially when a method to selectively inhibit the reactivity of byproducts is employed. In addition, C-terminal Leu-ethylenediamine motifs are identified as bona fide mimetics of native N-terminal sequences, enabling transpeptidase-catalyzed C-to-C ligations. This work significantly expands the synthetic scope of enzyme-catalyzed protein transpeptidation reactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Barindra Sana, Ding Ke, Eunice Hui Yen Li, Timothy Ho, Jayasree Seayad, Hung A. Duong, Farid J. Ghadessy
Summary: Halogenation of peptides can be achieved through selective halogenase enzymes, providing potential for post-synthesis/expression halogenation. The C-terminal (G/S)GW motif is identified as the preferred substrate. Improved halogenation of the (G/S)GW motif can be achieved through rational design of PyrH halogenase mutants.
Review
Biotechnology & Applied Microbiology
Zhenzhen Zhang, Zitong Zhao, Kunlun Huang, Zhihong Liang
Summary: Enzymes have promising applications in various industries due to their high efficiency, specificity, and environmentally friendly properties. However, their application range is limited due to the complexity of raw materials. This review discusses strategies for obtaining acid-resistant enzymes and their industrial applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Fabian B. H. Rehm, Tristan J. Tyler, Kuok Yap, Thomas Durek, David J. Craik
Summary: The use of enzymes, specifically asparaginyl endopeptidases (AEPs), for site-specific modification of proteins/peptides has become a popular method in studying protein/peptide functions or generating therapeutic conjugates. A novel approach using metal-complexation-based strategy has been developed to shift the AEP-catalyzed transpeptidation equilibrium towards product formation, allowing efficient peptide/protein labeling and enhancing protein-protein ligation. This method shows promise in facilitating the formation of transpeptidation products that are typically challenging to attain.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Abigail Roldan-Salgado, Liya Muslinkina, Sergei Pletnev, Nadya Pletneva, Vladimir Pletnev, Paul Gaytan
Summary: An engineered violet fluorescent protein from the lancelet Branchiostoma floridae (bfVFP) is described, which is the first example of a GFP-like fluorescent protein with a stable chromophore lacking an imidazolinone ring. bfVFP has the simplest chromophore reported in fluorescent proteins and could be used for multicolor experiments and expanding the excitation range of available FP biomarkers.
Article
Chemistry, Physical
Franziska Stegemann, Martin Grininger
Summary: This study investigates the mechanisms of FASs and PKSs in synthesizing important products and the substrate selectivity and enzymatic properties of different ATs. Findings reveal that ATs in PKS systems occurring in bacteria are slower than ATs in mammalian FASs, reflecting the respective purposes and metabolic contexts within the organism.
Review
Biotechnology & Applied Microbiology
Jingjie Jiang, Guangyu Yang, Fuqiang Ma
Summary: Fluorescence-activated droplet sorting (FADS) is a powerful tool for high-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) play a key role in developing new FADS methods by linking analyte properties to fluorescence signals. This review highlights recent advances in FCS for different analyte types and discusses successful FADS applications.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Computer Science, Information Systems
Ran Wang, Suhe Ye, Ke Li, Sam Kwong
Summary: This paper introduces a new Bayesian network-based Classifier chain (CC) method, which describes label dependencies using conditional entropy, optimizes the BN structure and derives label order through topological sorting, demonstrating its feasibility and effectiveness.
INFORMATION SCIENCES
(2021)
Article
Biochemical Research Methods
Sadat Hasan, Maximilian E. Blaha, Sebastian K. Piendl, Anish Das, David Geissler, Detlev Belder
Summary: This research introduces a label-free detection technique using time-resolved two-photon excitation (TPE) fluorescence detection at 532 nm in droplet microfluidics. A polydimethylsiloxane-fused silica (FS) hybrid chip was developed to provide high optical transparency in the deep-UV range and suitable surface properties for droplet microfluidics. The system incorporating a 532-nm picosecond laser, time-correlated single-photon counting (TCSPC), and a chip-integrated dielectrophoretic pulsed actuator was utilized to sort droplets containing specific compounds and screen yeast cells based on their protein autofluorescence.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Nadim Massad, Scott Banta
Summary: There is a growing interest in upgrading inexpensive and abundant C-1 feedstocks to higher carbon products. Linear carbon ligation routes are favored due to their simplicity and potential for high carbon efficiencies. This study provides a theoretical framework for comparing the performance of FLS enzymes, which is crucial for designing and implementing novel carbon ligation pathways.
BIOTECHNOLOGY AND BIOENGINEERING
(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
Biochemistry & Molecular Biology
Nardiah Rizwana Jaafar, Nashriq Jailani, Roshanida A. Rahman, Ebru Toksoy Oner, Abdul Munir Abdul Murad, Rosli Md Illias
Summary: A combined strategy of computational, protein engineering and cross-linked enzyme aggregates (CLEAs) approaches was used to investigate the preferred amino acids and orientation of the cross-linker in constructing stable and efficient biocatalyst. The study found that amino acids on the enzyme's surface play a crucial role in the construction of highly stable, efficient and recyclable CLEAs.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Biotechnology & Applied Microbiology
Zaigao Tan, Jian Li, Jin Hou, Ramon Gonzalez
Summary: Metabolic engineering manipulates catalytic and regulatory elements to improve specific cellular functions, particularly the synthesis of interesting chemicals. While naturally occurring pathways are valuable resources, they are often inefficient and have inherent drawbacks. Designing artificial pathways provides a promising alternative, but requires a comprehensive understanding of physical, chemical, and biological principles. However, these artificial pathways often suffer from low efficiencies, limiting their applications in host cells.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Food Science & Technology
Wanling Cui, Guodong Hu, Enguang Lv, Chonghui Li, Zhenxing Wang, Qiang Li, Zhaohong Qian, Jihua Wang, Shicai Xu, Rui Wang
Summary: A label-free and enzyme-free fluorescent aptasensor was developed for quantifying kanamycin in milk, with high sensitivity and selectivity. It has the potential for wide application in ensuring food safety.
Article
Multidisciplinary Sciences
Jennifer Park, Michael B. Cleary, Danyang Li, Joseph A. Mattocks, Jiansong Xu, Huan Wang, Somshuvra Mukhopadhyay, Eric M. Gale, Joseph A. Cotruvo Jr
Summary: The design of selective metal-binding sites is challenging in both small-molecule and macromolecular chemistry. In this study, researchers successfully engineered lanmodulin into genetically encoded fluorescent sensors for selective detection of MnII. These sensors have potential applications in studying photosynthesis, host-pathogen interactions, and neurobiology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Karla Ilic Durdic, Raluca Ostafe, Olivera Prodanovic, Aleksandra Durdevic Delmas, Nikolina Popovic, Rainer Fischer, Stefan Schillberg, Radivoje Prodanovic
Summary: Enzymatic degradation of azo dyes is a promising alternative to traditional chemical and physical remediation methods. By conducting protein engineering on lignin peroxidase, mutants with improved efficiency in breaking down azo dyes were selected. Cell wall fragments coated with mutant LiP enzymes maintained high dye degradation activity in multiple reaction cycles.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Nevena Pantic, Radivoje Prodanovic, Karla Ilic Durdic, Natalija Polovic, Milica Spasojevic, Olivera Prodanovic
Summary: Removal of phenolic compounds from water is a major concern, with horseradish peroxidase being a commonly studied biocatalyst for this purpose. Immobilization of HRP on tyramine-alginate microbeads showed promising results in terms of phenol removal efficiency and reusability. Internal generation of hydrogen peroxide using glucose and glucose oxidase enhanced the phenol removal process with immobilized HRP.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Biochemistry & Molecular Biology
Nikolina Popovic, Dunja Przulj, Maja Mladenovic, Olivera Prodanovic, Selin Ece, Karla Ilic Durdic, Raluca Ostafe, Rainer Fischer, Radivoje Prodanovic
Summary: Researchers focused on removing toxic textile dyes from the environment and wastewaters by applying immobilized enzymes. Laccases, with their wide substrate specificity, were expressed on the surface of yeast cells for degradation of different dye types. By modifying alginate and dopamine, cell wall laccase was effectively immobilized within hydrogel beads, showing increased activity and efficiency in dye decolorization.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Multidisciplinary
Milan Sencanski, Vladimir Perovic, Jelena Milicevic, Tamara Todorovic, Radivoje Prodanovic, Veljko Veljkovic, Slobodan Paessler, Sanja Glisic
Summary: Finding effective drugs to prevent or treat COVID-19 is of highest priority in the current pandemic. In this study, we used in silico virtual screening to identify 44 potential SARS-CoV-2 PLpro inhibitors, which should be further tested experimentally.
Article
Engineering, Environmental
Nevena Pantic, Milica Spasojevic, Zeljko Stojanovic, Dorde Veljovic, Jugoslav Krstic, Ana Marija Balaz, Radivoje Prodanovic, Olivera Prodanovic
Summary: Novel macroporous copolymers with mean pore size diameters ranging from 150 to 310 nm were synthesized and modified with ethylenediamine for horseradish peroxidase (HRP) immobilization. The activity and stability of immobilized HRP were greatly affected by the pore size of the carrier, and the highest specific activities were obtained for carriers with pore size diameters of 234 and 297 nm. HRP immobilized on the copolymer with a pore size of 234 nm showed higher activities than the native enzyme and exhibited good stability.
JOURNAL OF POLYMERS AND THE ENVIRONMENT
(2022)
Article
Chemistry, Physical
Gordana Kovacevic, Reyadh Gomah Amar Elgahwash, Marija Blazic, Nevena Pantic, Olivera Prodanovic, Ana Marija Balaz, Radivoje Prodanovic
Summary: This study focuses on utilizing Saccharomyces cerevisiae cell walls as a platform for creating biocatalyst cells for sucrose conversion. By crosslinking with invertase and catalase, and expressing glucose oxidase, high yield conversion of sucrose to gluconic acid can be achieved. The use of a mutant glucose oxidase showed higher productivity, and under optimized conditions, almost 100% conversion of glucose to gluconic acid was achieved.
MOLECULAR CATALYSIS
(2022)
Article
Biochemical Research Methods
Lidija Filipovic, Milica Spasojevic, Radivoje Prodanovic, Aleksandra Korac, Suzana Matijasevic, Goran Brajuskovic, Ario de Marco, Milica Popovic
Summary: The purification of extracellular vesicles (EV) is crucial for the study of physiological and pathological processes. Current methods are time-consuming and low-yield. This study presents an immuno-capture based chromatography system for efficient purification of EVs from different biological samples. The purified EVs were confirmed to be exosomes based on their morphological features and biomarker presence.
Article
Biochemistry & Molecular Biology
Nevena Kalicanin, Gordana Kovacevic, Milica Spasojevic, Olivera Prodanovic, Suzana Jovanovic-Santa, Dusan Skoric, Dejan Opsenica, Radivoje Prodanovic
Summary: The aim of this research was to improve the operational stability and enable the reusability of omega-transaminase for synthesis of new enantiopure chiral amines of steroids. The enzyme was immobilized on a methacrylate-based carrier and showed higher stability compared to the soluble form in organic solvents. The immobilized enzyme also retained high activity after multiple synthesis cycles.
PROCESS BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sara Protic, Nevena Kalicanin, Milan Sencanski, Olivera Prodanovic, Jelena Milicevic, Vladimir Perovic, Slobodan Paessler, Radivoje Prodanovic, Sanja Glisic
Summary: Finding an effective drug to prevent or treat COVID-19 is crucial. This study used a virtual screening protocol and identified gramicidin D as a potential PLpro inhibitor. It was found to be active against the target protein in vitro. These findings are important for discovering efficient and affordable therapies for COVID-19.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Marija D. Stanisic, Nikolina Popovic Kokar, Predrag Ristic, Ana Marija Balaz, Milos Ognjanovic, Veljko R. Dokic, Radivoje Prodanovic, Tamara R. Todorovic
Summary: This article investigates the isoenzyme composition of commercial HRP and the influence of the carbohydrate component of the protein molecule on biomineralization. The findings suggest that purified HRP yields enzyme@ZIF-8 biocomposites with higher activity, while oxidation of the carbohydrate component of both commercial HRP and purified HRP-C produces biocomposites with very high activity in acetate buffer, without degradation of the ZIF-8 structure. Therefore, the impact of isoenzyme composition and carbohydrate component of the protein molecule should be considered when studying the biomineralization process.
Article
Chemistry, Multidisciplinary
R. G. Rosenthal, X. Diana Zhang, K. Ilic Durdic, J. J. Collins, D. A. Weitz
Summary: Enzymes are catalysts that have high specificity and are used to improve drugs and industrial processes. Optimizing naturally occurring enzymes usually involves a labor- and capital-intensive process called directed evolution. We introduce a continuous evolution platform that enables the controlled exploration of fitness landscapes to evolve enzymes at a high throughput. This platform relies on direct measurement of enzymatic activity and uses drop-based microfluidics technology, reducing the need for human intervention.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Reyadh Gomah Amar Elgahwash, Marija Blazic, Ana Marija Balaz, Radivoje Prodanovic
Summary: This study used CDH mutants derived from Phanerochaete chrysosporium produced in Pichia pastoris to determine the production rate of LBA with varying number of redox mediators. The highest specific productivity was observed for the triple mutant CDH, with hydroquinone showing the highest specific productivity.
BIOCATALYSIS AND BIOTRANSFORMATION
(2023)
Article
Polymer Science
Minjun Chen, Conner Thacker, Ksenija R. Kumric, Radivoje Prodanovic, Guido Bolognesi, Goran T. Vladisavljevic
Summary: Monodispersed PEGDA/AA microgels with a controllable negative charge and macroporous internal structure were produced using a Lego-inspired droplet microfluidic device. The microgels exhibited tunable surface charge and macroporosity, thereby showing improved adsorption properties towards organic dyes and high removal capacity of Cu(II) ions.
Article
Chemistry, Multidisciplinary
Gheorghita Menghiu, Radivoje Prodanovic, Marija Blazic, Manuela Mincea, Cristina Moraru, Vasile Ostafe
Summary: Chitinases are important enzymes that can be used to extract valuable derivatives from chitin wastes. In this study, the chiA gene was successfully cloned and expressed in Saccharomyces cerevisiae INVSc1, confirming the production of recombinant enzyme. The optimal expression time was identified as 24 hours, and the purified enzyme showed a heterogeneous diffuse band on SDS-PAGE.
JOURNAL OF THE SERBIAN CHEMICAL SOCIETY
(2022)
