Article
Biotechnology & Applied Microbiology
Shangshang Sun, Chun You
Summary: Disaccharide phosphorylases (DSPs) are carbohydrate-active enzymes with the potential to convert common table sugar into products with attractive properties. Most DSPs have strict stereo- and regiospecificities, making them useful in synthesizing specific disaccharides. Protein engineering of DSPs is currently being pursued in various laboratories to create a toolbox of new catalysts for glycoside synthesis.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michela Cantiello, Monica Carletti, Mery Giantin, Giulia Gardini, Francesca Capolongo, Paolo Cascio, Marianna Pauletto, Flavia Girolami, Mauro Dacasto, Carlo Nebbia
Summary: This study provides a comprehensive characterization of phenobarbital's (PB) effects on drug-metabolizing enzyme (DME) catalytic activities in cattle liver. The findings show that PB increases the protein amounts and enzyme activities of certain target enzymes, but has contradictory effects on others. The study also reveals an increase in 26S proteasome activity, suggesting a potential role in cattle DME regulation. The results further confirm species differences in DME expression and activity between cattle, humans, and rodents.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Shinya Ariyasu, Kai Yonemura, Chie Kasai, Yuichiro Aiba, Hiroki Onoda, Yuma Shisaka, Hiroshi Sugimoto, Takehiko Tosha, Minoru Kubo, Takashi Kamachi, Kazunari Yoshizawa, Osami Shoji
Summary: This study reports the catalytic oxidation of methane to methanol by wild-type P450BM3 without mutagenesis. The findings have significant implications for the development of biological methane oxidation technology.
Article
Chemistry, Physical
Stefan R. Marsden, Luuk Mestrom, Hein J. Wijma, Sander J. Noordam, Duncan G. G. McMillan, Ulf Hanefeld
Summary: This passage discusses the synthesis and epimerization of diastereomers under thermodynamic and kinetic conditions, highlighting the influence of reaction conditions on product formation and the less deterministic role of the catalyst in determining the selective formation of thermodynamic and kinetic products.
Article
Chemistry, Multidisciplinary
Jingru Lu, Sofia Donnecke, Irina Paci, David C. Leitch
Summary: Making accurate predictions of chemical reactivity based on molecular structure is still a challenging task. This article presents an approach to reactivity prediction for catalytic reactions using quantitative structure-reactivity models. The authors demonstrate this approach with a mechanistically based model for a key step in catalytic processes.
Article
Chemistry, Physical
Binhao Wang, Cuiping You, Guochao Xu, Ye Ni
Summary: This study identifies two self-sufficient P450 enzyme variants with high catalytic activity and selectivity, reveals the catalytic mechanisms among different backbones through molecular simulation, and provides useful information for exploring unnatural reactions.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Agricultural Engineering
Misa Mojca Cajnko, Jost Oblak, Miha Grilc, Blaz Likozar
Summary: Enzymes play a crucial role in lignin valorization, with different enzymes involved in various elementary reaction mechanisms. Degradation of lignin depends on enzyme activity and the interaction with proteins in ways that target specific covalent bonds in lignin. Various factors influence enzymatic activity, which must be taken into consideration for optimal functionality and synthesis yields.
BIORESOURCE TECHNOLOGY
(2021)
Review
Chemistry, Applied
Angel M. Villalba-Rodriguez, Lidia Yaritza Martinez-Zamudio, Saul Antonio Hernandez Martinez, Jesus Alfredo Rodriguez-Hernandez, Elda M. Melchor-Martinez, Elda A. Flores-Contreras, Reyna Berenice Gonzalez-Gonzalez, Roberto Parra-Saldivar
Summary: Nanomaterials possess unique properties such as special geometries, higher surface area, and special mechanical, optical, and physicochemical properties, making them important contributors to the development of various technological and industrial sectors. They have increasing interest in biomedical research, particularly in chronic inflammations, disease detection, drug delivery, and infections treatment, where their catalytic applications as nanozymes or nanobiocatalysts play a crucial role. This review discusses the construction of nanozymes and nanobiocatalysts using different forms of nanomaterials, including carbon-based, metal-based, and polymer-based nanocomposites, and examines successful examples of their employment in biomedical research. The analysis of the role of nanomaterials in catalytic applications provides insights into future research directions and practical developments in the field.
TOPICS IN CATALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Andrew J. O'Donnell, Ruiqi Huang, Jessica J. Barboline, Todd J. Barkman
Summary: Resurrected ancient enzymes of the caffeine synthase shed light on how ancestral biosynthetic catalytic capabilities lead to the convergent evolution of similar biochemical pathways. It appears that modern-day pathways likely originated from ancestral pathways with different inferred flux, and the modern enzymes independently evolved via gene duplication with convergent catalytic characteristics differentiating multiple ancestral activities through mutations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Chemistry, Physical
Richiro Ushimaru, Ikuro Abe
Summary: This review summarizes recent discoveries that have significantly expanded our understanding of unusual nonheme iron enzyme catalysis in natural product biosynthesis.
Article
Biochemical Research Methods
Antonio J. M. Ribeiro, Ioannis G. Riziotis, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton
Summary: The rich literature on enzyme reaction mechanisms can serve as the foundation for new knowledge-based approaches to investigate enzyme mechanisms. In this study, a tool called EzMechanism is presented, which can automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction based on catalytic rules compiled from a database of enzyme mechanisms. EzMechanism facilitates and improves the generation of hypotheses by considering relevant information derived from literature on both related and unrelated enzymes.
Article
Agronomy
Qinqin Wang, Changhui Rui, Li Wang, Shahzad Ali Nahiyoon, Weiling Huang, Junshu Zhu, Xuejiao Ji, Qingjie Yang, Huizhu Yuan, Li Cui
Summary: The study evaluated the sensitivity of five field populations of cotton bollworm to several insecticides and investigated the biochemical and molecular mechanisms of field-evolved resistance in H. armigera. The results showed moderate resistance in these populations to certain insecticides, with specific correlations between resistance ratio and enzyme activity observed. Additionally, certain genes were found to be overexpressed in the resistant populations, indicating a potential link to resistance development.
PEST MANAGEMENT SCIENCE
(2021)
Article
Microbiology
Adeline Pichard-Kostuch, Violette Da Cunha, Jacques Oberto, Ludovic Sauguet, Tamara Basta
Summary: The TsaC/Sua5 family of enzymes catalyzes the initial step in the synthesis of a crucial tRNA modification. While TsaC is a single domain protein, Sua5 contains an additional domain of unclear function. The evolutionary path and distribution of these enzymes are complex, involving losses, transfers, and adaptations.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Anming Xu, Xiaoxiao Zhang, Shilei Wu, Ning Xu, Yan Huang, Xin Yan, Jie Zhou, Zhongli Cui, Weiliang Dong
Summary: Treatment of environmental pollution using microorganisms and their enzymes is an innovative and efficient method to mitigate various pollutants. Further research and understanding of the catalytic mechanisms of these degrading enzymes is necessary to enhance degradation efficiency.
Review
Food Science & Technology
Blanca Abril, Ricard Bou, Jose V. Garcia-Perez, Jose Benedito
Summary: Meat processing involves various enzymatic reactions that determine the quality of the final product. Enzymes such as glycolysis, proteolysis, and lipolysis play a crucial role in the conversion of muscle into meat. Additionally, exogenous enzymes are used in the meat industry for different purposes. Emerging technologies like ultrasound, electric fields, high-pressure processing, and supercritical CO2 have been employed to enhance enzymatic reactions in food applications.
Article
Chemistry, Physical
Daniel J. Fowles, David S. Palmer, Rui Guo, Sarah L. Price, John B. O. Mitchell
Summary: The research demonstrates that physics-based calculations of intrinsic aqueous solubility can rival machine learning predictions. By improving the sublimation free-energy model through crystal phonon mode calculations and using model-potential-based Psi(mol) method, accurate estimates of sublimation free energy are obtained, leading to solubilities comparable to both experiment and informatics predictions. This approach shows flexibility and can extend to applications not covered by informatics methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Medicinal
Benjamin J. Read, Gemma Fisher, Oliver L. R. Wissett, Teresa F. G. Machado, John Nicholson, John B. O. Mitchell, Rafael G. da Silva
Summary: ATP phosphoribosyltransferase (ATPPRT) plays a crucial role in histidine biosynthesis in bacteria, and its inhibition could be a promising strategy for specific antibiotic development. Studying the mechanisms of ATPPRT and related proteins like HisZ in Acinetobacter baumannii lays the foundation for inhibitor design.
ACS INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
E. A. Videla Rodriguez, John B. O. Mitchell, V. Anne Smith
Summary: Differences in gene expression patterns in poultry have been used to study the effects of stress conditions. This study aimed to identify a small set of stress-related genes in chickens using bioinformatic analysis and Bayesian networks. Several genes were identified and their biological functions suggest their potential as stress biomarkers.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Emiliano A. Videla Rodriguez, Fabio Pertille, Carlos Guerrero-Bosagna, John B. O. Mitchell, Per Jensen, V. Anne Smith
Summary: This study explores the relationships between epigenetic features and a stressful condition in chickens using a Bayesian network approach. Differentially methylated regions (DMRs) were identified and analyzed, revealing functional relationships and epigenetic features associated with the stressful condition. The DMRs interacting with the stress condition may serve as potential biomarkers of stress in poultry species.
BMC BIOINFORMATICS
(2022)
Article
Health Care Sciences & Services
Inti Pedroso, Shreyas Vivek Kumbhare, Bharat Joshi, Santosh K. Saravanan, Dattatray Suresh Mongad, Simitha Singh-Rambiritch, Tejaswini Uday, Karthik Marimuthu Muthukumar, Carmel Irudayanathan, Chandana Reddy-Sinha, Parambir S. Dulai, Ranjan Sinha, Daniel Eduardo Almonacid
Summary: Neuropsychiatric diseases and obesity are associated with genetic, lifestyle, and gut microbiome factors. This study aimed to identify the genetic and gut microbiome factors that explain individual differences in mental health improvement after a dietary and lifestyle intervention for weight loss. The results showed significant correlations between genetic scores and mental health symptoms, as well as gut microbial functions and mental health improvement.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Eugene Shrimpton-Phoenix, John B. O. Mitchell, Michael Buehl
Summary: Is-PETase is an enzyme capable of degrading PET, and its low energy barriers for PET degradation suggest its potential application value.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Pharmacology & Pharmacy
Shreyas V. Kumbhare, Inti Pedroso, Juan A. Ugalde, Valeria Marquez-Miranda, Ranjan Sinha, Daniel E. Almonacid
Summary: This review discusses the evolving understanding of drug-microbe relationships, highlighting the potential of microbes as drugs or targets, and covering various aspects such as drugs for targeting gut pathogens, probiotics, drugs derived from microbes, and other types of drug-microbe interactions. It also provides insights into future translational research, particularly in the field of efficient companion diagnostics in pharmaceutical interventions.
DRUG DISCOVERY TODAY
(2023)
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: This paper examines the emergent structures of random networks that have undergone a finite number of bond percolation processes. Two types of sequential branching processes, competitive and collaborative, are defined and their behavior and topological properties are investigated using generating functions. The model can be applied to explain seasonal disease spreading.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: This paper investigates the correlations among degrees of vertices in random graphs, particularly when clustering is present. By defining a joint-degree correlation function and using clustered configuration model networks, the organization among nearest-neighbor subgraphs in random graphs is studied in detail. Additionally, a novel edge-disjoint clique decomposition algorithm is introduced, and the correlations between subgraphs in empirical networks are investigated.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: This paper introduces a description of the equilibrium state of a bond percolation process on random graphs using the exact method of generating functions. The study examines the expected size of the giant connected component in two sequential bond percolation processes and interactions between diseases. The emergence of the second strain is highly dependent on the details of coupling between the strains, with contact clustering impacting outbreak size.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Christopher Jefferson, Simon Dobson
Summary: This study presents exact solutions for the size of the giant connected component in complex networks and locates the percolation threshold of the model. The results derived here are expected to be useful in various fields such as graph theory, epidemiology, percolation, and fragmentation theory. Additionally, the Erdos-Gallai theorem is examined as a necessary condition for the graphicality of configuration model networks consisting of clique subgraphs.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: This study explored the impact of clustering on the spread of pathogens in social networks, revealing that clustering reduces the coexistence threshold and outbreak size of the second strain while increasing its ability to spread.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: Coinfection refers to the process where a host infected with one pathogen is later infected with a second pathogen. The social contact patterns greatly influence the dynamics of emergent diseases. Studies show that the effects of clustering on coinfection levels are determined by the details of the contact topology.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: In this paper, percolation theory is used to analyze clustered networks with simple cycles and cliques of any order, providing solutions for critical properties and giant component size of Poisson and power-law networks using the generating function formulation. The study finds that networks with larger simple cycles behave more like trees, while clustering with larger cliques deviates from treelike solutions, influenced by degree-assortativity.
Article
Physics, Fluids & Plasmas
Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson
Summary: This paper extends analytical solutions to percolation properties of random networks with homogeneous clustering to networks with non-degree equivalent clusters, including multilayer networks. The method presented allows for investigating properties of random complex networks with arbitrary clustering, beyond the traditional configuration model and generating function formulation.