Article
Biochemistry & Molecular Biology
Florian Labourel, Etienne Rajon
Summary: Enzyme efficiency is influenced by competition for resources and undergoes directional selection up to a certain point before evolving near-neutrality. Evolutionary outcomes for enzymes vary due to differences in the evolutionary context encountered by each enzyme, with drift and effective population size playing important roles. Joint evolution of enzyme concentration and efficiency does not lead to extensive variance in outcomes, suggesting that other factors such as the kinetics of nutrient transporters, tolerance to high concentrations of metabolites, and reversibility of reactions are also significant.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Multidisciplinary
Joanna Afokai Quaye, Daniel Ouedraogo, Giovanni Gadda
Summary: The commercial food and l-amino acid industries use bioengineered d-amino acid oxidizing enzymes to detect and remove d-amino acid contaminants. This study successfully engineered a faster biocatalyst through mutation and kinetic methods, which has potential applications in industrial settings.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Engineering, Chemical
Abir Lal Bose, Debapriya Bhattacharjee, Debajyoti Goswami
Summary: This review explores the effects of process parameters on lipase catalysis, including enzyme concentration, substrate concentration and type, pH, temperature, agitation speed, and pressure. These parameters have significant impacts on the rate of reaction, kinetics, interfacial area, and thermal denaturation of enzymes. Statistical optimization can be used to control the effects of variables. Immobilization support and nonionic surfactant can alter the significance of enzyme concentration. Furthermore, the type of lipase controls the impact of enzyme, substrate, and water concentrations. The water content is crucial during lipase-catalyzed hydrolysis and esterification. Agitation mode influences the significance of enzyme concentration and temperature, while time plays a remarkable role during hydrolysis. Temperature, substrate type, and chain length notably control kinetic parameters.
CHEMBIOENG REVIEWS
(2023)
Article
Mathematical & Computational Biology
Darius Linge, Marius Gedgaudas, Andrius Merkys, Vytautas Petrauskas, Antanas Vaitkus, Algirdas Grybauskas, Vaida Paketuryte, Asta Zubriene, Audrius Zaksauskas, Aurelija Mickeviciute, Joana Smirnoviene, Lina Baranauskiene, Edita Capkauskaite, Virginija Dudutiene, Ernestas Urniezius, Aleksandras Konovalovas, Egidijus Kazlauskas, Kirill Shubin, Helgi B. Schioeth, Wen-Yih Chen, John E. Ladbury, Saulius Grazulis, Daumantas Matulis
Summary: We introduce a protein-ligand binding database (PLBD) that provides thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with human carbonic anhydrase isozymes. In addition to binding affinities, the database also provides calorimetrically measured binding enthalpies, enhancing mechanistic understanding.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Environmental Sciences
Xing Ma, Haixia Tian, Yunchao Dai, Yizhe Yang, Mallavarapu Megharaj, Wenxiang He
Summary: Antimony is a toxic metalloid that is widely present in the environment and poses a threat to human and ecological health. This study investigated the effect of Sb contamination on the kinetic parameters of soil arylsulfatase. The results showed that Sb inhibited the activity of soil arylsulfatase and affected its kinetic parameters.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Engineering, Environmental
Xiaonan Hu, Yang Ye, Yanxi Chen, Min Liu, Wenchao Zhang, Mingshan Zhu
Summary: Reaction parameters such as catalyst dosage, oxidant amount, and initial contaminant concentration play crucial roles in heterogeneous persulfate oxidation processes. Adjusting these parameters can establish inherent connections and generate different synergistic interactions. The study revealed that different reaction parameters can form various reaction modes under specific conditions, significantly enhancing the efficiency of wastewater treatment.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Food Science & Technology
Cesar Augusto Avellaneda Bohorquez, Herminia Emilia Prieto Martinez, Ricardo Henrique Silva Santos
Summary: Nitrogen is the most demanded nutrient by coffee plants with a recovery rate of about 50% from the soil. High doses of nitrogenous fertilizers are used for high production, leading to significant nitrogen loss to the environment. Determining the kinetic parameters of nitrate absorption in different fruit development stages can help adjust fertilizer doses and improve nitrogen recovery rates.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Gvantsa Chkadua, Eka Nozadze, Leila Tsakadze, Lia Shioshvili, Marine Leladze, Nana Arutinova, Sopio Dzneladze, Maia Javakhishvili, Sopio Kupradze
Summary: This study conducted a comparative analysis of the Na,K-ATPase in albino rat brain synaptic and kidney plasma membrane fractions, revealing different sensitivity levels to the neurotransmitter noradrenaline. While noradrenaline inhibits the rat brain synaptic membrane Na,K-ATPase and alters its enzyme system, the kidney plasma membrane fraction Na,K-ATPase is unaffected by noradrenaline and does not exhibit an Mg2+ dependent cycle. These findings suggest that noradrenaline has distinct modulatory effects on the enzyme systems in the two fractions.
CELL BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Materials Science, Characterization & Testing
Samir Abbas Ali Noma, Omur Acet, Ahmet Ulu, Burcu Onal, Mehmet Odabasi, Burhan Ates
Summary: L-asparaginase was successfully immobilized on cryogels with high efficiency and stability, showing improved catalytic activity and thermal stability compared to the soluble enzyme. The immobilized enzyme also exhibited good storage stability and reusability, making it a promising carrier matrix for enzyme immobilization.
Article
Biochemistry & Molecular Biology
Samir Abbas Ali Noma
Summary: Uricase loaded into responsive nanopolymers improves stability and catalytic efficiency.
PROCESS BIOCHEMISTRY
(2023)
Article
Chemistry, Applied
Huei-Chin Huang, Chun-Guey Wu
Summary: This study synthesized different types of reactive dyes and conducted a kinetic study on their hydrolysis reactions, finding that the hydrolysis rate constant of the dyes is influenced by the substituents, with stronger electron-donating substituents leading to lower hydrolysis rate constants.
Article
Biochemistry & Molecular Biology
Mikhail M. Solovyev, Elena N. Kashinskaya, Eugene A. Rogozhin, Francisco J. Moyano
Summary: The study found that trypsin in freshwater fish shows functional adaptations to seasonal changes in order to maximize protein digestion, with differences in response between Carassius gibelio and Perca fluviatilis.
FISH PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: The structure of the hydrophobic core in proteins is formed by hydrophobic residues oriented towards the center of the molecule, while polar residues are exposed. The folding process is influenced by the polar water environment. Proteins adopt a micelle-like structure based on hydrophobicity distribution, with the regions responsible for solubility resembling micelles. The determination of biological activity relies on identifying the location and contribution of orderliness to disorder in proteins.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Energy & Fuels
Ningbo Gao, Cui Quan, Zoltan Eller, Orsolya Toth, Nobert Miskolczi, Mohammed Al-asadi
Summary: The decomposition of waste polymers and the kinetic parameters of pyrolysis were discussed using Me/Ni/ZSM-5 catalysts, with a focus on the effects of raw materials and catalysts on weight loss. Different tendencies were found in different raw materials, and the La/Ni/ZSM-5 catalyst was further investigated at different ratios and temperatures to study gas composition and syngas yield. The lowest activation energy and highest syngas yield were found with a raw material:catalyst ratio of 2:1.
INTERNATIONAL JOURNAL OF ENERGY RESEARCH
(2021)
Article
Chemistry, Physical
Xuehua Yu, Yu Ren, Di Yu, Maozhong Chen, Lanyi Wang, Ruidan Wang, Xiaoqiang Fan, Zhen Zhao, Kai Cheng, Yongsheng Chen, Joanna Grybos, Andrzej Kotarba, Zbigniew Sojka, Yuechang Wei, Jian Liu
Summary: Soot particles are a major source of air pollution, and catalytic combustion is an effective strategy for reducing them. The study successfully developed novel catalysts with high catalytic activity and stability.
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)