Review
Biochemistry & Molecular Biology
Tohru Yoshimura
Summary: Enzymology, the study of enzyme structures and reaction mechanisms, is a classical discipline that has not yet reached its full potential. This review focuses on the reaction mechanisms of pyridoxal enzymes related to D-amino acid metabolism, highlighting the significance and interest of enzymology.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Chemistry, Physical
Natalia N. Kuranova, Daria Petrova, Maksim N. Zavalishin, Aleksei N. Kiselev, George A. Gamov
Summary: Hydrazones and Schiff bases are potent metal chelators with various biological activities. This paper collects protonation constant data of these compounds and proposes a chemometric model to describe the protolytic equilibria constants.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Immunology
Suneeta Devi, Priya Tomar, Khaja Faisal Tarique, Samudrala Gourinath
Summary: The dependence of Entamoeba histolytica on vitamin B-6 makes it a potential drug target, with two compounds identified through in-silico screening showing inhibitory activity against the parasite in vitro. These compounds hinder the growth of the parasite by targeting the enzyme pyridoxal kinase and blocking the binding of substrate.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Akram A. Da'dara, Manal Elzoheiry, Samar N. El-Beshbishi, Patrick J. Skelly
Summary: The research shows that schistosomes are able to cleave exogenous vitamin B6 and produce pyridoxal, which helps the parasites participate in essential, vitamin B6-driven metabolism. When the surface enzyme SmAP in schistosomes is suppressed, their ability to cleave exogenous vitamin B6 significantly decreases, indicating the important role of SmAP in parasite's vitamin B6 metabolism.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Hao-Hua Deng, Hui-Jing Yang, Kai-Yuan Huang, Yi-Jing Zheng, Ying-Ying Xu, Hua-Ping Peng, Yin-Huan Liu, Wei Chen, Guo-Lin Hong
Summary: Silicon nanoparticles (SiNPs) are currently attracting extensive research as a low toxicity, stable, and environmentally friendly sensing and imaging fluorescent probe. In this study, mitoxantrone-SiNPs (MXT-SiNPs) with green emission were synthesized under mild temperature conditions. The luminescence of MXT-SiNPs was enhanced using a pyridoxal phosphate (PLP)-based antenna, which also served as a novel sensing strategy for alkaline phosphatase (ALP). The activity of ALP was measured by the relationship between antenna formation ability and PLP hydrolysis degree.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Polymer Science
Anda Mihaela Craciun, Simona Morariu, Luminita Marin
Summary: This paper focuses on the preparation of chitosan self-healing hydrogels as carriers for local drug delivery. Through varying the ratio of glucosamine units and aldehyde and the water content, 30 hydrogels were prepared using chitosan and pyridoxal 5-phosphate (P5P). The driving forces of hydrogelation, stability, degradability, and self-healing ability were evaluated through various measurements. The results suggest that chitosan crosslinking with pyridoxal 5-phosphate is a suitable method to obtain self-healing hydrogels with good mechanical properties, structural recovery, stability, and pH-controlled degradability.
Article
Chemistry, Physical
O. N. Krutova, A. Lytkin, V. V. Chernikov, A. V. Volkov, Yu Mokhova, P. D. Krutov
Summary: The study measured the enthalpies of dissolution of crystalline pyridoxine and pyridoxal-5'-phosphate in water and KOH aqueous solutions using a direct calorimetric method. The standard enthalpies of combustion and formation were calculated based on group systematics and the effect of primary environment for atoms were taken into account. Additionally, the standard enthalpies of formation and dissociation products in aqueous solutions were also calculated.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Multidisciplinary Sciences
Elesha R. Hoffarth, Kersti Caddell Haatveit, Eugene Kuatsjah, Gregory A. MacNeil, Simran Saroya, Charles J. Walsby, Lindsay D. Eltis, K. N. Houk, Marc Garcia-Borras, Katherine S. Ryan
Summary: Recent study uncovers a mechanism by which the organic cofactor PLP activates molecular oxygen for oxidation reactions, particularly in the desaturation or hydroxylation of arginine. The proposed mechanism suggests the precise positioning of a water molecule in the active site plays a crucial role in controlling the final reaction outcome. This mechanism provides a unified framework to understand the activation of oxygen by PLP-dependent enzymes and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Agriculture, Dairy & Animal Science
Rong-Ju Yang, Na Wang, Xiao Ma, Meng-Die Gong, Yi-Rong Wang, Si-Yu Meng, Zhao-Ying Liu, Qi Tang
Summary: In this study, a two-dimensional liquid chromatography-UV detector was used to establish a method for simultaneous detection of PLP, PA, and PL. The method exhibited good performance in sample processing, separation, and detection, making it suitable for applications in pharmacological, pharmaceutical, and clinical research.
Article
Biochemistry & Molecular Biology
Amanda L. Darbyshire, Kirsten R. Wolthers
Summary: In Fusobacterium nucleatum, the clustering of aromatic residues is critical for the catalytic activity of serine synthase, an enzyme involved in the biosynthesis of noncanonical amino acids. Substituting these aromatic residues affects the reaction rate and the scope of nucleophilic substrates.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Nutrition & Dietetics
Donghui Yang, Yan Liu, Yafeng Wang, Yudiyang Ma, Jianjun Bai, Chuanhua Yu
Summary: The study found that participants with higher levels of vitamin B6 had a lower risk for all-cause mortality. Maintaining a sufficient level of serum vitamin B6 may lower the all-cause mortality risk in the general population.
Article
Nutrition & Dietetics
Christopher J. Cifelli, Sanjiv Agarwal, Victor L. Fulgoni
Summary: This study found that higher intake of dairy products, especially milk and yogurt, is positively associated with adequate levels of vitamin B-6, B-12, and folate, and lowers the risk of deficiency or inadequacy of these vitamins.
Review
Biochemistry & Molecular Biology
Juan Miguel Villa-Suarez, Cristina Garcia-Fontana, Francisco Andujar-Vera, Sheila Gonzalez-Salvatierra, Tomas de Haro-Munoz, Victoria Contreras-Bolivar, Beatriz Garcia-Fontana, Manuel Munoz-Torres
Summary: HPP is a rare genetic disease characterized by decreased TNSALP activity, caused by high allelic heterogeneity of the ALPL gene. The complications are mainly due to the accumulation of inorganic pyrophosphate (PPi) and pyridoxal-5 '-phosphate (PLP).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xingyu Chen, Nathan Ferchaud, Pierre Briozzo, David Machover, Thomas Simonson
Summary: Methionine gamma-lyase (MGL) is a therapeutic protein that can break down methionine to damage cancer cells. The presence of methionine affects the structure and active site of MGL, enhancing the enzyme reaction.
Article
Biochemistry & Molecular Biology
Pathum M. Weerawarna, Matthew J. Moschitto, Richard B. Silverman
Summary: OV329 is a highly efficient inactivator of GABA-AT with a structural difference from CPP-115 in an endocyclic double bond. The rate-limiting step of the inactivation mechanism is the deprotonation step, and QM calculations and KIE experiments accurately represent the enhancement of this step. Additionally, QM cluster models successfully capture the ground state destabilization and transition state stabilization in the enzyme.
ACS CHEMICAL BIOLOGY
(2021)
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)