Article
Biochemistry & Molecular Biology
Anna Barile, Philippa Mills, Martino L. di Salvo, Claudio Graziani, Victoria Bunik, Peter Clayton, Roberto Contestabile, Angela Tramonti
Summary: The study characterized the catalytic, allosteric, and structural properties of PNPO variants, including D33V, R161C, P213S, and E50K. D33V and E50K variants had mildly altered catalytic properties, while P213S had lower thermal stability and reduced cofactor binding capability. The R161C variant significantly decreased substrate affinity and abolished allosteric feedback inhibition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Biochemistry & Molecular Biology
Giovanni Bisello, Katarzyna Kusmierska, Marcel M. Verbeek, Jolanta Sykut-Cegielska, Michel A. A. P. Willemsen, Ron A. Wevers, Krystyna Szymanska, Jaroslaw Poznanski, Jakub Drozak, Katarzyna Wertheim-Tysarowska, Agnieszka Magdalena Rygiel, Mariarita Bertoldi
Summary: Aromatic amino acid decarboxylase (AADC) deficiency is a rare monogenic disease that causes intellectual disability, movement disorders, and autonomic dysfunction. In this study, a novel mutation of AADC was identified, which resulted in a significant decrease in enzymatic activity. The defect was found to be due to the mispositioning of the catalytically competent intermediate. These findings provide insights into the pathogenesis of AADC deficiency and a potential target for precision therapy.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Vijay Kumar Saxena, G. V. Vedamurthy, Raghvendar Singh
Summary: The study indicated that PLP has a significant impact on the expression and catalytic activity of PLP-dependent proteins in E. coli, with a positive correlation between PLP concentration and expression levels. E. coli does not secrete any dephosphorylation factor for PLP, suggesting internalization of PLP in the cells. The transport mechanism of PLP remains unknown and requires further investigation.
PROCESS BIOCHEMISTRY
(2022)
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
Prajakatta Mulay, Cindy Chen, Vijay Krishna
Summary: This study discovered that pyridoxal-5'-phosphate (PLP) has catalytic activity and can breakdown cysteine to produce hydrogen sulfide (H2S) in the absence of enzymes and multivalent metal ions. The reaction of PLP with cysteine forms a thiazolidine product, which can slowly decompose to produce H2S. This research provides important insights into the role of PLP in metabolic pathways.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
G. A. Gamov, A. N. Kiselev, M. N. Zavalishin, D. N. Yarullin
Summary: This paper reports on the prediction and stability study of the equilibrium and rate constants of the formation and hydrolysis reactions of hydrazones and Schiff bases derived from aldehyde species of the B6 vitamin family. It also investigates their applications in aqueous solutions at different pH values. The proposed additive model proves to be effective in considering the presence or absence of the amine or hydrazide group and five-or six-membered aromatic cycles.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Jingjie Xu, Huaxia Wang, Chengpeng Wu, Ailing Wang, Wei Wu, Jia Xu, Chenqi Luo, Shuang Ni, Ke Yao, Xiangjun Chen
Summary: The G91del variant of the CRYBA1/BA3 gene compromises protein solubility and stability, making it prone to proteolysis and aggregation under stress, ultimately leading to cellular apoptosis. Additionally, this mutation impairs the ability of beta A3 to form homo-oligomers, indicating its role in the pathogenic mechanism of congenital cataracts.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Microbiology
Tomokazu Ito, Honoka Ogawa, Hisashi Hemmi, Diana M. Downs, Tohru Yoshimura
Summary: PLPBP plays a crucial role in vitamin B-6 homeostasis. This study reveals the mechanism of intracellular accumulation of PNP due to the loss of PLPBP and suggests that disruption of PLPBP perturbs PMP homeostasis.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Natalia N. Kuranova, Daniil N. Yarullin, Maksim N. Zavalishin, George A. Gamov
Summary: This paper investigates the chemical reaction of gold(III) complexes with five hydrazones and confirms the formation of complexes in aqueous solutions. This contributes to further studies on the interaction between gold(III) complexes and biomacromolecules.
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
Nutrition & Dietetics
Lei Xu, Yu-Jing Fang, Meng-Meng Che, Alinuer Abulimiti, Chu-Yi Huang, Cai-Xia Zhang
Summary: This study investigated the relationship between vitamin B-6 and colorectal cancer risk using biomarkers PLP, PL, and PAr. The results showed that serum PLP and the sum of PLP and PL were inversely associated with colorectal cancer risk, while PAr was positively associated with colorectal cancer risk. The study suggested that vitamin B-6 may have a protective role in reducing colorectal cancer risk in the Chinese population, and that inflammation and oxidative stress may play a potential role in colorectal carcinogenesis.
Article
Green & Sustainable Science & Technology
Xingwang Ding, Ya Wen, Xuan Ma, Yuepei Zhang, Yuting Cheng, Zhaofeng Liu, Weiyue Hu, Yankai Xia
Summary: Pyridaben exposure during pregnancy can lead to anxiety-like behaviors in offspring by disrupting vitamin B6 metabolism, reducing pyridoxal 5'-phosphate (PLP) concentration, inhibiting the production of GABA, and down-regulating the expression of Pdxk and Gad1. Supplementation of PLP can restore normal behavior in PY offspring.
ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY
(2023)
Article
Engineering, Environmental
Guoguang Wei, Yan Chen, Ning Zhou, Qiuhao Lu, Sheng Xu, Alei Zhang, Kequan Chen, Pingkai Ouyang
Summary: This study successfully constructed a self-sufficient biocatalyst co-immobilizing PLP and LDC on chitin by regulating the DDA of chitin and using a chitin-binding domain for enzyme immobilization. The co-immobilized LDC and PLP showed good stability and retained over 55% of its original activity after multiple cycles. This strategy provides a new approach for co-immobilization of PLP-dependent enzymes.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Chengfeng Xue, I-Son Ng
Summary: For the first time, Pyridoxal 5'-phosphate (PLP) was used as a protein decoy to enhance enzyme expression and activity. By introducing new substrates and altering metabolic pathways, the growth and protein yield of the strain were further improved.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Chiara Gasbarri, Serena Rosignoli, Giacomo Janson, Dalila Boi, Alessandro Paiardini
Summary: Protein-peptide interactions are crucial for cell processes and functions, and in silico predictions offer an affordable alternative to experimental methods. This study presents a new algorithm, PepThreader, for predicting and analyzing PPIs and PpIs. It achieved an accuracy of 80% on a benchmark dataset and adds to the existing tools for identifying and characterizing PPIs and PpIs.
Article
Biochemical Research Methods
Fabiana Rossi, Alessandro Paiardini
Summary: G-quadruplexes are specific structures found in DNA and RNA sequences that play a key role in gene expression. Characterizing and predicting these structures can help understand their mechanism of action and discover potential therapeutic drugs. Machine learning and artificial neural networks offer accurate analysis methods.
CURRENT BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Benedetta Mattorre, Silvana Caristi, Simona Donato, Emilia Volpe, Marika Faiella, Alessandro Paiardini, Rosa Sorrentino, Fabiana Paladini
Summary: The common expression of ERAP1 and IRAP in humans, as well as the evolution of ERAP2 under balancing selection leading to the generation of a short form, suggest a significant yet debated role of these metalloproteases in antigen presentation and other cellular processes, as evidenced by their complex interactions in macrophages and some cancer cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Chiara Scribani Rossi, Laura Barrientos-Moreno, Alessio Paone, Francesca Cutruzzola, Alessandro Paiardini, Manuel Espinosa-Urgel, Serena Rinaldo
Summary: Bacterial biofilm is a multicellular community that provides protection to bacterial cells against harsh environments. Pseudomonas genus is known for its strong biofilm formation and metabolic versatility. Nutrient availability can be sensed by a Pseudomonas biofilm, which adjusts its metabolism accordingly. L-arginine, an amino acid, plays a crucial role in bacterial growth and is associated with biofilm formation, virulence, and antibiotic resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Serena Rosignoli, Alessandro Paiardini
Summary: This article introduces an open-source PyMOL plugin called DockingPie, which is used for individual and consensus docking analysis. The plugin supports multiple docking engines and provides an integrated docking environment and GUI for easy use.
Article
Genetics & Heredity
Niccolo Di Giosaffatte, Michele Valiante, Stefano Tricarico, Giulia Parise, Anna Maria De Negri, Guido Ricciotti, Lara Florean, Alessandro Paiardini, Irene Bottillo, Paola Grammatico
Summary: Choroideremia is an X-linked recessive condition that primarily affects males, causing progressive visual loss due to degeneration of retinal and choroidal tissues. The disease is caused by alterations in the CHM gene, leading to dysfunction of the protein REP1, which is crucial for prenylation of Rab. While female carriers are usually unaffected, this study identified a novel CHM pathogenic variant in a family with affected females. The variant resulted in a shorter CHM isoform, impairing REP1/Rab binding and potentially explaining the complex manifestations of Choroideremia in females.
Article
Cell Biology
Carola Amormino, Valentina Tedeschi, Giorgia Paldino, Stefano Arcieri, Maria Teresa Fiorillo, Alessandro Paiardini, Loretta Tuosto, Martina Kunkl
Summary: The SARS-CoV-2 spike protein does not exhibit superantigen-like activity, contradicting the superantigen theory of MIS-C.
Article
Biochemistry & Molecular Biology
Leonardo Gatticchi, Mirco Dindo, Gioena Pampalone, Carolina Conter, Barbara Cellini, Tatsuya Takayama
Summary: Primary Hyperoxaluria Type 1 (PH1) is a rare autosomal disease caused by mutations in AGXT gene that result in deficiency of alanine:glyoxylate aminotransferase (AGT) activity. A novel mutation c.1093G > T (p.Gly365Cys) was identified in a Japanese patient, which affected the folding and catalytic efficiency of AGT. The mutation resulted in a conformational change at the active site and led to reduced specific activity and protein levels. The study suggests that patients with this mutation may not respond to vitamin B6 treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Elena Di Nisio, Valerio Licursi, Cecilia Mannironi, Valentina Buglioni, Alessandro Paiardini, Giulia Robusti, Roberta Noberini, Tiziana Bonaldi, Rodolfo Negri
Summary: KDM5B histone demethylase is overexpressed in many cancers and has a dual role in oncogenesis depending on the specific context. One particular isoform of KDM5B, called KDM5B-NTT, is found to be more stable in breast cancer cell lines compared to the canonical PLU-1 isoform. Overexpression of KDM5B-NTT leads to increased H3K4 methylation and the derepression of genes involved in tumor suppression and interferon response.
CANCER GENE THERAPY
(2023)
Review
Biochemistry & Molecular Biology
Serena Rosignoli, Alessandro Paiardini
Summary: The field of structural bioinformatics has seen an exponential growth in available tools and software, with PyMOL emerging as a key player in providing an open platform for expert knowledge implementation and supporting structural bioinformatics analyses.
Article
Biochemistry & Molecular Biology
Fulvio Floriani, Carla Borri Voltattorni, Barbara Cellini, Riccardo Montioli
Summary: Deficiency of human ornithine aminotransferase (hOAT) causes gyrate atrophy of the choroid and retina (GA). Six pathogenic variants (G51D, G121D, R154L, Y158S, T181M, and P199Q) were analyzed in this study. All mutations resulted in a shift towards a dimeric structure and changes in tertiary structure, thermal stability, and PLP microenvironment. The impact of these mutations on the catalytic activity was also discussed based on computational information. These findings provide insight into the molecular defects and enzymatic phenotypes of GA patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Dalila Boi, Elisabetta Rubini, Sara Breccia, Giulia Guarguaglini, Alessandro Paiardini
Summary: Myc transcription factors play crucial roles in many cellular processes and its overexpression is frequently associated with cancer. The interplay between Myc and kinases is essential for tumor cell proliferation, with kinase inhibitors showing potential for cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Italia Anna Asteriti, Federica Polverino, Venturina Stagni, Valentina Sterbini, Camilla Ascanelli, Francesco Davide Naso, Anna Mastrangelo, Alessandro Rosa, Alessandro Paiardini, Catherine Lindon, Giulia Guarguaglini
Summary: AurkA kinase is frequently overexpressed in tumors and its nuclear localization in interphase is correlated with its oncogenic potential. The mechanisms leading to AurkA nuclear accumulation are poorly explored, but it is influenced by the cell cycle phase and nuclear export, and not by its kinase activity. Co-overexpression of AURKA and TPX2 or impairment of proteasome activity can induce AurkA nuclear accumulation.
LIFE SCIENCE ALLIANCE
(2023)
Article
Microbiology
Chiara Scribani-Rossi, Maria Antonia Molina-Henares, Simone Angeli, Francesca Cutruzzola, Alessandro Paiardini, Manuel Espinosa-Urgel, Serena Rinaldo
Summary: Recent research has found that arginine can affect the biofilm status of P. putida by modulating the intracellular levels of 3'-5' cyclic diguanylic acid (c-di-GMP). It has also been discovered that arginine can regulate c-di-GMP levels by using the transducer protein RmcA, thereby influencing biofilm architecture. This study provides a preliminary understanding of the molecular mechanisms linking biofilm formation and environmental adaptation.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Biochemical Research Methods
Serena Rosignoli, Luisa di Paola, Alessandro Paiardini
Summary: PyPCN is a PyMOL plugin that wraps over twenty PCN algorithms and metrics in an easy-to-use graphical user interface for PCN analysis. The plugin accepts 3D structures from the Protein Data Bank, user-provided PDBs, or precomputed adjacency matrices. The results are directly mapped to 3D protein structures and presented in interactive diagrams for visualization. The combination of a dedicated graphical user interface and PyMOL's visual support makes analysis more intuitive and accessible, expanding the applicability of PCNs.