The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site

Bubić, Ante; Narczyk, Marta; Petek, Ana; Wojtyś, Marta Ilona; Maksymiuk, Weronika; Wielgus‐Kutrowska, Beata; Winiewska-Szajewska, Maria; Pavkov‐Keller, Tea; Bertoša, Branimir; Štefanić, Zoran; Luić, Marija; Bzowska, Agnieszka; Ašler, Ivana Leščić

doi:10.1016/j.ijbiomac.2022.12.001

Cited by 7 publications

(5 citation statements)

References 61 publications

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“…Simultaneously, high purity soluble ADSS protein was obtained through denaturation and renaturation. Subsequently, we will optimize the refolding method to obtain a more active form of the ADSS protein and demonstrate its enzymatic activity by catalyzing the reaction between IMP and ASP [15] . The foundation was laid for constructing in vitro enzymatic reaction to produce adenosine.…”

Section: Discussionmentioning

confidence: 99%

Expression and Renaturation Analysis of Adenylosuccinate Synthetase from Cordyceps cicadae

Han,

Ruan

2024

BIO Web Conf.

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In this study, the objective was to obtain adenylosuccinate synthase (ADSS) in the adenosine biosynthesis pathway of Cordyceps cicadae. The coding sequence (CDS) information of the protein was obtained from transcriptome sequencing. Bioinformatics analysis were employed to predict and analyze the physicochemical properties, hydrophobicity, signal peptide, and advanced structure of ADSS. The ADSS coding sequence was chemically synthesized and a prokaryotic expression vector containing N-terminal His tag (pET28a-ADSS) was constructed. Induction of ADSS expression occurred with 0.1 mmol/L IPTG at 37°C for 2 hours. SDS-PAGE was utilized to detect soluble protein expression levels. Although ADSS primarily expressed as inclusion bodies, soluble proteins were successfully obtained after denaturation and renaturation.

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Section: Discussionmentioning

confidence: 99%

Expression and Renaturation Analysis of Adenylosuccinate Synthetase from Cordyceps cicadae

Han,

Ruan

2024

BIO Web Conf.

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“…29 Given that H. pylori is an invasive bacterium, PNP becomes an interesting target for the develop-ment of new antibiotics. 30 Understanding the dynamics of the PNP is crucial for this purpose. Crystallographic structures revealed two distinct conformations of the active site of this enzyme: open and closed.…”

Section: Phosphorylase (Pnp)mentioning

confidence: 99%

“…Some bacteria, such as Helicobacter pylori , lack enzymes in the de novo pathway and therefore rely on the purine salvage pathway, making PNP essential for their survival . Given that H. pylori is an invasive bacterium, PNP becomes an interesting target for the development of new antibiotics . Understanding the dynamics of the PNP is crucial for this purpose.…”

Section: Case Study 2: Purine Nucleoside Phosphorylase (Pnp)mentioning

confidence: 99%

MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams

Gomaz,

Pandini,

Maršavelski

et al. 2024

J. Chem. Inf. Model.

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Extracting meaningful information from atomistic molecular dynamics (MD) simulations of proteins remains a challenging task due to the high-dimensionality and complexity of the data. MD simulations yield trajectories that contain the positions of thousands of atoms in millions of steps. Gaining a comprehensive understanding of local dynamical events across the entire trajectory is often difficult. Here, we present a novel approach to visualize MD trajectories in the form of timedependent Ramachandran plots. Specialized data aggregation techniques are employed to address the challenge of plotting millions of data points on a single image, thereby ensuring that the analysis is independent of the molecule size and/or length of the MD simulation. This approach facilitates quick identification of flexible and dynamic regions, and its strength is the ability to simultaneously observe the movements of all amino acids over time. The Python program MDavocado is freely available at GitHub (https://github.com/zoranstefanic/MDavocado).

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“…In the latest United States Department of Health and Human Services (HHS) carcinogen report, H. pylori is listed as a carcinogen. At present, the resistance and adverse reactions towards H. pylori -related drugs, such as clarithromycin, metronidazole, and levofloxacin, are increasing ( Bubić et al, 2023 ). Therefore, finding safe, reliable, and effective drugs to treat the disease is particularly important.…”

Section: Health Benefitsmentioning

confidence: 99%

Chinese olive (Canarium album Rauesch.): a critical review on its nutritional value, phytochemical composition, health benefits, and practical applications

Yu,

Wang,

et al. 2023

Front. Pharmacol.

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Chinese olive is a popular fruit with a long history of cultivation and consumption. As a fruit with edible, nutritional, and even medicinal value, the Chinese olive has attracted increased interest from both nutrition researchers and health-conscious consumers. Chinese olive is a rich nutrient source, including essential and non-essential amino acids, various fatty acids, organic acids, vitamins, microelements, and high-quality dietary fibers. It is also an important natural source of phytochemicals such as phenolic acids, flavonoids, phenylpropanoids, and other bioactive compounds. The nutritional and phytochemical compounds obtained from the Chinese olive exhibit unique and potent biological activities, explaining its various benefits to human health, including anti-Helicobacter pylori, anti-influenza, anti-diabetes, anti-inflammatory, anti-tumor effects, among others. This review focuses on recent studies on Chinese olives and aims to summarize the major advances in their nutritional value, phytochemical composition, health benefits, and practical applications. It provides a reference for further research on Chinese olives and their properties and the development of novel functional products.

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The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site

Cited by 7 publications

References 61 publications

Expression and Renaturation Analysis of Adenylosuccinate Synthetase from Cordyceps cicadae

Expression and Renaturation Analysis of Adenylosuccinate Synthetase from Cordyceps cicadae

MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams

Chinese olive (Canarium album Rauesch.): a critical review on its nutritional value, phytochemical composition, health benefits, and practical applications

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