Article
Biochemistry & Molecular Biology
David Ortega-Alarcon, Rafael Claveria-Gimeno, Sonia Vega, Olga C. Jorge-Torres, Manel Esteller, Olga Abian, Adrian Velazquez-Campoy
Summary: Hydroxymethylated cytosine (5hmC) is a stable DNA epigenetic mark that interacts with MeCP2 in a distinct mode with a specific thermodynamic signature. Mutations associated with Rett syndrome alter the interaction between MeCP2 and dsDNA in a cytosine modification-specific manner, which may be correlated with disease onset time and clinical severity score.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Jennifer T. J. Freitas, Luan F. Diniz, Daniele S. Gomes, Pedro M. A. F. de Paula, Sergio H. A. de Castro, Larissa S. Martins, Daniely F. Silva, Ana L. M. Horta, Felipe A. S. Guimaraes, Victoria F. M. Calisto, Renata Diniz
Summary: This study proposes a new physicochemical approach to predict the solubility of drugs. By calculating the intermolecular interaction energy of crystalline solids, it can be correlated with their aqueous solubility. The results show that the greater the solubility, the lower the interaction energy, validating the feasibility of this approach.
Article
Biochemistry & Molecular Biology
Safikur Rahman, Sana Iram, Md Tabish Rehman, Afzal Hussain, Arif Tasleem Jan, Jihoe Kim
Summary: This study investigates the interaction between the sodium channel blocker amiloride and human serum albumin. The results show that amiloride specifically binds to a specific site on HSA and the complex is stabilized by van der Waals hydrogen-bonding and hydrophobic interactions. FRET analysis demonstrates that the distance between amiloride and Trp214 is crucial for efficient quenching. UV-Vis spectroscopy and circular dichroism indicate minor structural changes in HSA after binding. Molecular dynamics simulations provide further evidence of stable HSA-AML complex formation.
Article
Biochemistry & Molecular Biology
Anna Sandner, Khang Ngo, Christoph P. Sager, Frithjof Scheer, Michael Daude, Wibke E. Diederich, Andreas Heine, Gerhard Klebe
Summary: The study demonstrates that the transient specificity pocket of aldose reductase has unique opening characteristics for specific ligands, and confirms that an electron-deficient aromatic group is an important prerequisite for occupying the pocket. Additionally, the binding position of the ligand in the pocket is not affected by a pH shift between 5 and 8.
Article
Biochemistry & Molecular Biology
Tao Shi, Paulien E. Polderman, Marc Pages-Gallego, Robert M. Van Es, Harmjan R. Vos, Boudewijn M. T. Burgering, Tobias B. Dansen
Summary: Reversible cysteine oxidation is crucial in redox signaling and plays a role in altering protein structure and function. The tumor suppressor p53 is known to be redox-sensitive and can form disulfide-dependent interactions with other proteins under oxidizing conditions, potentially playing a role in regulating p53 activity.
Article
Plant Sciences
Shuting Ding, Xiangqi Shao, Jianxin Li, Golam Jalal Ahammed, Yanlai Yao, Jian Ding, Zhangjian Hu, Jingquan Yu, Kai Shi
Summary: Nitrogen levels influence tomato plant immunity against pathogens, with low nitrogen conditions and NO3- as the sole nitrogen source enhancing resistance. Modulating nitrogen metabolism genes can alter disease susceptibility, with the defense mechanism dependent on the salicylic acid pathway.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Chemistry, Physical
K. Geethika, Angel Rose Thomas, T. Srividya Vyjayanthi, Soumit S. Mandal
Summary: Archaea use histone homologues and chromatin proteins to compact their DNA and survive in extreme environments. Cren7, a conserved chromatin protein, binds to DNA and induces structural changes. The binding process is driven by entropy and is independent of the anions present in the solution. Cren7 binding increases DNA flexibility and thermal stability.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Review
Chemistry, Multidisciplinary
Amy J. Thompson, Analia I. Chamorro Orue, Akshay Jayamohanan Nair, Jason R. Price, John McMurtrie, Jack K. Clegg
Summary: The discovery of molecular single crystals with interesting elastic behaviour has challenged the common perception of crystals as brittle objects. However, there is still a lack of comprehensive understanding of their mechanical properties and some contention regarding the atomic-scale mechanism of elasticity.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Medicinal
Rosanna Maccari, Gerhard Wolber, Massimo Genovese, Gemma Sardelli, Valerij Talagayev, Francesco Balestri, Simone Luti, Alice Santi, Roberta Moschini, Antonella Del Corso, Paolo Paoli, Rosaria Ottana
Summary: Type 2 diabetes mellitus (T2DM) is a serious chronic disease with a growing prevalence worldwide. Current treatment relies on drug combinations, but recently there has been interest in developing multiple-targeted drugs for complex diseases like T2DM. In this study, the researchers designed new compounds that inhibit both PTP1B and AKR1B1, two enzymes crucially involved in the development of T2DM and its complications.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Valeria Scardino, Juan I. Di Filippo, Claudio N. Cavasotto
Summary: A crucial component in structure-based drug discovery is high-quality three-dimensional structures of protein targets. When experimental structures are not available, homology modeling has been the preferred method. AlphaFold, an AI-based protein structure prediction method, has shown impressive accuracy. However, our evaluation using docking-based drug discovery revealed that AF models consistently performed worse compared to experimental structures. Post-modeling refinement strategies may be crucial to increase the chances of success.
Article
Biochemistry & Molecular Biology
Hossein Lanjanian, Shadi Hosseini, Zahra Narimani, Sogol Meknatkhah, Gholam Hossein Riazi
Summary: The study aimed to develop a pipeline to identify potential protein-protein interaction inhibitors by screening phytochemicals from Middle Eastern antiviral herbs. A series of simulations were performed to determine candidate molecules for inhibiting PPIs involved in COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Kentaroh Yoshiwara, Seiya Watanabe, Yasunori Watanabe
Summary: The crystal structures of RhaDH from Azotobacter vinelandii were investigated, showing a preference for binding to NADP+ over NAD+ and specific interactions with l-rhamnose residues. These interactions contribute to the substrate specificity of RhaDH and provide insights into the metabolic pathway mechanism.
Article
Chemistry, Physical
Christopher Paslack, Lars Schafer, Matthias Heyden
Summary: This study used molecular dynamics simulations to investigate how internal protein motions and their coupling to the surrounding solvent impact the dynamics of ligand binding to biomolecular surfaces. The results showed that protein flexibility modulates water density fluctuations near the hydrophobic surface patch, smoothing out the friction profile of ligand binding. Internal protein motions were found to shape the effects of enhanced friction in the vicinity of the protein, similar to idealized hydrophobic surfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Catriona M. A. Thompson, Richard H. Little, Clare E. M. Stevenson, David M. Lawson, Jacob G. Malone
Summary: This study reveals the regulatory mechanism of the RimK system in bacteria and the structural differences among different bacteria, providing insights into the impact of protein sequence and structure on protein activity.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Bijo Mathew, Jong Min Oh, Mohamed A. Abdelgawad, Ahmed Khames, Mohammed M. Ghoneim, Sunil Kumar, Lekshmi R. Nath, Sachithra Thazhathuveedu Sudevan, Della Grace Thomas Parambi, Clement Agoni, Mahmoud E. S. Soliman, Hoon Kim
Summary: Fifteen multiconjugated dienones were synthesized and evaluated for their inhibitory activities against MAO-A and MAO-B. The compounds showed potent and highly selective inhibition of MAO-B. MK6 and MK12 exhibited the most effective inhibition of MAO-B, with high selectivity indices. The study concluded that these compounds have potential as neurodegenerative disorder treatments.
Article
Biochemistry & Molecular Biology
A. Prabakaran, Amit Alexander
Summary: The molecular interactions and mucoadhesive nature of chitosan-coated liposomes with mucin are crucial for the development of an effective drug delivery system. The positively charged SA-CH-LPs showed stronger interaction and better mucoadhesive properties compared to negatively charged SALPs, thereby improving drug retention in the nasal cavity and enhancing therapeutic efficacy.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Maryam Noei-Khesht Masjedi, Esmaeil Sadroddiny, Jafar Ai, Saeed Balalaie, Yazdan Asgari
Summary: This study discovered an effective strategy for cargo sorting within exosomes by incorporating an appropriate cleavage site, providing further insight into the potential of exosomes as nano-shuttles bearing therapeutic biomolecules.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Pei -Gee Yap, Chee-Yuen Gan
Summary: This study collected the sequences of 128 tyrosinase inhibitory peptides and analyzed their hydrophobicity/hydrophilicity properties and amino acid profiles. Molecular docking analysis was used to investigate the binding interactions between peptides and tyrosinase. The study found that hydrophobic and/or polar neutral properties facilitate or stabilize peptide binding with tyrosinase, and short peptides with cysteine and tyrosine tend to bind to the active site of tyrosinase. These findings provide detailed explanations for the relationship between peptide/amino acid structures and tyrosinase inhibition, as well as potential anti-melanogenesis mechanisms for peptide-based treatments against skin hyperpigmentation.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ye Yang, Hai-Lian Chen, Su Fang Wu, Wei Bao
Summary: The study found that CHMP4B and VPS4A play an important role in reversing GSDMD-mediated pyroptosis by facilitating cell membrane remodeling in endometrial carcinoma.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aya Al Othman, Dmitry Bagrov, Julian M. Rozenberg, Olga Glazova, Gleb Skryabin, Elena Tchevkina, Alexandre Mezentsev, Mikhail Durymanov
Summary: Arc protein is found in glutamatergic neurons of vertebrates and can be transferred between neurons in extracellular vesicles (EVs). In glioma cells, Arc protein is also present in EVs and can facilitate the transfer of mRNA, potentially contributing to tumor progression and affecting synaptic plasticity in cancer patients.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Nan Zhang, Meng-yu Shen, Qing-li Meng, Hao-ping Sun, Fang-yi Fan, Hai Yi, Yong-jian Yang
Summary: In this study, it was demonstrated for the first time that FAT1 inhibited AML proliferation by reducing autophagy level. FAT1 achieved this by decreasing the expression of ATG4B, which is related to autophagy. Mechanistically, FAT1 decreased the levels of phosphorylated and intranuclear smad2/3, thus decreasing the activity of the ATG4B gene promoter. It was also found that FAT1 competitively bound to TGF-beta R II, leading to reduced phosphorylation of TGF-beta R I and smad2/3. Knockdown of FAT1 promoted AML autophagy and proliferation in vivo.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Oleh Demianchuk, Myroslava Vatashchuk, Dmytro Gospodaryov, Viktoria Hurza, Marian Ivanochko, Vitalii Derkachov, Vladyslav Berezovskyi, Oleh Lushchak, Kenneth B. Storey, Maria Bayliak, Volodymyr I. Lushchak
Summary: This study investigated the effects of a high-fat high-fructose diet (HFFD) on the behavior, energy metabolism, and oxidative stress markers in the cerebral cortex of mice. The results showed that HFFD stimulated locomotion and defecation, while an AKG-supplemented diet had a tendency to promote anxiety-like behavior. Additionally, there were significant differences in glutathione-dependent detoxification and processes related to autophagy between the two diets.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Yusaku Chukai, Ginga Ito, Yasuo Miki, Koichi Wakabayashi, Ken Itoh, Eriko Sugano, Hiroshi Tomita, Tomokazu Fukuda, Taku Ozaki
Summary: The study found that mitochondrial calpain-5 plays an important role in the occurrence and development of ischemia-reperfusion injury and is expressed in the human and mouse brains. Targeting the expression or activity of mitochondrial calpain-5 may have significant implications for suppressing inflammation during I/R injuries such as cerebrovascular diseases.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aline Dias da Purificaca, Victor Debbas, Leonardo Yuji Tanaka, Gabriele Veronica de Mello Gabriel, Joao Wosniak Junior, Tiphany Coralie De Bessa, Sheila Garcia-Rosa, Francisco Rafael Martins Laurindo, Percillia Victoria Santos Oliveira
Summary: The ER transmembrane chaperones DNAJB12 and DNAJB14 play important roles in protein folding and ER stress response. They are regulated by thiol redox processes and are involved in ER protein reflux.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ekaterina O. Bryanskaya, Andrey Y. Vinokurov, Angelina I. Dolgikh, Andrey Dunaev, Plamena R. Angelova, Andrey Y. Abramov
Summary: FAD autofluorescence in cells can assess enzymatic activity, and its intensity variations may be related to different cell types and tissues. High levels of FAD autofluorescence can indicate cell pathology and potentially predict the occurrence of apoptosis and necrosis.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Rumei Luan, Manyu Luo, Dongyan Ding, Xin Su, Junling Yang
Summary: Zinc deficiency can worsen obesity-related lung damage, and Nrf2 activation is one of the important mechanisms of this protective effect. Regulating zinc homeostasis can contribute to the prevention and treatment of obesity-related lung injury.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)