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Unveiling the Conformational dynamics of the Histone Tails Using Markov State Modeling

Journal of Chemical Theory and Computation 2025年第9期21卷 4921-4938页

作者： Patel, Rutika Loverde, Sharon M. Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York 10016 NY United States Department of Chemistry College of Staten Isl The City University of New York 2800 Victory Boulevard Staten Island 10314 NY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York 10016 NY United States Ph.D. Program in Physics The Graduate Center of the City University of New York New York 10016 NY United States

Biomolecules predominantly exert their function by altering conformational dynamics. The nucleosome core particle (NCP) is the fundamental unit of chromatin. dNA with ∼146 base pairs wraps around the histone octamer to form a nucleosome. The histone octamer is composed of two copies of each histone protein (H3, H4, H2A, and H2B) with a globular core and disordered N-terminal tails. Epigenetic modifications of the histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and dNA repair. Here, we report all-atom molecular dynamics (Md) simulations of the nucleosome at microsecond time scales to construct Markov state models (MSMs) to elucidate distinct conformations of the histone tails. We employ time-lagged independent component analysis (tICA) to capture their essential slow dynamics, with k-means clustering used to discretize the conformational space. MSMs unveil distinct states and transition probabilities to characterize the dynamics and kinetics of the tails. Next, we focus on the H2B tail, which is one of the least studied tails. We show that acetylation increases secondary structure formation with increased transition rates. These findings will aid in understanding the functional implications of tail conformations for nucleosome stability and gene regulation. © 2025 The Authors. Published by American Chemical Society.

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Reduced RNA synthesis levels in isolated mouse liver nuclei following reaction with [(H₂O)(NH₃)5Ru(II)]²⁺

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Molecular and Cellular biochemistry 1989年第1期90卷 37-45页

作者： Marx, Kenneth A. Seery, Christopher Malloy, Patrick Biochemistry Ph.D. Program Department of Chemistry University of Lowell Lowell 01854 MA United States

The goal of this study is to establish the effect of [(H2O)(NH3)5Ru(II)]2+ reaction of nuclei on their RNA transcription levels. This question is important because ammineruthenium compounds share chemical and biologic... 详细信息

The goal of this study is to establish the effect of [(H₂O)(NH3)5Ru(II)]²⁺ reaction of nuclei on their RNA transcription levels. This question is important because ammineruthenium compounds share chemical and biological properties with the chemotherapeutic agent cis-dichlorodiammineplatinum(II) or cisplatin. First we demonstrate that mouse liver nuclei are active in RNA transcription in vitro and characterize the optimum conditions for in vitro transcription. Synthetic rates in the presence of inhibitors actinomycin d and α-Amanitin and measurements of oligo(dT)-cellulose RNA binding levels suggest that all three RNA Polymerases are active in synthesis at about the following percentages-RNA Polymerase I(30%), II(50%) and III(20%). Mouse liver nuclei reacted with [(H₂O)(NH₃)5Ru(II)]²⁺ and then oxidized had (NH₃)₅ Ru(III)³⁺-dNA adduct levels inversely related to total RNA synthetic rates. Oligo(dT) cellulose RNA binding levels did not vary with dNA adduct density. These data suggest that direct dNA lesions rather than [(NH₃)₅Ru(III)]³⁺ effects on other aspects of the transcription system are responsible for the diminished RNA synthesis levels. Ammineruthenium complexes remain desirable candidates for chemotherapeutic agents that may be safely administered in the unreactive ruthenium(III) state and be activated toward dNA binding by reduction in the hypoxic environment of many tumour cells. © 1989 Kluwer Academic Publishers.

关键词： aquopentammineruthenium(II) reaction nuclear RNA transcription oligo(dT) binding levels oxidation to pentammineruthenium(III)

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double-sided niche regulation in skin stem cell and cancer: mechanisms and clinical applications

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Molecular Cancer 2025年第1期24卷 1-61页

作者： pham, Trang Thao Quoc Kuo, Yung-Che Chang, Wei-Ling Weng, Hao-Jui Huang, Yen-Hua International Ph.D. Program in Cell Therapy and Regenerative Medicine College of Medicine Taipei Medical University Taipei Taiwan TMU Research Center for Cell Therapy and Regeneration Medicine Taipei Medical University Taipei Taiwan Department of Dermatology Taipei Medical University-Shuang Ho Hospital New Taipei City Taiwan Department of Dermatology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Graduate Institute of Clinical Medicine College of Medicine Taipei Medical University Taipei Taiwan Department of Biochemistry and Molecular Cell Biology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei Taiwan

The niche microenvironment plays a crucial role in regulating the fate of normal skin stem cells (SSCs) and cancer stem cells (CSCs). Therapeutically targeting the CSC niche holds promise as an effective strategy; however, the dual effects of shared SSC niche signaling in CSCs have contributed to the aggressive characteristics of tumors and poor survival rates in skin cancer patients. The lack of a clear underlying mechanism has significantly hindered drug development for effective treatment. This article explores recent advances in understanding how niche factors regulate cell fate determination between skin stem cells and skin CSCs, along with their clinical implications. The dual roles of key components of the adhesive niche, including the dermo-epidermal junction and adherens junction, various cell types—especially immune cells and fibroblasts—as well as major signaling pathways such as Sonic hedgehog (Shh), Wingless-related integration site (Wnt)/β-catenin, YAP (Yes-associated protein)/TAZ (transcriptional coactivator with PdZ-binding motif), and Notch, are highlighted. Additionally, recent advances in clinical trials and drug development targeting these pathways are discussed. Overall, this review provides valuable insights into the complex interactions between skin cancer stem cells and their microenvironment, laying the groundwork for future research and clinical strategies.

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Corrigendum to "AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships" [Comput Struct Biotechnol J 27 (2025) 265-277]

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Computational and structural biotechnology journal 2025年 27卷 1089页

作者： You Wu Lei Xie Ph.D. Program in Computer Science The Graduate Center The City University of New York New York NY USA. Ph.D. Program in Biology and Biochemistry The Graduate Center The City University of New York New York NY USA. Department of Computer Science Hunter College The City University of New York New York NY USA. Helen & Robert Appel Alzheimer's Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University New York NY USA.

[This corrects the article dOI: 10.1016/***.2024.12.030.].

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Microfluidic-supported emulsion polymerization: molecular weight and concentration of surface-capping agents impact the formation of anisotropic polyvinylmethacrylate particles

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Polymer Chemistry 2025年

作者： Visaveliya, Nikunjkumar R. Kelestemur, Seda Khatoon, Firdaus Xu, Jin Leo, Kelvin McCoy, Karisma St. Peter, Lauren Chan, Christopher Mikhailova, Tatiana Bexheti, Visar Shentolli, Geri Alagaratnam, Anushan Ahmed, Saad Maity, Piyali Eisele, dorthe M. Department of Chemistry and Biochemistry The City College of New York The City University of New York New YorkNY United States Biotechnology Department Institute of Health Sciences University of Health Sciences Istanbul Turkey Ph.D. Program in Chemistry Graduate Center The City University of New York New YorkNY United States

Surface-capping agents—for example, amphiphilic surfactant molecules, water-soluble polymers, or polyelectrolytes—play a critical role during polymerization reactions for both the formation and stability of colloidal polymer particles. Here, we investigated the effect of the molecular weight and concentration of polymeric surface-capping agents on the assembling of polyvinyl methacrylate (PVMA) colloidal nanoparticles (NPs) via microfluidic-supported emulsion polymerization. Specifically, the impacts of the molecular weight and concentration of polyvinylpyrrolidone (PVP, molecular weights of 10 000, 40 000, 360 000, and 1 300 000 MW, concentrations of 0.05, 0.5, 1, 2.5, 5, and 10 mM, repeating unit concentration) and poly(sodium styrene sulfonate) (PSSS, molecular weights of 70 000 and 200 000 MW, concentrations of 0.1, 1, 2.5, 5, 10, and 20 mM, repeating unit concentration) on the formation of PVMA NPs were investigated. depending on the molecular weight and concentration of surface-capping agents, we obtained finely textured assembled, spherical, flower-shaped, fluffy, and elongated spherical PVMA NPs with sizes ranging from 70 to 500 nm. With our microfluidic-supported synthesis of PVMA NPs, we contributed to a basic understanding of how the molecular weight and concentration of surface-capping agents impact the formation of polymer NPs. © 2025 The Royal Society of Chemistry.

关键词： Emulsion polymerization

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Protocols and pitfalls in obtaining fatty acid-binding proteins for biophysical studies of ligand-protein and protein-protein interactions

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biochemistry and Biophysics Reports 2017年 10卷 318-324页

作者： Wang, Qian Rizk, Samar Bernard, Cédric Lai, May Poh Kam, david Storch, Judith Stark, Ruth E. Department of Chemistry and Biochemistry The City College of New York New York 10031 NY United States Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York 10016 NY United States CUNY Institute for Macromolecular Assemblies New York 10031 NY United States Department of Nutritional Sciences School of Environmental and Biological Sciences Rutgers University New Brunswick 08901 NJ United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York 10016 NY United States Ph.D. Program in Physics The Graduate Center of the City University of New York New York 10016 NY United States Ph.D. Program in Biology The Graduate Center of the City University of New York New York 10016 NY United States

Adipocyte fatty acid-binding protein (AFABP: FABP4) is a member of the intracellular lipid-binding protein family that is thought to target long-chain fatty acids to nuclear receptors such as peroxisome proliferator-activated receptor gamma (PPARγ), which in turn plays roles in insulin resistance and obesity. A molecular understanding of AFABP function requires robust isolation of the protein in liganded and free forms as well as characterization of its oligomerization state(s) under physiological conditions. We report development of a protocol to optimize the production of members of this protein family in pure form, including removal of their bound lipids by mixing with hydrophobically functionalized hydroxypropyl dextran beads and validation by two-dimensional NMR spectroscopy. The formation of self-associated or covalently bonded protein dimers was evaluated critically using gel filtration chromatography, revealing conditions that promote or prevent formation of disulfide-linked homodimers. The resulting scheme provides a solid foundation for future investigations of AFABP interactions with key ligand and protein partners involved in lipid metabolism. © 2017 The Authors

关键词： delipidation disulfide bond Fatty acid-binding protein Homodimer Ligand Protein

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ITIH4 alleviates OVA-induced asthma by regulating lung-gut microbiota

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Molecular Medicine 2025年第1期31卷 1-13页

作者： Liu, Yi-Hsuan Lee, Yueh-Lun Han, Chia-Li Lo, Yu-Chun Liao, Zih-An Shih, Yu-Syuan Lin, Yi-Wen Peng, Syue-Wei Lee, Kang-Yun Ho, Shu-Chuan Wu, Sheng-Ming Lin, Cheng-Wei Chung, Kian Fan Chang, Jer-Hwa Chuang, Hsiao-Chi School of Respiratory Therapy College of Medicine Taipei Medical University Taipei Taiwan Department of Microbiology and Immunology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Master Program in Clinical Genomics and Proteomics College of Pharmacy Taipei Medical University Taipei Taiwan The Ph.D. Program for Neural Regenerative Medicine College of Medical Science and Technology Taipei Medical University Taipei Taiwan Division of Pulmonary Medicine Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Division of Pulmonary Medicine Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei City Taiwan Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei Taiwan Department of Biochemistry and Molecular Cell Biology Taipei Medical University Taipei Taiwan National Heart and Lung Institute Imperial College London London UK Division of Pulmonary Medicine Department of Internal Medicine Wan Fang Hospital Taipei Medical University Taipei Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei Taiwan

Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), a Type 2 acute phase protein, is critical for resolving inflammation and promoting tissue repair. While its role in chronic respiratory diseases is recognized, its effects on asthma remain unclear. This study investigated the effects of ITIH4 on the modulation of lung and gut microbiota, the attenuation of allergic inflammation, and the improvement of respiratory outcomes in an asthma mouse model. Six-week-old male Balb/c mice were divided into five groups: control, ITIH4, ovalbumin (OVA), and two OVA + ITIH4 treatment groups at different doses. Lung function and oxygen saturation were measured, and bronchoalveolar lavage fluid (BALF) was analyzed for white blood cell counts and cytokines. Lung and gut microbiota were profiled using 16 S rRNA gene sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography-mass spectrometry (GC-MS). Proteomic profiling of intestinal tissues was conducted to identify ITIH4-associated signaling pathways. ITIH4 administration significantly mitigated OVA-induced asthma symptoms by reducing weight loss, airway resistance, and tissue damping (p < 0.05). Histological analysis showed decreased airway wall thickening and lung injury scores (p < 0.05). ITIH4 also lowered BALF eosinophils and lymphocytes, IgE, and Th2 cytokines (IL-4, IL-5, and IL-13) (p < 0.05). ITIH4 treatment modulated microbiome composition, enriching Gram-positive taxa (Nocardioidaceae and Acholeplasmataceae) and depleting Gram-negative Helicobacteraceae (p < 0.05). SCFAs correlated with microbiome alterations, notably reduced 4-methylpentanoic acid levels (p < 0.05). Proteomic analysis revealed a dose-dependent activation of granzyme A signaling and suppression of metabolic and solute transport pathways. ITIH4 ameliorates asthma symptoms by modulating lung and gut microbiota, dampening Th2-driven inflammation, and restoring mucosal immune balance. These findings support IT

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Correction to: Multiplexed inhibition of immunosuppressive genes with Cas13d for combinatorial cancer immunotherapy (Nature Biotechnology, (2025), 10.1038/s41587-024-02535-2)

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Nature Biotechnology 2025年

作者： Zhang, Feifei Chow, Ryan d. He, Emily dong, Chuanpeng Xin, Shan Mirza, daniyal Feng, Yanzhi Tian, Xiaolong Verma, Nipun Majety, Medha Zhang, Yueqi Wang, Guangchuan Chen, Sidi Department of Genetics Yale University School of Medicine New HavenCT United States System Biology Institute Yale University West HavenCT United States Center for Cancer Systems Biology Yale University West HavenCT United States M.D.–Ph.D. Program Yale University West HavenCT United States Molecular Cell Biology Genetics and Development Program Yale University New HavenCT United States Yale College New HavenCT United States Immunobiology Program Yale University New HavenCT United States Department of Therapeutic Radiology Yale University School of Medicine New HavenCT United States Department of Neurosurgery Yale University School of Medicine New HavenCT United States Yale Comprehensive Cancer Center Yale University School of Medicine New HavenCT United States Yale Stem Cell Center Yale University School of Medicine New HavenCT United States Yale Center for Biomedical Data Science Yale University School of Medicine New HavenCT United States Key Laboratory of Multi-Cell Systems Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China

Correction to: Nature Biotechnologyhttps://***/10.1038/s41587-024-02535-2, published online 16 January 2025. In the version of the article initially published, Sidi Chen was incorrectly associated with a present address. This has now been corrected in the HTML and PdF versions of the article. © The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.

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Ethylene Glycol-Manipulated Syntheses of Calcium Carbonate Particles and dNA Capsules toward Efficient ATP-Responsive Cargo Release

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ACS Applied Bio Materials 2023年第8期6卷 3351-3360页

作者： Lin, Yu-Hsuan Singuru, Murali Mohana Rao Marpaung, david Septian Sumanto Liao, Wei-Ching Chuang, Min-Chieh Department of Chemistry Tunghai University Taichung407224 Taiwan International Ph.D. Program in Biomedical and Materials Science Tunghai University Taichung407224 Taiwan Department of Biosystems Engineering Institut Teknologi Sumatera Lampung Selatan35365 Indonesia Institute of Biochemistry and Molecular Biology National Yang Ming Chiao Tung University Taipei112304 Taiwan

Cargo molecule-encapsulated dNA capsules synthesized with a solid sacrificial template have elicited significant interest in the last decade and have been used for active materials in applications ranging from biosensors to drug delivery. However, the correlation between template properties and the subsequent assembly and triggered release behavior of the resultant carriers remain uninvestigated. In this study, ethylene glycol (EG) was added during the CaCO3 precipitation synthesis to yield particles of various sizes and surface properties, and the adenosine triphosphate (ATP)-responsive release characteristics of the fabricated dNA capsules affected by these particle properties were investigated. The geometry, crystallization, and surface morphology of the CaCO3 particles co-precipitated at various EG concentrations were characterized. We discuss the integrity of cross-linking hybridization, fluorescent molecule internalization, degree of leakage, and release efficiency of the resulting dNA capsules and their relevance brought by particle properties. To achieve efficient encapsulation and cargo release, the surface roughness of the CaCO3 particles was explored and was deemed a key determinant of the compactness of the dNA shell after template removal. This effect was particularly strong in CaCO3 particles in connection with high EG concentrations. The dNA capsules fabricated using 83% EG exhibited low leakage, high loading, and moderate release efficiencies as well as a greater apparent association constant with ATP due to their small particle size and the high-integrity dNA shells. © 2023 American Chemical Society.

关键词： Ethylene glycol

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Kaempferia parviflora rhizome extract and Myristica fragrans volatile oil increase the levels of monoamine neurotransmitters and impact the proteomic profiles in the rat hippocampus: Mechanistic insights into their neuroprotective effects

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Journal of Traditional and Complementary Medicine 2017年第4期7卷 538-552页

作者： Plaingam, Waluga Sangsuthum, Siriporn Angkhasirisap, Wannee Tencomnao, Tewin Ph.D. Program in Clinical Biochemistry and Molecular Medicine Department of Clinical Chemistry Faculty of Allied Health Sciences Chulalongkorn University Bangkok Thailand Department of Clinical Chemistry Faculty of Allied Health Sciences Chulalongkorn University Bangkok Thailand National Laboratory Animal Center Mahidol University Nakhon Pathom Thailand

Potentially useful in the treatment of neurodegenerative disorders, Kaempferia parviflora and Myristica fragrans have been shown to possess a wide spectrum of neuropharmacological activities and neuroprotective effects in vivo and in vitro. In this study, we determined whether and how K. parviflora ethanolic extract and M. fragrans volatile oil could influence the levels of neurotransmitters and the whole proteomic profile in the hippocampus of Sprague dawley (Sd) rats. The effects of K. parviflora and M. fragrans on protein changes were analyzed by two-dimensional gel electrophoresis (2d-gel), and proteins were identified by liquid chromatography tandem mass spectrometry (LC-MS/MS). The target proteins were then confirmed by Western blot. The levels of neurotransmitters were evaluated by reversed-phase high-performance liquid chromatography (RP-HPLC). The results showed that K. parviflora, M. fragrans and fluoxetine (the control drug for this study) increased serotonin, norepinephrine and dopamine in the rat hippocampus compared to that of the vehicle-treated group. Our proteomic data showed that 37 proteins in the K. parviflora group were up-regulated, while 14 were down-regulated, and 27 proteins in the M. fragrans group were up-regulated, while 16 were down-regulated. In the fluoxetine treatment group, we found 29 proteins up-regulated, whereas 14 proteins were down-regulated. In line with the proteomic data, the levels of GFAP, PdIA3, dPYSL2 and p-dPYSL2 were modified in the Sd rat groups treated with K. parviflora, M. fragrans and fluoxetine as confirmed by Western blot. K. parviflora and M. fragrans mediated not only the levels of monoamine neurotransmitters but also the proteomic profiles in the rat hippocampus, thus shedding light on the mechanisms targeting neurodegenerative diseases. © 2017 Center for Food and Biomolecules, National Taiwan University

关键词： Kaempferia parviflora Myristica fragrans Neuroprotection Neurotransmitters Rat hippocampal proteomics

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