Article
Chemistry, Physical
Tokio Watanabe, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, Koichi Kato
Summary: This research developed a non-linear multivariate analysis using a kernel method to classify the conformations of oligosaccharides, allowing for a systematic comparison and understanding of the contributions of intraresidue conformational factors to their global dynamics. It sheds light on exploring the conformational spaces of oligosaccharides and other molecules with high degrees of motional freedom.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Yu-Cheng Liu, Dah-Yen Yang, Sheh-Yi Sheu
Summary: G-quadruplexes have become attractive drug targets in cancer therapy, but the polymorphic nature of their structures makes understanding their conformational conversion mechanisms challenging. This study used molecular dynamics simulation to show that as salt concentration increases, the mechanism of conformational conversion shifts from multi-pathway to sequential pathways, with conformational conversion being more feasible upon K+ binding compared to Na+ binding in high-salt solutions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biology
Hiromitsu Shimoyama, Yasuteru Shigeta
Summary: Calmodulin is a multifunctional calcium-binding protein that regulates biochemical processes through conformational changes and complex formation with target enzymes. The free-energy landscape obtained by MSDC-MD technique reveals the structural changes of CaM and can provide insights into important interactions during these changes.
Article
Mathematics, Applied
Andrew Cleary, Jacob Page
Summary: This paper presents a new method for systematically exploring the free-energy landscape in the study of superfluids. It discovers new equilibrium states and evaluates the likelihood of observing certain states in experiments. Additionally, it investigates the dynamics near the minimizing state.
Article
Chemistry, Multidisciplinary
Miki Kato, Yasuhiro Ueta, Shigekazu Ito
Summary: This study investigated the complexation of phosphanoxy-substituted phosphaalkenes with gold and evaluated their catalytic activity. It was found that a pseudo coordinating interaction exists between the gold center and the P=C unit, and the bis(chlorogold) complexes can catalyze various reactions without activation treatment.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Engineering, Environmental
Hanyu Zhao, Wenjun Cao, Cen Liang, Changyuan Wang, Chunchang Wang
Summary: High-entropy engineering alone is insufficient for good energy storage performance in dielectric capacitors. A combined entropy engineering + poly-phase strategy is proposed, where medium-entropy materials with introduced polyphases show good energy storage performance. The introduction of multiphase effectively refines the grain and domain sizes, leading to high polarization intensity and excellent energy storage performance. This work demonstrates the effectiveness of the entropy engineering + polyphase strategy and provides a pathway for developing new energy storage materials.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Esra Boz, Matthias Stein
Summary: The study utilized the CREST tool to calculate non-covalent ligand-receptor interactions and energy using the GFN2-xTB method, and blind predictions were made for the binding of 10 drug molecule ligands to the CB[8] receptor. The results demonstrate that the proposed method shows good agreement with experimental values for large molecules, showcasing the effectiveness of quantum chemistry in predicting molecular interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Genetics & Heredity
Ting-Ting Yang, Sebastian Yu, Chiao-Li Khale Ke, Shih-Tsung Cheng
Summary: With the help of advanced technologies such as next generation sequencing and single-cell sequencing, our understanding of the genetic landscape of melanoma and its tumor microenvironment has improved. This can explain the varied treatment outcomes in melanoma patients and provide insights for potential new therapeutic targets. This review summarizes the genetics related to melanoma tumorigenesis, metastasis, prognosis, and the influence of genetics on the tumor microenvironment and treatment.
Article
Multidisciplinary Sciences
Korak Kumar Ray, Colin D. Kinz-Thompson, Jingyi Fei, Bin Wang, Qiao Lin, Ruben L. Gonzalez
Summary: Biomolecular machines utilize thermal and chemical energy to perform cellular processes, and they require dynamic rearrangements of structural components. The physical and structural mechanisms through which ligands achieve repurposing of these dynamics remain unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Hisashi Ishida, Hidetoshi Kono
Summary: Nucleosome reconstitution is crucial for cellular functions, and the displacement of the H2A-H2B dimer is a key step. In this study, adaptive biased molecular dynamics and umbrella sampling simulations were used to investigate the free energy landscape of the dimer displacement. The docking domain of H2A and the C-terminal of H4 were identified as the main contributors to the free energy. The extent of nucleosomal DNA wrapping determined the different paths for the dimer displacement, suggesting that external factors such as histone chaperones can modulate the displacement path. Additionally, key residues involved in the free energy were found to be related to nucleosome assembly, reassembly, and posttranslational modifications (PTMs) in cancer cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Plant Sciences
Xiuxiu Li, Gongxian Yang, Xinyi Yuan, Fenghua Wu, Wenda Wang, Jian-Ren Shen, Tingyun Kuang, Xiaochun Qin
Summary: PSI plays a crucial role in photosynthesis with its high quantum efficiency and fast energy transfer speed. The study of its structure and function over the past decades has shed light on how energy is transferred in vascular plants, providing important insights for future research.
FUNCTIONAL PLANT BIOLOGY
(2021)
Article
Materials Science, Ceramics
T. Odagaki, Y. Saruyama, T. Ishida
Summary: The free energy landscape is reorganized with temperature modulation, impacting the relaxation process and physical properties. The relaxation time of dielectric response depends on the relaxation of the FEL, converging to equilibrium in the long term. In temperature modulation spectroscopy, the dynamics are influenced by the relaxation time of FEL.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Environmental Sciences
Shira Biton Seror, Dror Shamir, Yael Albo, Haya Kornweitz, Ariela Burg
Summary: This study investigated the mechanism of an electro-Fenton reaction with a FeLaO3 catalyst entrapped in a sol-gel matrix, shedding light on the degradation process of toxic compounds. The findings have significant implications for environmental protection and wastewater treatment.
Article
Chemistry, Multidisciplinary
Dezhi Yang, Hongjuan Wang, Qiwen Liu, Penghui Yuan, Ting Chen, Li Zhang, Shiying Yang, Zhengzheng Zhou, Yang Lu, Guanhua Du
Summary: The specific crystalline form of a compound has a significant impact on its physicochemical properties. This study reports the characterization and analysis of three novel cocrystal salt solvates of rhein and berberine. Experimental and theoretical computations were conducted to understand the intermolecular interactions. The results show that the solubility improvement is mainly attributed to the ionic interactions between rhein and berberine in the cocrystal salt.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Emir Al-Sayed, Sreejith P. Nandan, Elias Tanuhadi, Gerald Giester, Marco Arrigoni, Georg K. H. Madsen, Alexey Cherevan, Dominik Eder, Annette Rompel
Summary: In this study, three abundant-metal-based germanotungstate clusters were synthesized using a PO43- template. These clusters showed activity as molecular water oxidation catalysts, with Co-9 and Co-20 outperforming a well-known catalyst by a factor of 2. Among them, Co-9 currently represents the fastest Co-GT-based water oxidation catalyst, with a turnover frequency of 0.608 s(-1) and a turnover numbers (TONs) up to 159.9.