Article
Biochemical Research Methods
Jan Van Slambrouck, Charlotte Schoenaers, Lies Laenen, Xin Jin, Kurt Beuselinck, Ann Verdonck, Joost Wauters, Geert Molenberghs, Bart M. Vanaudenaerde, Robin Vos, Peter Mombaerts, Katrien Lagrou, Laurens J. Ceulemans
Summary: The ability to detect SARS-CoV-2 RNA or antigen in BAL fluid samples using point-of-care tests (POCTs) can reduce the risk of developing severe COVID-19 after lung transplantation.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Krishna Chaturvedi, Caroline S. Anthony, Pankaj Pandey, Robert J. Doerksen, Murrell Godfrey
Summary: This study evaluated the interactions between the CB1 receptor and ligands from the JWH synthetic cannabinoid family, as well as newly designed JWH-like virtual compounds. The results revealed important structural characteristics that influenced the predicted CB1 binding affinity, including the carbonyl group and the length of the alkyl chain.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.
Article
Biochemical Research Methods
Michel V. F. Sucupira, Ana P. C. Argondizzo, Mariana Miguez, Anna E. de Araujo, Leila B. R. Silva, Marcelle B. Mello, Christiane F. S. Marques, Danielle Brito Cunha, Renata C. Bastos, Vanessa S. de Paula, Luciane A. Amado Leon
Summary: This study focuses on improving the purification, solubility, and protein expression levels of recombinant VP1-2A, a hepatitis A virus (HAV) structural protein with immunogenic activity. The results show that the modified approach successfully produces biologically active HAV VP1-2A, which can be used as a diagnostic tool for HAV infection.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Yunlong Shen, Ruirui Zhang, Xiaohua Jiang, Jinliang Yang
Summary: The study developed a monoclonal antibody, B1M023, that can bind to LILRB1 with high affinity and block its binding to HLA-G. This antibody can promote the activation and IFN-gamma secretion of T cells, suggesting its potential applications in concomitant diagnosis and tumor immunotherapy.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Xianghua Xiong, Yujin Qiu, Jiahao Zheng, Ling Zhou, Qingyang Wang, Jinglun Pang, Weicai Zhang, Huipeng Chen, Gang Liu, Xiaodong Han
Summary: A specific monoclonal antibody ML419 has been found to disrupt the recognition between Botulinum neurotoxin serotype A (BoNT/A) and FGFR3, effectively preventing BoNT/A from entering neurons. In vivo experiments show that ML419 has a strong protective effect, making it a promising candidate for the development of therapeutics against BoNT/A.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Weijian Wang, Yong Feng, Xiaoyang Li
Summary: In this study, the mechanical properties of recycled concrete (RC) were improved through two different modification methods. The results showed that the compressive and shear strength of RC modified by Silane Coupling Agent (KH560)/Ethylene vinyl acetate copolymer (EVA) was higher than that of RC modified by EVA alone. The effects of separate and co-modification on RC were analyzed through multi-scale methods, and the results provided insights into the macro-mechanical properties, microstructure, chemical composition, and molecular mechanism of the modified RC.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jun Jiang, Zhengqiang Jiang, Qiaojuan Yan, Susu Han, Shaoqing Yang
Summary: A novel alginate lyase gene from a marine bacterium showed efficient enzyme activity and stability, producing high conversion ratios of alginate oligosaccharides.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Xue-Fen Zhang, Ning Wang, Xu-Dong Li, Xiang Li, Chen-Xiang Wang
Summary: In this study, the protection behaviors of superhydrophobic dodecyltrimethoxysilane for mild steel were explored using molecular dynamics simulation. The results showed that the absorption orientations of the silane and the wetting behaviors of water clusters played important roles in the protection mechanism. The superhydrophobic silane film exhibited a repulsive effect on water droplets, confining corrosive species to specific regions and reducing their diffusion coefficient, thereby improving the corrosion protection of the underlying metal substrate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Oinam Sangita Devi, Senjam Sunil Singh, K. Rana, Sorokhaibam Jibankumar Singh, Wayenbam Sobhachandra Singh
Summary: A new lectin with hemagglutination activity was purified from the rhizome of Xanthosoma violaceum Schott. The lectin showed different reactions towards human red blood cells of different blood groups. It exhibited optimal hemagglutination activity at specific temperature and pH range, and showed good stability.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Biyu Xu, Luguang Liang, Yirong Jiang, Zuguo Zhao
Summary: This study investigates the underlying mechanisms of resistance to ibrutinib caused by the BTK L528W mutation using bioinformatics analysis and molecular dynamics simulations. The results demonstrate that the L528W mutation reduces BTK stability, decreases binding affinity, and leads to drug resistance and potential disease recurrence.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
V. Nagarajan, M. Vaishnavi, R. Bhuvaneswari, R. Chandiramouli
Summary: Amino acids are essential for protein synthesis and their deficiency can affect sleep and mood. This study investigates the adsorption properties of alanine and asparagine amino acids on one-dimensional chair graphene nanotubes. The results show that alanine and asparagine are physically adsorbed on the nanotubes, which act as electron donors. Additionally, changes in the band gap and electron density of the graphene nanotubes are observed.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
