Article
Biochemistry & Molecular Biology
Zsuzsanna Rethi-Nagy, Edit Abraham, Zoltan Lipinszki
Summary: This method involves immobilizing the protein/domain of interest to a carrier, incubating it with a labelled putative binding partner, and visualizing the interacting proteins through SDS/PAGE autoradiography, offering a simple, cheap, and easily performed in vitro analysis suitable for wet labs.
Article
Multidisciplinary Sciences
Elizabeth M. Bailey, Emanuel Salazar-Cavazos, Rachel M. Grattan, Michael J. Wester, David J. Schodt, Julian A. Rojo, Keith A. Lidke, Diane S. Lidke
Summary: Phosphorylation is a crucial posttranslational modification that regulates protein function and cell signaling outcomes. Existing methods for measuring protein phosphorylation lack the ability to account for heterogeneity across individual proteins. The single-molecule pull-down (SiMPull) assay allows for investigating macromolecular complex composition and provides a robust quantification of the phosphorylation state of full-length membrane receptors at the single-molecule level.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Neurosciences
Eve Honore, Ines Belo do Nascimento, Isabel Laplante, Jean-Claude Lacaille
Summary: Protein synthesis, regulated by mTORC1, plays a crucial role in controlling synaptic inputs in the hippocampus. The induction of long-term potentiation (LTP) at SOM-INs requires protein synthesis and is dependent on mTORC1.
Article
Food Science & Technology
Xiaochao Tang, Dianmei Yu, Haiyan Wang, Wenwen Meng, Yiwen Zhai, Zhixiang Lei, Zhen Liu, Xianchun Wang
Summary: LETX-VI interacts with 164 proteins in PC12 cells, enhancing dopamine synthesis, cell division, and proliferation, while negatively regulating cell cycle arrest, cell death, and apoptotic processes.
Article
Cell Biology
Tamotsu Tsukahara, Yasuka Sahara, Nigel Ribeiro, Ryoko Tsukahara, Mari Gotoh, Satoshi Sakamoto, Hiroshi Handa, Kimiko Murakami-Murofushi
Summary: This study identified the interaction between a metabolically stabilized cPA derivative, 2ccPA, and ANT2 in microglial cells, showing its ability to inhibit apoptosis induced by phenylarsine oxide and improve cell survival.
CELLULAR SIGNALLING
(2021)
Article
Chemistry, Multidisciplinary
Jinyoung Byun, Srivithya Vellampatti, Prathit Chatterjee, Sun Ha Hwang, Byoung Choul Kim, Juyong Lee
Summary: A significant difference between APP695 and APP751 isoforms is the presence of the Kunitz type protease inhibitor (KPI) domain, which affects the dimerization of APP isoforms. Through experiments and simulations, it was discovered that homo-dimerization is favored for both isoforms, while hetero-dimerization is limited between APP751 and APP695. The KPI domain has a stronger attractive interaction with itself and other domains in APP751, leading to its predominant homo-dimer formation.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Virology
Tucker Hansen, Jodie Baris, Min Zhao, Richard E. Sutton
Summary: This study developed both cell-intact and cell-free systems that can reliably, rapidly, and reproducibly quantify Rev-Rev interaction. The results of mutant Revs tested in the cell-based assay correlated strongly with the results of a functional Rev trans-complementation infectivity assay. These assays may be useful in screening and identifying compounds that inhibit Rev function on a high throughput basis.
Article
Multidisciplinary Sciences
Vidyasagar Koduri, Leslie Duplaquet, Benjamin L. Lampson, Adam C. Wang, Amin H. Sabet, Mette Ishoey, Joshiawa Paulk, Mingxing Teng, Isaac S. Harris, Jennifer E. Endress, Xiaoxi Liu, Ethan Dasilva, Joao A. Paulo, Kimberly J. Briggs, John G. Doench, Christopher J. Ott, Tinghu Zhang, Katherine A. Donovan, Eric S. Fischer, Steven P. Gygi, Nathanael S. Gray, James Bradner, Jeffrey A. Medin, Sara J. Buhrlage, Matthew G. Oser, William G. Kaelin
Summary: Some undruggable proteins can be targeted by compounds that degrade them. Current assays for identifying degraders have limitations, but a new gain of signal assay has been developed to facilitate the discovery of drugs that degrade undruggable proteins directly or indirectly.
Review
Neurosciences
Chiara Lanzillotta, Ilaria Zuliani, Antonella Tramutola, Eugenio Barone, Carla Blarzino, Valentina Folgiero, Matteo Caforio, Diletta Valentini, Alberto Villani, Franco Locatelli, D. Allan Butterfield, Elizabeth Head, Marzia Perluigi, Jose F. Abisambra, Fabio Di Domenico
Summary: Abnormal activation of the PERK pathway in neurodegenerative disorders is associated with reduced protein synthesis, cell death, and altered antioxidant response. In Down syndrome, PERK activation is linked to the early development of Alzheimer's disease, suggesting that dysregulation of the PERK pathway may play a key role in DS pathology.
PROGRESS IN NEUROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Laura Grasemann, Barbora Lavickova, M. Carolina Elizondo-Cantu, Sebastian J. Maerkl
Summary: The PURE system is a promising chassis for cell-free synthetic biology, but commercially available systems are expensive while homemade methods are time-consuming and laborious. Streamlining protein purification through coculturing and co-purification can minimize time and labor requirements.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Multidisciplinary Sciences
Joongoo Lee, Jaime N. Coronado, Namjin Cho, Jongdoo Lim, Brandon M. Hosford, Sangwon Seo, Do Soon Kim, Camila Kofman, Jeffrey S. Moore, Andrew D. Ellington, Eric Anslyn, Michael C. Jewett
Summary: This study reveals the plasticity of the ribosome in polymerization reactions and demonstrates its ability to synthesize various non-canonical polymeric backbones. It opens up new possibilities for applications in synthetic biology.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Giuseppe Gianini Figueiredo Leite, Bianca Lima Ferreira, Alexandre Keiji Tashima, Erika Sayuri Nishiduka, Edecio Cunha-Neto, Milena Karina Colo Brunialti, Murillo Assuncao, Luciano Cesar Pontes Azevedo, Flavio Freitas, Tom van der Poll, Brendon P. Scicluna, Reinaldo Salomao
Summary: Sepsis, a global health emergency, causes changes in gene expression, protein coding, and metabolism due to various infections. Through transcriptome and proteome profiling, this study identified 170 co-differentially expressed genes/proteins, with 122 showing the same expression trend. Pathway analysis revealed decreased lymphocyte functions and increased defense processes. Additionally, an upregulated module related to LDNs was identified.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Isam Elamri, Chahinez Abdellaoui, Jasleen Kaur Bains, Katharina Felicitas Hohmann, Santosh Lakshmi Gande, Elke Stirnal, Josef Wachtveitl, Harald Schwalbe
Summary: PPGs are essential in biochemical studies for controlled release of effector molecules. The new TPOM method allows for both release and suppression of effector molecules through orthogonal photolysis of two PPGs. This strategy provides a precise and valuable tool for regulating biological processes with light.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Roberto Natale, Mariangela Coppola, Nunzio D'Agostino, Youjun Zhang, Alisdair Robert Fernie, Valeria Castaldi, Rosa Rao
Summary: ProSys interacts with multiple proteins in tomato plants, contributing to defense responses and revealing the molecular mechanisms underlying ProSys-associated defense.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Rei Nishiguchi, Toyohisa Tanaka, Jun Hayashida, Tomoya Nakagita, Wei Zhou, Hiroyuki Takeda
Summary: In this study, a wheat cell-free membrane protein production system was used to synthetize 250 clones of human channels, including various types of channel proteins. 95% of the channels were successfully synthesized, including very large channels with molecular weights of over 200 kDa. Functional analysis revealed that the majority of the synthesized voltage-gated potassium ion channels displayed voltage-dependent opening. The results demonstrate that cell-free protein synthesis provides a promising solution for channel studies.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)