Protein interaction surface mapping using MS is widely applied but comparatively resource-intensive. Here, a workflow adaptation for use of isotope-coded tandem mass tags for the purpose is reported. The key benefit of improved throughput derived from sample acquisition multiplexing and automated analysis is shown to be maintained in the new application. Mapping of the epitopes of two monoclonal antibodies on their respective targets serves to illustrate the novel approach. We conclude that the approach enables mapping of interactions by MS at significantly larger scales than hereto possible.
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http://dx.doi.org/10.1021/acs.analchem.5b01410 | DOI Listing |
J Chem Inf Model
December 2024
School of Physics, Shandong University, Jinan 250100, China.
In recent years, the deep learning (DL) technique has rapidly developed and shown great success in scoring the protein-ligand binding affinities. The protein-ligand conformation optimization based on DL-derived scoring functions holds broad application prospects, for instance, drug design and enzyme engineering. In this study, we evaluated the robustness of a DL-based ligand conformation optimization protocol (DeepRMSD+Vina) for optimizing structures with input perturbations by examining the predicted ligand binding poses and scoring.
View Article and Find Full Text PDFChembiochem
December 2024
Hunan University, College of Chemistry and Chemical Engineering, Yuelu, 410082, Changsha, CHINA.
Adeno-associated virus (AAV) has emerged as a powerful and effective tool for the delivery of exogenous genes into various cells or tissues. To improve the gene delivery efficiency, as well as the safety and specificity of AAV's cell-targeting capabilities, extensive investigations have been conducted into its molecular biological characteristics, including capsid structure, cellular tropism, and the mechanisms underlying its entry, replication, DNA packaging, and capsid assembly. Significant differences exist between human and non-human primate AAVs regarding tissue targeting and transduction efficiency.
View Article and Find Full Text PDFCell Biol Toxicol
December 2024
Department of General Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, People's Republic of China.
The prevalence of breast cancer (BRCA) is notable in the female population, being a commonly diagnosed malignancy, where the management of copper levels is crucial for treatment success. This research aims to explore the influence of copper homeostasis on BRCA therapy, with a specific focus on the role of Cyclin-Dependent Kinase 1 (CDK1) and its relationship to copper regulation. A novel thermosensitive hydrogel incorporating nanoparticles (NPs) was engineered to synergize with the chemotherapy drug vincristine (VCR) in inhibiting tumor growth and metastasis.
View Article and Find Full Text PDFProtein Sci
January 2025
Department of Physical Chemistry, Institute of Biotechnology, and Unit of Excellence in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Granada, Spain.
The ubiquitin E2 variant domain of TSG101 (TSG101-UEV) plays a pivotal role in protein sorting and virus budding by recognizing PTAP motifs within ubiquitinated proteins. Disruption of TSG101-UEV/PTAP interactions has emerged as a promising strategy for the development of host-oriented broad-spectrum antivirals with low susceptibility to resistance. TSG101 is a challenging target characterized by an extended and flat binding interface, low affinity for PTAP ligands, and complex binding energetics.
View Article and Find Full Text PDFJ Cell Mol Med
December 2024
Department of Critical Care Medicine, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China.
Sevoflurane's potential impact on cognitive function and neurodevelopment, especially in susceptible populations such as infants and the elderly, has raised widespread concern. This study focuses on how sevoflurane induces ferroptosis in astrocytes and identifies solute carrier family 7 member 11 (SLC7A11) as a mediator of ferroptosis, providing new insights into sevoflurane-related neurotoxic pathways. We analysed single-cell sequencing (scRNA-seq) data from sevoflurane-exposed mice and control mice, supplemented with bulk RNA-seq data, to assess gene expression alterations.
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