pFind Studio: a computational solution for mass spectrometry-based proteomics
2024
2024. Lyu, Mingming et al.
College of Computer Science and Technology, Shandong University of Technology, Zibo, China
ABSTRACT:
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Advanced Science2024. Zhou, Wen et al.
lihuazhang@dicp.ac.cn
ABSTRACT:The study of in situ conformations and interactions of mitochondrial proteins plays a crucial role in understanding their biological functions. Current chemical cross-linking mass spectrometry (CX-MS) has difficulty in achieving in-depth analysis of mitochondrial proteins for cells without genetic modification. Herein, this work develops the reactive oxygen species (ROS)-responsive cross-linker delivery nanoparticles (R-CDNP) targeting mitochondria. R-CDNP contains mitochondria-targeting module triphenylphosphine, ROS-responsive module thioketal, loading module poly(lactic-co-glycolic acid) (PLGA), and polyethylene glycol (PEG), and cross-linker module disuccinimidyl suberate (DSS). After targeting mitochondria, ROS-triggered cross-linker release improves the cross-linking coverage of mitochondria in situ. In total, this work identifies 2103 cross-linked sites of 572 mitochondrial proteins in HepG2 cells. 1718 intra-links reveal dynamic conformations involving chaperones with ATP-dependent conformation cycles, and 385 inter-links reveal dynamic interactions involving OXPHOS complexes and 27 pairs of possible potential interactions. These results signify that R-CDNP can achieve dynamic conformation and interaction analysis of mitochondrial proteins in living cells, thereby contributing to a better understanding of their biological functions.
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Journal of Lipid Research2024. Sarkar, Snigdha et al.
Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, USA
ABSTRACT:
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Acta Pharmaceutica Sinica B2024. Li, Li et al.
State Key Laboratory of Cellular Stress Biology,School of Life Sciences,Faculty of Medicine and Life Sciences,Xiamen University,Xiamen361102,China
ABSTRACT:
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Journal of Proteome Research2024. Hoenger Ramazanova, Runa D et al.
Functional Proteomics team, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, United Kingdom
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Scientific Data2024. de Oliveira Veloso Rezende, J{\'e}ssica et al.
Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz Paran, Paran, Brazil
ABSTRACT:
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Nature Communications2024. Chen, Ke et al.
Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
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Structure2024. Ludzia, Patryk et al.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Nature Communications2024. Tang, Di et al.
Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
ABSTRACT:
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Nature Communications2024. Le Bihan, Thierry et al.
Rapid Novor, Kitchener, ON, Canada
ABSTRACT:
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