Review
Cell Biology
Sylvain D. Vallet, Coline Berthollier, Sylvie Ricard-Blum
Summary: Glycosaminoglycans (GAGs) are complex linear polysaccharides that play important roles in the extracellular matrix and cell surface. By generating an expanded dataset, we have gained a better understanding of the interactions and functions of GAGs, as well as the biological processes and pathways involved.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sungyul Lee, Young-suk Lee, Yeon Choi, Ahyeon Son, Youngran Park, Kyung-Min Lee, Jeesoo Kim, Jong-Seo Kim, V. Narry Kim
Summary: The study reveals the interactions between SARS-CoV-2 and host RNA-binding proteins, provides a comprehensive list of RBPs regulating coronaviral replication, and opens new avenues for therapeutic interventions.
Review
Biochemistry & Molecular Biology
Susanna Tornroth-Horsefield, Clara Chivasso, Helin Strandberg, Claudia D'Agostino, Carla V. T. O'Neale, Kevin L. Schey, Christine Delporte
Summary: This review provides a comprehensive overview of the current knowledge of AQP interactomes and discusses the molecular basis and functional significance of these protein-protein interactions in health and diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Amira Moustafa, Sara Hashemi, Gurnoor Brar, Jorg Grigull, Siemon H. S. Ng, Declan Williams, Gerold Schmitt-Ulms, John C. McDermott
Summary: Transcriptional regulators encoded by the MEF2 gene family have a fundamental role in cardiac development, homeostasis, and pathology. Through a systematic screen, we identified a dynamic interaction between MEF2A and STAT3 proteins, which play an important role in the regulation of inflammation and cardiomyocyte cell survival. This study provides information about the MEF2A protein interactome in cardiomyocytes, enhancing our understanding of the hierarchical control of gene expression in normal and pathophysiological conditions.
CELL DEATH & DISEASE
(2023)
Review
Chemistry, Multidisciplinary
Ciaran P. Seath, Aaron D. Trowbridge, Tom W. Muir, David W. C. MacMillan
Summary: Biomolecular interactions are crucial for cellular processes, with a focus on protein-protein interactions playing a key role in cellular signaling pathways. Recent advancements in creating reactive intermediates that cross-link neighboring proteins have provided insights into the biomolecular makeup of cellular environments, accelerating the understanding of PPIs and their impact on cellular physiology.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Biochemistry & Molecular Biology
Colin A. Fox, Robert O. Ryan
Summary: Cardiolipin (CL) is a crucial component in the structure and function of mitochondria, inducing negative membrane curvature and interacting with various ligands. However, studying these interactions in intact mitochondria is challenging, thus the development of a soluble model membrane system called nanodisks (ND) provides an alternative approach.
PROGRESS IN LIPID RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Elise Malard, Samuel Valable, Myriam Bernaudin, Elodie Peres, Laurent Chatre
Summary: Helmut Sies introduced three definitions of reactive species challenges: oxidative stress, oxidative eustress, and oxidative distress. The Reactive Species Interactome (RSI) is a new redox regulatory system that identifies reactive species families and their interactions. Future studies should focus on understanding the contributions of reactive species through identification, concentration, and interactions, especially in the brain.
ANTIOXIDANTS & REDOX SIGNALING
(2021)
Article
Plant Sciences
Merve Yilmaz, Merle Paulic, Thorsten Seidel
Summary: This study reports a protein-protein interaction network of Arabidopsis thaliana, combining various types of information such as subcellular localization, gene ontologies, biochemical properties, and co-expression. The resulting network shows enrichment in nuclear, cytosolic, and plasma membrane proteins, while being depleted in extracellular and mitochondrial proteins. Additionally, proteins involved in transcription are highly abundant in the network.
Article
Biochemistry & Molecular Biology
Yang Du, Meng Cai, Xiaofang Xing, Jiafu Ji, Ence Yang, Jianmin Wu
Summary: The PINA platform has been updated to version 3.0, integrating a unified human interactome with cancer type-specific RNA-seq transcriptomes and mass spectrometry-based proteomes. New analytical tools have been developed to help users identify cancer-specific protein expression, potential biomarkers, and therapeutic targets.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Justina Sileikyt, Sunil Sundalam, Larry L. David, Michael S. Cohen
Summary: Nicotinamide adenine dinucleotide (NAD(+)) is a multifunctional molecule with important functions in redox metabolism and as a substrate for post-translational modification enzymes. Recent discoveries of noncanonical NAD-binding proteins suggest a larger NAD interactome than previously thought. Newly designed chemical tools, 2- and 6-ad-BAD, have been shown to efficiently profile NAD-binding proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Cell Biology
Yi Xin (Iris) Tu, Andrew M. Sydor, Etienne Coyaud, Estelle M. N. Laurent, Diana Dyer, Nora Mellouk, Jonathan St-Germain, Robert M. Vernon, Julie D. Forman-Kay, Taoyingnan Li, Rong Hua, Kexin Zhao, Neale D. Ridgway, Peter K. Kim, Brian Raught, John H. Brumell
Summary: This study identified a network of interactions among core human macroautophagy proteins using proximity-dependent biotin identification, highlighting the critical role of OSBPL family members in the macroautophagy process.
Article
Cell Biology
Catherine R. Dufour, Charlotte Scholtes, Ming Yan, Yonghong Chen, Lingwei Han, Ting Li, Hui Xia, Qiyun Deng, Mathieu Vernier, Vincent Giguere
Summary: An increasing number of studies support the direct role of nuclear mTOR in gene regulation and chromatin structure. However, the limited knowledge of chromatin-bound mTOR partners restricts our understanding of how nuclear mTOR controls transcription. This study comprehensively maps the mTOR chromatin-bound interactome in prostate cancer cellular models and identifies a 67-protein interaction network enriched with chromatin modifiers, transcription factors, and SUMOylation machinery. SUMO2/3 and nuclear pore protein NUP210 are among the strongest interactors, while the androgen receptor (AR) is the dominant androgen-inducible mTOR partner. Further investigation reveals the role of NUP210 in mTOR nuclear trafficking, the functional transcriptional module formed by mTOR, AR, and the nucleosome remodeling and deacetylase (NuRD) complex, and the androgen-dependent mTOR-SUMO2/3 promoter-enhancer association.
Article
Multidisciplinary Sciences
Milosz Chodkowski, Andrzej Zielezinski, Savani Anbalagan
Summary: By using a deep learning algorithm, we predicted the cellular localization of zebrafish reference proteome and created repositories of zebrafish ligands, membrane receptome, and interactome, as well as associated diseases and targeting drugs. These resources are available as R and Python scripts, providing a new resource for researchers interested in targeting cellular communication in zebrafish.
Article
Cell Biology
Laura M. Szczesniak, Caden G. Bonzerato, Richard J. H. Wojcikiewicz
Summary: The study revealed the interactome of Bok with various proteins, particularly those related to mitochondrial fission and cellular structures. It also identified novel physical and functional interactions between Bok and Mcl-1.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mason Stillman, Jonathan D. Lautz, Richard S. Johnson, Michael J. MacCoss, Stephen E. P. Smith
Summary: Neurons encode information by modifying synaptic protein complexes, and Homer1's binding to mGlu5 and Shank3 changes in response to synaptic activity. A study in the cerebral cortex found an activity-dependent protein network involving mGlu5, Shank2 and 3, and Homer1-3, with only mGlu5 and Shank3 significantly reduced after neuronal depolarization.
SCIENTIFIC REPORTS
(2022)
