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Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. MTX-211 purchase Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.Glucocorticoid receptor (GR) is a ligand-dependent transcription factor that plays a central role in inflammation. GR activity is also modulated via protein-protein interactions, including binding of 14-3-3 proteins induced by GR phosphorylation. However, the specific phosphorylation sites on GR that trigger these interactions and their functional consequences are less clear. Hence, we sought to examine this system in more detail. We used phosphorylated GR peptides, biophysical studies and X-ray crystallography to identify key residues within the ligand binding domain of GR, T524 and S617, whose phosphorylation results in binding of the representative 14-3-3 protein 14-3-3ζ. A kinase screen identified MINK1 as responsible for phosphorylating T524 and ROCK1 for phosphorylating S617; cell-based approaches confirmed the importance of both GR phosphosites and MINK1 but not ROCK1 alone in inducing GR-14-3-3 binding. Together our results provide molecular-level insight into 14-3-3-mediated regulation of GR and highlight both MINK1 and the GR-14-3-3 axis as potential targets for future therapeutic intervention.Advances in cancer biology are revealing the importance of the cancer cell microenvironment on tumorigenesis and cancer progression. Hyaluronan (HA), the main glycosaminoglycan in the extracellular matrix, has been associated with the progression of glioblastoma (GBM), the most frequent and lethal primary tumor in the central nervous system, for several decades. However, the mechanisms by which HA impacts GBM properties and processes have been difficult to elucidate. In this review, we provide a comprehensive assessment of the current knowledge on HA's effects on GBM biology, introducing its primary receptors CD44 and RHAMM and the plethora of relevant downstream signaling pathways that can scramble efforts to directly link HA activity to biological outcomes. We consider the complexities of studying an extracellular polymer, and the different strategies used to try to capture its function, including 2D and 3D in vitro studies, patient samples, and in vivo models. Given that HA affects not only migration and invasion, but also cell proliferation, adherence and chemoresistance, we highlight the potential role of HA as a therapeutic target. Finally, we review the different existing approaches to diminish its pro-tumor effects, such as the use of 4-methylumbelliferone, HA oligomers and hyaluronidases, and encourage further research along these lines in order to improve the survival and quality of life of GBM patients.Computational de novo protein design is increasingly applied to address a number of key challenges in biomedicine and biological engineering. Successes in expanding applications are driven by advances in design principles and methods over several decades. Here, we review recent innovations in major aspects of de novo protein design, and include how these advances were informed by principles of protein architecture and interactions derived from the wealth of structures in the PDB. We describe developments in de novo generation of designable backbone structures, in optimization of sequences, in design scoring functions, and in design of function. The advances not only highlight design goals reachable now but also point to the challenges and opportunities for the future of the field.Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1,198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.Preclinical models are a core feature of translational research, and patient-derived xenograft (PDX) models have increasingly been used with such purpose. PDX involves the transplantation of fresh human tumor samples into immunodeficient mice to overcome immunologic rejection. It is a valuable tool for basic as well as preclinical research, contributing to the establishment of models to characterize the neoplasms to drug screening and to allow the identification of therapeutic targets. The use of these models is justified because they retain the histological and genomic features of the primary tumor. PDX models are well described for malignant neoplasms, for which the advantages are clear and include the development of drug treatments. The establishment of malignant tumors PDX is undeniably important from a medical perspective. However, few studies have used such models for benign neoplasms. The use of PDX for benign neoplasm studies can help to clarify the pathobiology of these diseases, as well as invasion and malignant transformation mechanisms, which from a biological perspective is equally important to the study of malignant tumors.
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