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Kocak, D. D.

Publications and source records attributed to Kocak, D. D..

2 recordsLinked to original sources

Cryo-EM Structures of Brain-Derived G Protein-Coupled Receptors: The First Direct Visualization from Mammalian Brain Tissue

Glutamate is the main excitatory neurotransmitter in the brain and mediates its actions by both ionotropic (e.g. NMDA and AMPA) and metabotropic glutamate receptors (mGluRs). The Groups II and III mGluRs, which pre-synaptically inhibit glutamate release, are important for synaptic plasticity, modulating neuronal excitation, learning and memory. Our current understanding of the structural organization and dynamics of these and other mGluRs, as well as most other GPCRs, relies mainly on studies using recombinant and highly engineered systems in vitro. Here, we combine CRISPR-mediated protein tagging, proteomics and a rapid immunoaffinity purification method to isolate endogenous mGluR2-containing assemblies from mouse brain and visualize them via cryo-EM. Analysis of the particle sets reveals the molecular structures of at least 11 distinct endogenous receptor assemblies that span active and inactive states, homomeric and heteromeric dimers, and G protein-coupled and uncoupled species. We find that mGluR2 homodimers and mGluR2/3 heterodimers are the major endogenous mGluR2-containing species present in the brain, with the mGluR2/3 heterodimers detected only in active state complexes, potentially reflecting basal activation of mGluR3 containing dimers by chloride. Reconstructing a comprehensive conformational equilibrium for the brain-isolated receptors in detergent reveals endogenous ternary complexes comprising mGluR2 homodimers and mGluR2/3 heterodimers with a single GoA heterotrimer which exhibit significant differences from prior studies with recombinant systems. Our work illuminates the endogenous conformational, proteomic and compositional landscape of the heterogenous mGluR2 complexes in the brain, thereby providing a structural framework for the pathophysiology of psychiatric disorders. This information has the potential to be leveraged for therapeutic targeting of endogenous glutamatergic signaling complexes.

neuroscience↗

SMARCA2 is an essential and potent cofactor for a specific subset of the glucocorticoid response in A549 cells

Glucocorticoids are a widely used, potent class of anti-inflammatory drugs that modulate the expression of hundreds of genes across the genome. Although the glucocorticoid response is primarily carried out by the glucocorticoid receptor (NR3C1, a.k.a. GR), there are many glucocorticoid receptor co-factors that are also essential to the downstream effects. To identify novel factors necessary for the glucocorticoid gene expression response, we used a genome-wide CRISPR screen in A549 lung adenocarcinoma cells. In that screen, we knocked out every gene in the human genome, and measured the effect of expression of the glucocorticoid-induced leucine zipper (GILZ), a classic glucocorticoid-response gene. We identified two chromatin remodeling proteins, SMARCA2 and BPTF, that are essential for GILZ expression. We then evaluated the genome-wide effects of SMARCA2 and BPTF on glucocorticoid-mediated gene expression. BPTF had a highly specific role in the glucocorticoid response, affecting the expression of only a handful of genes, and having virtually no effect on dexamethasone-induced changes in chromatin accessibility. However, SMARCA2 was necessary for 27% of dexamethasone-induced transcriptional changes (152 genes), and [~]7% of dexamethasone-induced changes in chromatin accessibility (586 regions of the genome). Genomic regions with SMARCA2-dependent changes in chromatin accessibility were characterized by high dexamethasone-induced regulatory activity in a massively parallel reporter assay, and dexamethasone-induced increases in transcription factor binding and chromatin states. Taken together, these data suggest that SMARCA2 is critical for chromatin remodeling at a specific set of genomic regions with high regulatory activity, which in turn drive changes in expression for many glucocorticoid-responsive genes.

genomics↗