Search Results - "Deniz, Ashok A"

Reentrant Phase Transitions and Non-Equilibrium Dynamics in Membraneless Organelles by Milin, Anthony N, Deniz, Ashok A

“…Compartmentalization of biochemical components, interactions, and reactions is critical for the function of cells. While intracellular partitioning of…”
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Reentrant Phase Transition Drives Dynamic Substructure Formation in Ribonucleoprotein Droplets by Banerjee, Priya R., Milin, Anthony N., Moosa, Mahdi Muhammad, Onuchic, Paulo L., Deniz, Ashok A.

“…Intracellular ribonucleoprotein (RNP) granules are membrane‐less droplet organelles that are thought to regulate posttranscriptional gene expression. While…”
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Modulation of allostery by protein intrinsic disorder by Ferreon, Allan Chris M., Ferreon, Josephine C., Wright, Peter E., Deniz, Ashok A.

“…Single-molecule FRET is used to examine how an intrinsically disordered protein, the adenovirus E1A oncoprotein, interacts with two different protein partners…”
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Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation by Mitrea, Diana M., Cika, Jaclyn A., Stanley, Christopher B., Nourse, Amanda, Onuchic, Paulo L., Banerjee, Priya R., Phillips, Aaron H., Park, Cheon-Gil, Deniz, Ashok A., Kriwacki, Richard W.

“…Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes…”
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Physical Chemistry of Cellular Liquid‐Phase Separation by Bentley, Emily P., Frey, Benjamin B., Deniz, Ashok A.

“…Compartmentalization of biochemical processes is essential for cell function. Although membrane‐bound organelles are well studied in this context, recent work…”
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Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA by Mitrea, Diana M, Cika, Jaclyn A, Guy, Clifford S, Ban, David, Banerjee, Priya R, Stanley, Christopher B, Nourse, Amanda, Deniz, Ashok A, Kriwacki, Richard W

“…The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that…”
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Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence by Ferreon, Allan Chris M, Gambin, Yann, Lemke, Edward A, Deniz, Ashok A

“…We studied the coupled binding and folding of α-synuclein, an intrinsically disordered protein linked with Parkinson's disease. Using single-molecule…”
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FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices by Lerner, Eitan, Barth, Anders, Hendrix, Jelle, Ambrose, Benjamin, Birkedal, Victoria, Blanchard, Scott C, Börner, Richard, Sung Chung, Hoi, Cordes, Thorben, Craggs, Timothy D, Deniz, Ashok A, Diao, Jiajie, Fei, Jingyi, Gonzalez, Ruben L, Gopich, Irina V, Ha, Taekjip, Hanke, Christian A, Haran, Gilad, Hatzakis, Nikos S, Hohng, Sungchul, Hong, Seok-Cheol, Hugel, Thorsten, Ingargiola, Antonino, Joo, Chirlmin, Kapanidis, Achillefs N, Kim, Harold D, Laurence, Ted, Lee, Nam Ki, Lee, Tae-Hee, Lemke, Edward A, Margeat, Emmanuel, Michaelis, Jens, Michalet, Xavier, Myong, Sua, Nettels, Daniel, Peulen, Thomas-Otavio, Ploetz, Evelyn, Razvag, Yair, Robb, Nicole C, Schuler, Benjamin, Soleimaninejad, Hamid, Tang, Chun, Vafabakhsh, Reza, Lamb, Don C, Seidel, Claus Am, Weiss, Shimon

“…Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET…”
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Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB by Bentley, Emily P., Scholl, Daniel, Wright, Peter E., Deniz, Ashok A.

“…The cyclic AMP response element binding protein (CREB) contains a basic leucine zipper motif (bZIP) that forms a coiled coil structure upon dimerization and…”
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Divalent cations can control a switch-like behavior in heterotypic and homotypic RNA coacervates by Onuchic, Paulo L., Milin, Anthony N., Alshareedah, Ibraheem, Deniz, Ashok A., Banerjee, Priya R.

“…Liquid-liquid phase separation (LLPS) of RNA-protein complexes plays a major role in the cellular function of membraneless organelles (MLOs). MLOs are…”
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Single-molecule biophysics: at the interface of biology, physics and chemistry by Deniz, Ashok A, Mukhopadhyay, Samrat, Lemke, Edward A

“…Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to…”
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Topological Considerations in Biomolecular Condensation by Das, Debapriya, Deniz, Ashok A

“…Biomolecular condensation and phase separation are increasingly understood to play crucial roles in cellular compartmentalization and spatiotemporal regulation…”
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Reentrant DNA shells tune polyphosphate condensate size by Chawla, Ravi, Tom, Jenna K. A., Boyd, Tumara, Tu, Nicholas H., Bai, Tanxi, Grotjahn, Danielle A., Park, Donghyun, Deniz, Ashok A., Racki, Lisa R.

“…The inorganic biopolymer polyphosphate (polyP) occurs in all domains of life and affects myriad cellular processes. A longstanding observation is polyP’s…”
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natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures by Mukhopadhyay, Samrat, Krishnan, Rajaraman, Lemke, Edward A, Lindquist, Susan, Deniz, Ashok A

“…The yeast prion protein Sup35 is a translation termination factor, whose activity is modulated by sequestration into a self-perpetuating amyloid. The…”
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Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories by Fang, Jingru, Castillon, Guillaume, Phan, Sebastien, McArdle, Sara, Hariharan, Chitra, Adams, Aiyana, Ellisman, Mark H., Deniz, Ashok A., Saphire, Erica Ollmann

“…Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather…”
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Conserved features of intermediates in amyloid assembly determine their benign or toxic states by Krishnan, Rajaraman, Goodman, Jessica L, Mukhopadhyay, Samrat, Pacheco, Chris D, Lemke, Edward A, Deniz, Ashok A, Lindquist, Susan

“…Some amyloid-forming polypeptides are associated with devastating human diseases and others provide important biological functions. For both, oligomeric…”
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Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape by Ferreon, Allan Chris M, Moosa, Mahdi Muhammad, Gambin, Yann, Deniz, Ashok A

“…Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes…”
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Protocol for preparing cyclic-phospholipid decanoate and glyceryl-didecanoate-phosphate-containing vesicles by Veena, Kollery S., Pulletikurti, Sunil, Deniz, Ashok A., Krishnamurthy, Ramanarayanan

“…Cyclic-phospholipids-based vesicles can play a role in facilitating the chemical evolution of protocells from the structurally simple to the functionally more…”
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Forced Folding of a Disordered Protein Accesses an Alternative Folding Landscape by Moosa, Mahdi Muhammad, Ferreon, Allan Chris M., Deniz, Ashok A.

“…Intrinsically disordered proteins (IDPs) are involved in diverse cellular functions. Many IDPs can interact with multiple binding partners, resulting in their…”
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Percolation physics and density transition frameworks converge in biomolecular condensation by Deniz, Ashok A

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