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| http://dx.doi.org/10.1021/acscentsci.0c01499 | DOI Listing |
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Plasma membrane-associated ARAF condensates fuel RAS-related cancer drug resistance.
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Zhejiang Key Laboratory of Molecular Cancer Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
RAF protein kinases are major RAS effectors that function by phosphorylating MEK. Although all three RAF isoforms share a conserved RAS binding domain and bind to GTP-loaded RAS, only ARAF uniquely enhances RAS activity. Here we uncovered the molecular basis of ARAF in regulating RAS activation.
View Article and Find Full Text PDFA study of alpha-synuclein and poly(-isopropylacrylamide) complex formation through detailed atomistic simulations.
Soft Matter
January 2025
Computation-based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus.
This work presents an investigation of the influence of poly(-isopropylacrylamide) (PNIPAM) polymer on the structural dynamics of intrinsically disordered alpha-synuclein (α-syn) protein, exploring the formation and intricate features of the resulting α-syn/PNIPAM complexes. Using atomistic molecular dynamics (MD) simulations, our study analyzes the impact of initial configuration, polymer molecular weight, and protein mutations on the α-syn and the α-syn/PNIPAM complex. Atomistic simulations, of a few μs, of the protein/polymer complex reveal crucial insights into molecular interactions within the complex, emphasizing a delicate balance of forces governing its stability and structural evolution.
View Article and Find Full Text PDFOur current understanding of protein folding is based predominantly on studies of small (<150 aa) proteins that refold reversibly from a chemically denatured state. As protein length increases, the competition between off-pathway misfolding and on-pathway folding likewise increases, creating a more complex energy landscape. Little is known about how intermediates populated during the folding of larger proteins affect navigation of this more complex landscape.
View Article and Find Full Text PDFA variational graph-partitioning approach to modeling protein liquid-liquid phase separation.
Cell Rep Phys Sci
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Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs.
View Article and Find Full Text PDFMolecular Drivers of Aging in Biomolecular Condensates: Desolvation, Rigidification, and Sticker Lifetimes.
PRX Life
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Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
Biomolecular condensates are dynamic intracellular entities defined by their sequence- and composition-encoded material properties. During aging, these properties can change dramatically, potentially leading to pathological solidlike states, the mechanisms of which remain poorly understood. Recent experiments reveal that the aging of condensates involves a complex interplay of solvent depletion, strengthening of sticker links, and the formation of rigid structural segments such as beta fibrils.
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