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Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered proteins is an onerous task, primarily because these proteins adopt transient structures, which are difficult to capture in experiments. Simulations have emerged as a powerful tool for interpreting and augmenting experimental measurements of IDPs. In this review we focus on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today.
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http://dx.doi.org/10.1016/j.sbi.2016.11.006 | DOI Listing |
Open Res Eur
July 2025
REQUIMTE LAQV Porto, Porto, Porto District, Portugal.
The 2024 Nobel Prizes in Chemistry and Physics mark a watershed moment in the convergence of artificial intelligence (AI) and molecular biology. This article explores how AI, particularly deep learning and neural networks, has revolutionized protein science through breakthroughs in structure prediction and computational design. It highlights the contributions of 2024 Nobel laureates John Hopfield, Geoffrey Hinton, David Baker, Demis Hassabis, and John Jumper, whose foundational work laid the groundwork for AI tools such as AlphaFold.
View Article and Find Full Text PDFJ Neurochem
September 2025
Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
Memory formation involves a complex interplay of molecular and cellular processes, including synaptic plasticity mechanisms such as long-term potentiation (LTP) and long-term depression (LTD). These processes rely on activity-dependent gene expression and local protein synthesis at synapses. A central unresolved question in neuroscience is how memories can be stably maintained over time, despite the transient nature of the proteins involved in their initial encoding.
View Article and Find Full Text PDFBiophys Chem
September 2025
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway.
View Article and Find Full Text PDFJ Mol Biol
September 2025
Department of Biochemistry and Biophysics Oregon State University, Corvallis, Oregon, USA. Electronic address:
Ferlins are vesicle trafficking proteins composed of folded C2 domains conjugated by linkers which are largely disordered. Although a role for the C2 domains as calcium sensors has been established it remains unclear whether the linkers function beyond acting as passive spacers. We examined the C2A-C2B linker sequences of vertebrate ferlins and found both putative short linear motifs (SLiMs) as well as membrane binding sequences for members of the protein family.
View Article and Find Full Text PDFBiochemistry
September 2025
Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States.
SAMHD1 (SAM domain and HD domain-containing protein 1) is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) with functions in viral restriction, R-loop resolution, DNA repair, telomere maintenance, ssRNA homeostasis, and regulation of self-nucleic acids. As a dNTPase, SAMHD1 functions as an allosterically activated tetramer, where binding of GTP to the A1 activator site of each monomer initiates dNTP-dependent tetramerization. cEM structures reveal that the nucleic-acid-related functions of SAMHD1 involve binding of guanine residues to the A1 site, leading to oligomeric forms that appear as beads-on-a-string on single-stranded RNA and DNA.
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