A “Knob Switch” Model for the Phosphoregulatory Mechanism of KCC3 at the Carboxy-Terminal Domain

Biochemistry, Год журнала: 2025, Номер unknown

Опубликована: Фев. 26, 2025

Phosphorylation is a reversible post-translational modification that can modulate protein function. For example, phosphorylation modifications of solute carrier family 12 (SLC12) proteins function as molecular switches precisely regulate cation–chloride ion transport. Elucidating the phosphoregulatory mechanism SLC12 at carboxy-terminal domain (CTD) through structural determination approaches remains challenging due to domain's disordered and flexible nature. In this study, dynamics (MD) simulations enhanced sampling techniques were employed investigate CTD SLC12A6 (also known KCC3). Atomistic MD metadynamics revealed dephosphorylation residues T940 T997 stabilizes favorable state "switches on" solvent accessibility inward-facing pocket. Meanwhile, induces distinct orientations CTD, transitioning dimer into another off" accessibility. The alteration in pocket influences water dynamics. Based on these findings, we propose "knob switch" model illustrate how regulates transport KCC3.

Язык: Английский

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Coarse-Grained Simulations of Phosphorylation Regulation of p53 Autoinhibition

Biochemistry, Год журнала: 2025, Номер unknown

Опубликована: Март 18, 2025

Intrinsically disordered proteins (IDPs) are key components of cellular signaling and regulatory networks. They frequently remain dynamic even in complexes thus rely on potentially subtle shifts the conformational ensemble for function. Understanding molecular basis these fascinating mechanisms IDP function regulation requires a detailed characterization ensembles various biologically relevant states. Here, we study phosphorylation dependence interaction between N-terminal transactivation domain (NTAD) DNA-binding (DBD) tumor suppressor p53, which plays role autoinhibition p53 activation or termination during stages stress response. By extending hybrid-resolution (HyRes) coarse-grained (CG) protein force field to model phosphorylated side chains, show that HyRes simulations accurately recapitulate effects NTAD/DBD interactions. The simulated Thr55 as well Ser46 enhances interactions further induces promote trans two dimers drive dissociation from DNA. These CG provide strong support previous experimental studies suggesting central domains p53. success this also suggests provides an efficient viable tool studying post-translational modifications regulation.

Язык: Английский

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Assessing the relation between protein phosphorylation, AlphaFold3 models and conformational variability

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 18, 2025

Abstract Proteins perform diverse functions critical to cellular processes. Transitions between functional states are often regulated by post-translational modifications (PTMs) such as phosphorylation, which dynamically influence protein structure, function, folding, and interactions. Dysregulation of PTMs can therefore contribute diseases cancer Alzheimer’s. However, the structure-function relationship proteins their remains poorly understood due a lack experimental structural data, inherent diversity PTMs, dynamic nature proteins. Recent advances in deep learning, particularly AlphaFold, have transformed structure prediction with near-experimental accuracy. it unclear whether these models effectively capture PTM-driven conformational changes, those induced phosphorylation. Here, we systematically evaluated AlphaFold (AF2, AF3-non phospho, AF3-phospho) assess ability predict phosphorylation-induced diversity. By analysing experimentally derived ensembles, found that all predominantly aligned dominant states, failing phosphorylation-specific conformations. Despite its phosphorylation-aware design, AF3-phospho predictions provided only modest improvement over AF2 phospho predictions. Our findings highlight key challenges modelling landscapes underscore need for more adaptable frameworks capable capturing modification-induced variability.

Язык: Английский

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Intrinsically Disordered Peptide Nanofibers from A Structured Motif within Proteins

Angewandte Chemie International Edition, Год журнала: 2025, Номер unknown

Опубликована: Апрель 28, 2025

Intrinsically disordered regions (IDRs) are ubiquitous in proteins, orchestrating complex cellular signaling through higher-order protein assemblies. However, the properties and functions of intrinsically peptide (IDP) assemblies largely underexplored. This work unveiled a facile strategy for engineering IDP We demonstrate that conjugating structured motif derived from protein's phosphorylation site to self-assembling tripeptide unexpectedly yields self-assembled nanofibers with intrinsic disorder. Specifically, by using glycine linker attach pentapeptide within random coil region SRC kinase C-terminus widely used enabler, we generated phosphorylated octapeptide. The octapeptide exhibits cell compatibility forms hydrogel upon dephosphorylation phosphooctapeptide. Cryo-electron microscopy (cryo-EM) structural analysis reveals peptides adopt two types helical arrangements but exhibit disorder at periphery nanofibers. hydrogels decreased adsorption increasing concentration. study represents first instance transitioning into an state nanofibers, expanding pool sequences IDPs providing valuable insights development cell-compatible biomaterials.

Язык: Английский

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nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat

Journal of Chemical Information and Modeling, Год журнала: 2024, Номер 64(16), С. 6570 - 6582

Опубликована: Авг. 2, 2024

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity for microtubules, abnormal patterns involved Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared conformational landscapes explored R2 repeat domain (which comprises strong tubulin site) its native state with phosphorylations on S285, S289, S293 residues, four different standard force field (FF)/water model combinations. We find parameters used phosphate groups more or less flexible) these FFs specific interactions between bulk cations water lead formation type counterion bridge, termed

Язык: Английский

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Progress in Lactate Metabolism and Its Regulation via Small Molecule Drugs

Molecules, Год журнала: 2024, Номер 29(23), С. 5656 - 5656

Опубликована: Ноя. 29, 2024

Lactate, once viewed as a byproduct of glycolysis and metabolic “waste”, is now recognized an energy-providing substrate signaling molecule that modulates cellular functions under pathological conditions. The discovery histone lactylation in 2019 marked paradigm shift, with subsequent studies revealing lactate can undergo both non-histone proteins, implicating it the pathogenesis various diseases, including cancer, liver fibrosis, sepsis, ischemic stroke, acute kidney injury. Aberrant metabolism associated disease onset, its levels predict outcomes. Targeting production, transport, may offer therapeutic potential for multiple yet systematic summary small molecules modulating diseases lacking. This review outlines sources clearance lactate, well roles myocardial infarction, injury, summarizes effects on regulation. It aims to provide reference direction future research.

Язык: Английский

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