AIMC Topic: Phosphorylation

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Mechanistic Basis for GPCR Phosphorylation-Dependent Allosteric Signaling Specificity of β-Arrestin 1 and 2.

Journal of chemical information and modeling Oct 13, 2025
β-Arrestins (βarr1 and βarr2) are key transducers of G protein-coupled receptor (GPCR) signaling, orchestrating both shared and isoform-specific intracellular pathways. Phosphorylation of the receptor C-terminal tail by GPCR kinases encodes regulator...
Machine Learning Signal Transduction Receptors, G-Protein-Coupled Humans Allosteric Regulation beta-Arrestin 1 beta-Arrestin 2 Receptors, Vasopressin Phosphorylation Molecular Dynamics Simulation Protein Conformation
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Mapping Context-Aware Phosphosite Regulation of Protein-Protein Interactions Using Deep Learning and Pan-Cancer Proteomics.

Journal of chemical information and modeling Oct 10, 2025
Phosphorylation dynamically orchestrates the protein-protein interaction (PPI) network that governs cellular signaling, and its dysregulation frequently drives malignant transformation and neurodegeneration. We present PhosPPI-SEQ, an interpretable d...
Deep Learning Cell Line, Tumor Protein Interaction Maps Histone Deacetylase 1 Proteomics Histone Demethylases Phosphorylation Protein Interaction Mapping Humans Neoplasms
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Single-Molecule SERS Detection of Phosphorylation in Serine and Tyrosine Using Deep Learning-Assisted Plasmonic Nanopore.

The journal of physical chemistry letters Aug 8, 2025
Single-molecule detection of post-translational modifications (PTMs) such as phosphorylation plays a crucial role in early diagnosis of diseases and therapeutics development. Although single-molecule surface-enhanced Raman spectroscopy (SM-SERS) dete...
Deep Learning Spectrum Analysis, Raman Nanopores Phosphorylation Tyrosine Serine
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Protein Conformation Protein Kinase Inhibitors Thermodynamics Cyclin-Dependent Kinase 6 Protein Binding Phosphorylation Molecular Dynamics Simulation Humans Deep Learning
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Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.

Nature communications Mar 20, 2025
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, yet our limited knowledge about the regulation and function of most phosphosites hampers the extraction of meaningful biological insights. To address th...
Proteome Signal Transduction Phosphorylation Phosphoproteins Substrate Specificity Machine Learning Neoplasms Proteomics Humans
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Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.

PLoS computational biology Mar 17, 2025
Neutrophils, an essential innate immune cell type with a short lifespan, rely on continuous replenishment from bone marrow (BM) precursors. Although it is established that neutrophils are derived from the granulocyte-macrophage progenitor (GMP), the ...
Neutropenia Humans Mice, Inbred C57BL Protein Serine-Threonine Kinases Phosphorylation Computational Biology Machine Learning Cell Differentiation Intracellular Signaling Peptides and Proteins Neutrophils Animals Mice, Knockout Hematopoietic Stem Cells Apoptosis Mice
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GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks.

International journal of molecular sciences Jan 23, 2025
Phosphorylation is one of the most common protein post-translational modifications. The identification of phosphorylation sites serves as the cornerstone for protein-phosphorylation-related research. This paper proposes a protein-phosphorylation site...
Computational Biology Phosphorylation Neural Networks, Computer Protein Processing, Post-Translational Amino Acid Sequence Graph Neural Networks Software Proteins Algorithms
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Screening of Aβ and phosphorylated tau status in the cerebrospinal fluid through machine learning analysis of portable electroencephalography data.

Scientific reports Jan 15, 2025
Diagnosing Alzheimer's disease (AD) through pathological markers is typically costly and invasive. This study aims to find a noninvasive, cost-effective method using portable electroencephalography (EEG) to detect changes in AD-related biomarkers in ...
Male tau Proteins Electroencephalography Humans Female Amyloid beta-Peptides Middle Aged Alzheimer Disease Machine Learning Aged Phosphorylation Biomarkers Aged, 80 and over
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MMFuncPhos: A Multi-Modal Learning Framework for Identifying Functional Phosphorylation Sites and Their Regulatory Types.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jan 13, 2025
Protein phosphorylation plays a crucial role in regulating a wide range of biological processes, and its dysregulation is strongly linked to various diseases. While many phosphorylation sites have been identified so far, their functionality and regul...
Computational Biology Humans Phosphorylation Deep Learning
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Identification of STAT3 phosphorylation inhibitors using generative deep learning, virtual screening, molecular dynamics simulations, and biological evaluation for non-small cell lung cancer therapy.

Molecular diversity Dec 23, 2024
The development of phosphorylation-suppressing inhibitors targeting Signal Transducer and Activator of Transcription 3 (STAT3) represents a promising therapeutic strategy for non-small cell lung cancer (NSCLC). In this study, a generative model was d...
Lung Neoplasms Protein Binding Carcinoma, Non-Small-Cell Lung Antineoplastic Agents Deep Learning Cell Line, Tumor Binding Sites Phosphorylation Molecular Dynamics Simulation STAT3 Transcription Factor Humans Molecular Docking Simulation
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