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Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: Jul 4, 2026

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at

Shanlong Li, Shrishti Barethiya, Jianhan Chen

    Biorxiv : the Preprint Server for Biology
    |July 3, 2026
    PubMed
    Summary
    This summary is machine-generated.

    HyRes, a novel protein model, efficiently simulates intrinsically disordered proteins (IDPs) and their interactions. This tool aids in understanding cellular regulation and disease by providing large-scale disordered protein ensemble data.

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    Last Updated: Jul 4, 2026

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    Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

    Published on: July 8, 2025

    Area of Science:

    • Biophysics
    • Computational Biology
    • Structural Biology

    Background:

    • Intrinsically disordered proteins (IDPs) are crucial for cellular regulation but challenging to study due to their dynamic nature.
    • Existing methods struggle to balance accuracy and computational efficiency for large-scale IDP analysis.

    Purpose of the Study:

    • To develop a physics-based, hybrid-resolution protein model (HyRes) for efficient and accurate simulation of IDP conformational ensembles.
    • To assess HyRes's performance against established methods and its transferability across various biological environments.

    Main Methods:

    • Developed HyRes, a hybrid-resolution model with atomistic backbones and intermediate-resolution sidechains.
    • Validated HyRes across ~100 IDPs, comparing results to all-atom force fields.
    • Applied HyRes to generate ensembles for ~30,000 human proteome and DisProt IDPs.

    Main Results:

    • HyRes accurately reproduces experimental chain dimensions, transient contacts, and secondary structures of IDPs.
    • The model demonstrates exceptional transferability, capturing IDP dynamics in dilute, condensed, and amyloidogenic phases.
    • A strong correlation was found between residual structures and cellular function/localization in large-scale IDP analysis.

    Conclusions:

    • HyRes offers a computationally efficient and accurate approach for studying IDP dynamics and interactions.
    • The generated database of disordered ensembles provides valuable resources for IDP biology and deep learning applications.
    • HyRes facilitates a deeper understanding of the link between IDP structure, function, and cellular processes.