Search research articles

Related Concept Videos

Amyloid Fibrils

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins. Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils.
Amyloid deposits were observed as early as 1639 in the liver and the spleen. In 1854, Rudolph Virchow performed iodine staining,...

Amyloid Fibrils

Amyloid Fibrils

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.

bioRxiv : the preprint server for biology·2026

Same author

A principled basis for nonequilibrium network flows.

Nature communications·2026

Same author

"Excluded phenotypes" restrict genetic paths toward adaptation in declining populations.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Statistical Mechanical Theory of Liquid Water.

Journal of chemical theory and computation·2025

Same author

Brain aging shows nonlinear transitions, suggesting a midlife "critical window" for metabolic intervention.

Proceedings of the National Academy of Sciences of the United States of America·2025

Same author

MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.

Journal of chemical information and modeling·2025

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Oct 25, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

MELD-accelerated molecular dynamics help determine amyloid fibril structures.

Bhanita Sharma¹, Ken A Dill^2,3,4

¹Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.

Communications Biology

|August 6, 2021

Summary

Determining protein fibril structures is hard. MELD accelerated Molecular Dynamics (MD) accurately predicts amyloid structures using limited experimental data, paving the way for understanding mechanical properties.

More Related Videos

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

Published on: September 12, 2019

Related Experiment Videos

Last Updated: Oct 25, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

Published on: September 12, 2019

Area of Science:

Biophysics
Structural Biology
Computational Chemistry

Background:

Determining the structures of protein fibrils, such as amyloids, presents significant challenges.
Traditional Molecular Dynamics (MD) modeling is often impractical for large multi-molecular systems like fibrils.

Purpose of the Study:

To demonstrate the capability of MELD accelerated MD (MELD x MD) in predicting amyloid structures from limited experimental data.
To validate the accuracy of MELD x MD predictions against known fibril structures.

Main Methods:

Utilized MELD accelerated MD (MELD x MD) simulations.
Employed Nuclear Magnetic Resonance (NMR) and Solid State NMR (SSNMR) data for long-chain fibril predictions.
Used limited restraints information, including strand directions, for short-chain fibril predictions.

Main Results:

Accurately predicted five long-chain amyloid fibril structures using NMR and SSNMR data.
Successfully predicted ten short-chain amyloid fibril structures with more limited restraints.
The study validated predictions against available structure data.

Conclusions:

MELD x MD is a powerful and accurate method for predicting amyloid structures from limited experimental data.
This physical approach holds promise for elucidating mechanical properties, conformational ensembles, and relative stabilities beyond structure determination.