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Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Updated: Oct 3, 2025

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

Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.

Ana V Rojas¹, Gia G Maisuradze², Harold A Scheraga²

¹Schrodinger Inc., 120 West 45th Street New York, New York, 10036, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)

|February 15, 2022

Summary

This summary is machine-generated.

Investigating protein aggregation, a cause of neurodegenerative diseases, is challenging due to long timescales. This study uses coarse-grained models and the UNRES force field to simulate protein aggregation, aiding in understanding disease mechanisms.

Keywords:

Coarse graining Molecular dynamics Protein aggregation UNRES force field

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Area of Science:

Biophysics
Computational Biology
Molecular Medicine

Background:

Protein aggregation is implicated in lethal diseases like Alzheimer's and Parkinson's.
Understanding the toxic oligomeric intermediates of protein aggregation is crucial.
Simulating these processes is difficult due to the extensive timescales involved.

Purpose of the Study:

To apply the physics-based UNited RESidue (UNRES) force field for protein aggregation studies.
To investigate protein aggregation mechanisms using coarse-grained models.
To simulate both free and seeded aggregation processes.

Main Methods:

Utilized coarse-grained modeling to extend simulation timescales by orders of magnitude.
Applied the UNRES force field for physics-based simulations of protein aggregation.
Performed simulations of amyloid-beta (Aβ) peptide aggregation and tau (TauRD) peptide aggregation.

Main Results:

Demonstrated the utility of UNRES force field in simulating protein aggregation.
Successfully modeled Aβ-peptide aggregation.
Showcased Aβ-peptide-assisted aggregation of TauRD peptides.

Conclusions:

Coarse-grained models, specifically UNRES, are advantageous for studying protein aggregation.
The UNRES force field can effectively simulate complex aggregation pathways.
This approach provides insights into the mechanisms of protein misfolding diseases.