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Related Experiment Video

Updated: Sep 1, 2025

Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One α-Synuclein Monomer at a Time

Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One α-Synuclein Monomer at a Time

Published on: May 30, 2021

Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins.

Kasper B Pedersen¹, Jose C Flores-Canales¹, Birgit Schiøtt^1,2

¹Department of Chemistry, Aarhus University, Aarhus C, Denmark.

|August 11, 2022

Summary

Force field validation is crucial for Molecular Dynamics (MD) simulations. The ff19SB/TIP4P-D and a99SB-disp/TIP4P-disp force fields accurately model alpha-synuclein

Keywords:

OPC TIP4P-D a99SB-disp ff03CMAP ff19SB intrinsically disordered proteins α-synuclein

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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

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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:

Computational Chemistry
Biophysics
Structural Biology

Background:

Independent force field validation is essential for accurate Molecular Dynamics (MD) simulations.
Intrinsically disordered proteins (IDPs) present unique challenges for simulation due to their dynamic nature.

Purpose of the Study:

To evaluate the performance of different atomistic force fields for simulating the intrinsically disordered protein alpha-synuclein.
To compare simulation results against experimental data for key biophysical properties.

Main Methods:

Simulated alpha-synuclein using four protein-water force field combinations (ff19SB/OPC, ff19SB/TIP4P-D, ff03CMAP/TIP4P-D, a99SB-disp/TIP4P-disp) for 2.5 microseconds.
Compared simulation trajectories to a longer 73-microsecond simulation and experimental data (radius of gyration, hydration, intramolecular distances, NMR chemical shifts, 3J-couplings).

Main Results:

ff19SB/TIP4P-D and a99SB-disp/TIP4P-disp produced extended conformational ensembles agreeing well with experimental radius of gyration and intramolecular distances.
a99SB-disp/TIP4P-disp showed balanced secondary structure content, while ff19SB/OPC and ff03CMAP/TIP4P-D yielded overly compact ensembles with secondary structure discrepancies.

Conclusions:

The ff19SB/TIP4P-D and a99SB-disp/TIP4P-disp force fields are suitable for accurate MD simulations of alpha-synuclein.
Force field choice significantly impacts the conformational ensemble and secondary structure prediction of IDPs.