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Updated: Jun 10, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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A coarse-grained model for disordered and multi-domain proteins.

Fan Cao¹, Sören von Bülow¹, Giulio Tesei¹

¹Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Protein Science : a Publication of the Protein Society

|October 16, 2024

Summary

This summary is machine-generated.

We developed a fast coarse-grained model for simulating multi-domain proteins. Placing interaction sites at the center of mass accurately predicts protein behavior and phase separation.

Keywords:

coarse graining condensates molecular dynamics multi‐domain proteins protein dynamics

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Area of Science:

Biophysics
Computational Biology
Protein Science

Background:

Multi-domain proteins are crucial for expanding protein functions.
Simulating their conformational ensembles is challenging due to size and dynamics.

Purpose of the Study:

To develop a fast and accurate coarse-grained model for multi-domain proteins.
To investigate the impact of interaction site representation on simulation accuracy.
To simulate protein phase separation and domain stability.

Main Methods:

Developed a one-bead-per-residue coarse-grained model.
Optimized interaction site representation by locating them at the center of mass of residues.
Validated the model (CALVADOS) with experimental data.
Simulated phase separation of disordered and multi-domain proteins.

Main Results:

Accurate simulation of multi-domain protein conformational ensembles.
Center-of-mass representation improves agreement between simulations and experiments.
Successfully simulated protein phase separation and analyzed domain stability in different phases.

Conclusions:

The revised coarse-grained model provides an accurate and efficient method for studying multi-domain proteins.
Understanding domain interactions is key to predicting protein self-association and phase separation.
This model serves as a foundation for further research into protein behavior in solution.