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Published on: July 16, 2017
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Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.
R B Pandey1, D J Jacobs2, B L Farmer3
1Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA.
The Journal of Chemical Physics
|May 22, 2017
Summary
Solute binding to histone H3.1 protein causes abrupt structural collapse, altering protein dynamics and dimensions. This preferential binding significantly impacts protein folding compared to homogeneous solvent models.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Histone proteins are crucial for DNA packaging and gene regulation.
- Understanding protein behavior in solution is vital for molecular biology.
- Solute-protein interactions can significantly alter protein structure and function.
Purpose of the Study:
- To investigate the impact of preferential solute binding on histone H3.1 protein structure and dynamics.
- To compare simulation results between effective medium and explicit solute fluctuation models.
- To analyze how varying solute-solvent interaction strength affects protein physical quantities.
Main Methods:
- Coarse-grained Monte Carlo simulation.
- Utilized knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions.
- Analyzed local and global physical quantities, including radius of gyration (Rg) and structure factor S(q).
Main Results:
- Protein radius of gyration (Rg) showed non-monotonic dependence in an effective medium.
- Abrupt Rg collapse occurred in a narrow interaction strength range with preferential solute binding.
- Structure factor S(q) became oscillatory in the collapsed state, indicating segmental correlations.
- Spatial solute binding fluctuations modified the protein's effective dimension (D) across different conformational states.
Conclusions:
- Preferential solute binding induces significant structural changes in histone H3.1, distinct from homogeneous solvent effects.
- Explicit consideration of solute positional fluctuations is crucial for accurately modeling protein behavior.
- Solute-protein interaction strength dictates protein conformational ensembles and their dimensions.
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