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Related Experiment Video

Updated: Jun 8, 2025

Determination of the Gas-phase Acidities of Oligopeptides

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Statistics of protein electrostatics.

Taylor Colburn¹, Setare Mostajabi Sarhangi¹, Dmitry V Matyushov²

¹Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, USA.

The Journal of Chemical Physics

|November 4, 2024

Summary

Molecular dynamics simulations reveal that protein electrostatics exhibit weakly nonergodic behavior. While electrostatic potential is nearly Gibbsian/Gaussian, the electric field shows non-Gibbsian and non-Gaussian statistics due to protein-water interface instabilities.

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Area of Science:

Computational biophysics
Protein dynamics
Statistical mechanics

Background:

Understanding protein electrostatics is crucial for predicting protein function.
Previous studies have explored protein dynamics but often assume ideal Gibbsian and Gaussian statistics.
Investigating deviations from these statistical assumptions is key to refining molecular simulations.

Purpose of the Study:

To determine if protein electrostatics equilibrate to the Gibbsian ensemble.
To ascertain if electrostatic potential and electric field within proteins follow Gaussian distributions.
To probe the statistical behavior of electrostatic potential and electric field under perturbations.

Main Methods:

Utilized molecular dynamics simulations of the redox-active protein plastocyanin.
Applied small charge and dipole perturbations to various protein sites.
Analyzed deviations from fluctuation-dissipation relations and free-energy surface linearity.
Investigated temperature-dependent behavior around the glass transition temperature (Ttr).

Main Results:

Observed weakly nonergodic statistics for electrostatic potential over 0.4-1.0 μs simulation times.
Identified non-Gibbsian and non-Gaussian statistics for the electric field.
Dipolar perturbations induced structural instabilities at the protein-water interface.
Electrostatic potential variance showed a crossover at Ttr ≃ 170 K; dipolar susceptibility exhibited a sharp drop at Ttr.

Conclusions:

Protein electrostatic potential statistics are nearly Gibbsian/Gaussian.
Protein electric field statistics are significantly non-Gibbsian/non-Gaussian, particularly under dipolar perturbations.
Structural instabilities of the protein hydration shell are responsible for nonergodic electric field behavior.