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Development of an effective polarizable bond method for biomolecular simulation.

Xudong Xiao¹, Tong Zhu, Chang G Ji

¹State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.

The Journal of Physical Chemistry. B

|November 21, 2013

Summary

A new effective polarizable bond (EPB) model enhances protein simulations by accurately capturing molecular dynamics and structure. This robust model offers improved agreement with experimental data compared to traditional methods.

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Area of Science:

Computational Biology
Molecular Dynamics Simulations
Protein Structure and Dynamics

Background:

Accurate protein simulations require force fields that capture electrostatic interactions.
Traditional nonpolarizable force fields have limitations in describing protein behavior.
Previous polarizable models often suffer from numerical instability and high computational cost.

Purpose of the Study:

To develop and validate an effective polarizable bond (EPB) model for protein simulations.
To assess the EPB model's ability to reproduce experimental protein structures and dynamics.
To compare the EPB model's performance against nonpolarizable force fields and previous polarizable models.

Main Methods:

Developed a partial polarizable approach (EPB model) treating polar groups of amino acids as polarizable.
Parameterized the model using quantum-calculated electrostatic properties of polar groups.
Performed extensive molecular dynamics (MD) simulations on diverse protein systems.

Main Results:

The EPB model demonstrated robustness in MD simulations for both soluble and membrane proteins.
EPB simulations showed significantly better agreement with experimental data for hydrogen bond properties and protein dynamics.
Achieved a substantial reduction in deviation for the backbone N-H order parameter compared to Amber99SB.

Conclusions:

The EPB model effectively simulates protein structure and dynamics, offering improved accuracy over nonpolarizable force fields.
Implicit inclusion of polarization energy cost ensures numerical stability and efficiency, avoiding over-polarization issues.
The EPB model provides a computationally efficient and accurate alternative for large-scale protein simulations.