Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations

Area of Science:

• Computational Biophysics
• Structural Biology
• Molecular Dynamics

Background:

• Backbone N-H S(2) order parameters are crucial for understanding protein dynamics.
• Accurate calculation of these parameters from molecular dynamics (MD) simulations is essential for comparison with experimental data, such as NMR relaxation.
• Previous studies have not fully elucidated the optimal simulation parameters for reliable order parameter calculation.

Purpose of the Study:

• To investigate the influence of simulation methodology, starting conditions, and simulation length on calculated backbone N-H S(2) order parameters.
• To compare simulation-derived order parameters with experimental NMR relaxation data using galectin-3 as a model system.
• To determine optimal strategies for achieving sufficient sampling and reliable order parameter calculations in MD simulations.

Main Methods:

• Performed molecular dynamics simulations of the carbohydrate binding domain of galectin-3 in free and lactose-bound states.
• Varied starting structures, simulation lengths, and equilibration times.
• Compared four different methods for extracting order parameters: autocorrelation function and isotropic reorientational eigenmode dynamics with varying window sizes.

Main Results:

• Using multiple starting structures improved sampling, but the effect was limited, with single conformations often adequately sampling conformational space.
• Multiple short simulations (approx. 10 independent simulations of 10 ns) provided better agreement with experimental NMR data than single long simulations.
• An equilibration time of 0.25 ns was found to be sufficient, and the four order parameter calculation methods yielded comparable results, with discrepancies indicating potential unreliability.

Conclusions:

• Optimizing molecular dynamics simulation protocols, particularly by employing multiple shorter trajectories, enhances the accuracy of calculated backbone N-H S(2) order parameters.
• The study provides practical guidelines for simulation length and starting conditions to achieve reliable order parameter calculations.
• Discrepancies among different order parameter calculation methods can serve as indicators of simulation reliability.