Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation

Area of Science:

• Biophysics
• Computational Biology
• Statistical Mechanics

Background:

• Molecular dynamics (MD) simulations offer high-resolution insights into biomolecular motions.
• Statistical analysis is crucial for interpreting large MD datasets and understanding allosteric mechanisms.
• Current correlation methods often assume stationarity, limiting their ability to capture time-dependent dynamics.

Purpose of the Study:

• To investigate nonstationarity in biomolecular dynamics using MD simulations.
• To identify and characterize oscillatory variance in signed dihedral angular accelerations (SDAA).
• To explore the implications of these findings for understanding biomolecular information flow.

Main Methods:

• Utilized MD simulations of alanine tripeptide.
• Applied power spectrum, corrected squared envelope spectrum (CSES), and cross-CSES to analyze SDAA.
• Quantified the fraction of oscillatory motion and its transmission between dihedral angles.

Main Results:

• Identified significant oscillatory instantaneous variance in SDAA, interpreted as oscillatory diffusion.
• Found that oscillatory motion constitutes up to 40% of total motion at certain frequencies.
• Demonstrated that these oscillations transmit between dihedral angles.

Conclusions:

• Standard correlation analyses may overlook significant nonstationary dynamics in biomolecules.
• Oscillatory variance is a key feature of biomolecular motion that needs to be considered.
• These findings advance the understanding of biomolecular dynamics and allosteric mechanisms.