Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.

Area of Science:

• Biophysics
• Computational Biology

Background:

• Protein dynamics are key to understanding the link between structure and function.
• Elastic network models (ENMs) are established tools for predicting protein flexibility and conformational changes.
• Existing ENM methods typically analyze free vibrations or static perturbations.

Purpose of the Study:

• To integrate free vibration and static perturbation approaches in ENMs.
• To evaluate the complete protein response to dynamic perturbations.
• To investigate the role of low-frequency dynamics in protein conformational changes.

Main Methods:

• Applied harmonic forces simulating particle collisions to protein ENMs.
• Solved dynamic equations in the underdamped regime, considering mass, damping, and stiffness.
• Analyzed protein motion in coordinate and principal component spaces.

Main Results:

• Dynamic perturbations, particularly in the low-frequency range, effectively drive protein conformational changes.
• High direction similarity was observed between applied perturbations and resulting motions.
• The study demonstrates a connection between external dynamic forces and protein structural rearrangements.

Conclusions:

• Protein conformational changes may be initiated by external collisions.
• The inherent low-frequency dynamics of protein structures facilitate these conformational changes.
• This integrated ENM approach offers a more comprehensive view of protein dynamics and function.