Simulating energy flow in biomolecules: application to tuna cytochrome c

Area of Science:

• Computational Biophysics
• Molecular Dynamics Simulations
• Protein Dynamics

Background:

• Understanding energy flow in biomolecules is crucial for deciphering their function.
• Previous methods lacked detailed insights into energy transfer pathways.
• Molecular dynamics simulations offer a powerful tool for studying atomic-level processes.

Purpose of the Study:

• To develop and apply a method for calculating energy flux in biomolecules.
• To investigate the pathways and mechanisms of energy flow in tuna ferrocytochrome c following oxidation.
• To analyze the speed and characteristics of energy propagation in proteins.

Main Methods:

• Constructed a continuity equation for energy flow.
• Utilized molecular dynamics simulation data to compute energy flux.
• Applied the method to a small argon cluster and subsequently to tuna ferrocytochrome c.

Main Results:

• Energy initially propagated rapidly perpendicular to the heme plane via a through-bond mechanism.
• Electrostatic interactions facilitated long-range through-space energy transfer, affecting distant polar groups.
• Bridging mechanisms involving coupled atoms enabled efficient long-range responses.
• Energy propagation speed in tuna cytochrome c was approximately 10^5 m/s.
• All protein atoms sensed oxidation effects within 40 femtoseconds.

Conclusions:

• The study successfully calculated energy flux, revealing complex energy transfer pathways in biomolecules.
• Multiple mechanisms, including through-bond, through-space, and bridging, contribute to energy dissipation.
• Energy transfer is not simply correlated with distance from the initial site, highlighting intricate biological processes.