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Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation
K Kuczera1, J C Lambry, J L Martin
1Department of Chemistry, Harvard University, Cambridge, MA 02138.
Summary
Molecular dynamics simulations reveal myoglobin
Area of Science:
- Biophysics
- Computational Chemistry
Background:
- Myoglobin's function involves ligand binding and release.
- Understanding protein dynamics is crucial for elucidating biological mechanisms.
Purpose of the Study:
- To investigate the dynamics of myoglobin's heme iron after ligand photodissociation.
- To correlate protein relaxation with geminate recombination kinetics.
Main Methods:
- Utilizing molecular dynamics simulations.
- Analyzing the out-of-plane motion of the heme iron over 100 picoseconds.
- Comparing simulation results with experimental spectroscopic data (band III frequency shift).
Main Results:
- Observed a rapid subpicosecond phase and a slower nonexponential phase in heme iron motion.
- Identified an inhomogeneous component in protein relaxation based on individual trajectories.
- Demonstrated excellent agreement between simulated iron motion and experimental band III shifts.
- Simulated time dependence explains nonexponential nitric oxide (NO) recombination.
Conclusions:
- Heme iron motion is characterized by multi-phasic relaxation.
- Protein relaxation dynamics are heterogeneous.
- The out-of-plane iron position influences the rebinding barrier, explaining NO recombination kinetics.