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Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics
Kusai A Merchant1, W G Noid, Ryo Akiyama
1Department of Chemistry, Stanford University, Stanford, California 94305, USA.
Journal of the American Chemical Society
|November 6, 2003
Summary
Infrared spectroscopy reveals how histidine-64 dynamics in sperm whale carbonmonoxymyoglobin (MbCO) influence CO ligand vibrations. Molecular dynamics simulations confirm these findings, explaining vibrational dephasing mechanisms.
Area of Science:
- Biophysics
- Computational Chemistry
- Spectroscopy
Background:
- Carbonmonoxymyoglobin (MbCO) is a crucial model for studying protein dynamics and ligand interactions.
- Understanding vibrational dephasing of ligands provides insights into protein conformational substates.
Purpose of the Study:
- To investigate the vibrational dephasing dynamics of the CO ligand in sperm whale MbCO at 300 K.
- To correlate experimental spectroscopic data with molecular dynamics (MD) simulations.
- To elucidate the role of histidine-64 (His64) protonation and dynamics in CO ligand vibrational dephasing.
Main Methods:
- Spectrally resolved infrared stimulated vibrational echo spectroscopy.
- All-atom molecular dynamics (MD) simulations.
- Analysis of vibrational dephasing dynamics and protein conformational substates.
Main Results:
- Experimental dephasing dynamics of the CO ligand agree with MD simulations for protonated His64 (N(epsilon)-H).
- Two MD conformational substates (B(epsilon) and R(epsilon)) are assigned to spectroscopic substates A(1) and A(3), respectively.
- His64 dynamics are identified as the primary source of CO vibrational dephasing in the A(3) state and a significant factor in the A(1) state.
Conclusions:
- The protonation state and dynamics of His64 play a critical role in the vibrational dephasing of the CO ligand in MbCO.
- MD simulations accurately predict experimental observations, validating the model.
- Distinct conformational substates of MbCO exhibit different dephasing mechanisms influenced by His64 and solvent interactions.