Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin.
The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol and a nonpolar solvent, and two forms of the heme, one native and one lacking acidic side chains, were studied. Structural alteration of the protein was observed in native myoglobin glycerol solution and native myoglobin water solution. The single-exponential decay of the excess kinetic energy of the heme following ligand photolysis was observed in all systems studied. The relaxation rate depends on the solvent used. However, this dependence cannot be explained using bulk transport properties of the solvent including macroscopic thermal diffusion. The rate and mechanism of heme cooling depends upon the detailed microscopic interaction between the heme and solvent. Three intermolecular energy transfer mechanisms were considered: (i) energy transfer mediated by hydrogen bonds, (ii) direct vibration-vibration energy transfer via resonant interaction, and (iii) energy transfer via vibration-translation or vibration-rotation interaction, or in other words, thermal collision. The hydrogen bond interaction and vibration-vibration interaction between the heme and solvent molecules dominates the energy transfer in native myoglobin aqueous solution and native myoglobin glycerol solutions. For modified myoglobin, the vibration-vibration interaction is also effective in glycerol solution, different from aqueous solution. Thermal collisions form the dominant energy transfer pathway for modified myoglobin in water solution, and for both native myoglobin and modified myoglobin in a nonpolar environment. For native myoglobin in a nonpolar solvent solution, hydrogen bonds between heme isopropionate side chains and nearby protein residues, absent in the modified myoglobin nonpolar solvent solution, are key interactions influencing the relaxation pathways.
Zhang
Yong
Y
Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA. zhangy@bu.edu
Fujisaki
Hiroshi
H
Straub
John E
JE
D000818:Animals; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004058:Diffusion; D004735:Energy Transfer; D006418:Heme / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D010782:Photolysis; D017785:Photons; D011487:Protein Conformation; D012997:Solvents; D014907:Whales
D008024:Ligands; D009211:Myoglobin; D012997:Solvents; D006418:Heme