Single-atom test of all-atom empirical potentials: Fe in myoglobin.
The measured Fe vibrational density of states in deoxy-myoglobin, obtained from nuclear resonance vibrational spectroscopy, is compared to results from a normal-mode analysis using an all-atom empirical potential. Substantial disagreement reveals that for this one atom, the empirical potential does not accurately describe the actual forces. A Green function technique is developed to calculate the iron vibrational spectrum of deoxy-myoglobin by coupling the independently calculated heme and globin normal modes; nonbonded interactions between the heme molecule and the protein are essential for a good fit to the measurements. A projection of the eigenvectors from this potential onto the displacements induced by binding of CO demonstrates that normal modes over a broad range centered around 50-150 cm(-1) may drive the ligand-induced structural changes.
Rai
Brajesh K
BK
Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA.
Prohofsky
Earl W
EW
Durbin
Stephen M
SM
D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry; D007501:Iron / Q000737:chemistry*; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009211:Myoglobin / Q000737:chemistry*; D012680:Sensitivity and Specificity; D014732:Vibration
D008024:Ligands; D009211:Myoglobin; C055547:deoxymyoglobin; D002248:Carbon Monoxide; D007501:Iron