Single-atom test of all-atom empirical potentials: Fe in myoglobin

Published in:

Journal of Physical Chemistry B 109,40 (2005) 18983-18987;


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 deoxymyoglobin 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.


nuclear resonant scattering;; normal-mode analysis;; inelastic neutron-scattering;; density-of-states;; x-ray-scattering;; vibrational spectroscopy;; heme-proteins;; synchrotron-radiation;; dynamics;; hemoglobin

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