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

Authors :
Rai BK
Prohofsky EW
Durbin SM
Source :
The journal of physical chemistry. B [J Phys Chem B] 2005 Oct 13; Vol. 109 (40), pp. 18983-7.
Publication Year :
2005

Abstract

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.

Details

Language :
English
ISSN :
1520-6106
Volume :
109
Issue :
40
Database :
MEDLINE
Journal :
The journal of physical chemistry. B
Publication Type :
Academic Journal
Accession number :
16853444
Full Text :
https://doi.org/10.1021/jp052950i