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Biophys. J. BioFAST: First Published February 16, 2007. doi:10.1529/biophysj.106.098442
© 2007 by the Biophysical Society.

A more recent version of this article appeared on May 15, 2007.
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BIOPHYSICAL THEORY AND MODELING

Theoretical characterization of Carbon Monoxide vibrational spectrum in Sperm Whale Myoglobin distal pocket

Massimiliano Anselmi 1, Massimiliano Aschi 2, Alfredo Di Nola 3 and Andrea Amadei 4*

1 Università di Roma
2 Universita' di L'Aquila
3 University of Rome
4 University of Rome Tor Vergata

* To whom correspondence should be addressed. E-mail: andrea.amadei{at}uniroma2.it.

Submitted on October 2, 2006
Revised on November 9, 2006
Accepted on 18 January 2007


  Abstract
In this paper we use the Perturbed Matrix Method and an extended Molecular Dynamics sampling of the carbon monoxide (CO) in Myoglobin distal pocket, in order to characterize the CO vibrational spectrum and hence to relate its spectroscopic features with the atomic-molecular behavior. Results show the accuracy of the method employed and confirm the assignment of the spectroscopic B1 and B2 states proposed by Lim et al. (Lim, M., T.A. Jackson, and P.A. Anfinrud. 1997. Nat. Struct. Biol. 4:209-214).

Key Words: MD simulation, binding sites, carboxy myoglobin, cavities, ligands, perturbed matrix method




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Copyright © 2007 by the Biophysical Society.