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Biophys. J. BioFAST: First Published February 29, 2008. doi:10.1529/biophysj.107.124529
© 2008 by the Biophysical Society.

A more recent version of this article appeared on June 1, 2008.
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BIOPHYSICAL THEORY AND MODELING

The Kinetics of ligand migration in crystallized Myoglobin as revealed by Molecular Dynamics simulations

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

1 University of Rome "La Sapienza"
2 University of Rome
3 University of Rome Tor Vergata

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

Submitted on October 26, 2007
Revised on December 4, 2007
Accepted on 28 January 2008


  Abstract
By using multiple Molecular Dynamics (MD) trajectories of photolized carbon monoxide (CO) within crystallized myoglobin, a quantitative description of CO diffusion and corresponding kinetics were obtained. MD results allowed to construct a detailed kinetic model of the migration process shading light on the kinetic mechanism and relevant steps of CO migration and remarkably well reproducing the available experimental data as provided by time-resolved Laue X-ray diffraction.

Key Words: MD simulations, binding sites, cavities, ligand diffusion, myoglobin, photolysis




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M. Anselmi, M. Brunori, B. Vallone, and A. Di Nola
Molecular Dynamics Simulation of the Neuroglobin Crystal: Comparison with the Simulation in Solution
Biophys. J., November 1, 2008; 95(9): 4157 - 4162.
[Abstract] [Full Text] [PDF]


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Copyright © 2008 by the Biophysical Society.