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Molecular Dynamics Calculations on Metalloproteins

  • Lucia Banci
  • Giovanni Gori Savellini
Part of the NATO ASI Series book series (ASHT, volume 41)

Abstract

Molecular Dynamics (MD) simulations have been and are extensively applied to biological molecules, and they are very useful and precious for the determination of structural properties when experimental data are not available. They can also, in a fast and efficient way, predict structural changes induced by mutations, inhibitor binding or interaction with a substrate. Furthermore, they can provide information on the internal motions of macromolecules. With the algorithms presently available for MD calculations, only motions on fast time scales (i.e. up to nanoseconds) can be calculated. Still, these motions can be relevant for the comprehension of the biological function. They can be important for the determination of the molecular recognition for the substrate or the partner in biological reactions. Also the dynamic behavior of residue-residue interactions, which can affect the biological process, can be successfully addressed by MD calculations. Finally, MD can be useful for the characterization of solvation properties, specifically the structure of internal water molecules which cannot easily be addressed experimentally.

Keywords

Water Molecule Molecular Dynamics Superoxide Dismutase Lignin Peroxidase Axial Ligand 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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© Springer Science+Business Media Dordrecht 1997

Authors and Affiliations

  • Lucia Banci
    • 1
  • Giovanni Gori Savellini
    • 1
  1. 1.Department of ChemistryUniversity of FlorenceFlorenceItaly

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