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Protein Science (2001), 10:1927-1935.
Copyright © 2001 The Protein Society

Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study

Patricia Amara1, Pierre Andreoletti2, HéLène Marie Jouve2 and Martin J. Field1

1 Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale, Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
2 Laboratoire d'Enzymologie Moléculaire, Institut de Biologie Structurale, Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France

Reprint requests to: Hélène Marie Jouve, Laboratoire d'Enzymologie Moléculaire, Insitut de Biologie Structurale—Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex I, France; e-mail: jouve{at}ibs.frmjfield{at}ibs.fr

The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 ->1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X-ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H2O and O2 are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol-1 for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface.

Keywords: Catalase; cavities; channels; ligand diffusion; molecular dynamics; free energy


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Copyright © 2001 by The Protein Society.