Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation |
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Authors: | Mattia Falconi Ruggero Gallimbeni Emanuele Paci |
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Institution: | (1) Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica e Tecnologica, I-00133 Rome, Italy;(2) Centre Européen de Calcul Atomique et Moleculaire (CECAM), École Normale Supérieure de Lyon, F-69364 Lyon, France;(3) SBPM/DBCM/DSV, CEA Centre d'Étude Saclay, F-91191 Gif-sur-Yvette Cédex, France;(4) Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica e Tecnologica, I-00133 Rome, Italy |
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Abstract: | Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits. |
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Keywords: | Cu Zn superoxide dismutase Molecular dynamics Active site asymmetry Atomic displacement covariance matrix |
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