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Active site modeling in copper azurin molecular dynamics simulations

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Abstract

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion.

The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent Nδ1 atoms of His46 and His117.

The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions.

Figure Model of azurin active site. Copper ligand residues are cut off at Cα position except Gly45, for which the portion of backbone connecting it to His46 is shown. Only polar H atoms are shown. All atoms are in standard colors (Cu in violet), and the five ligands are labeled

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Acknowledgements

B.R. is grateful to Alan Mark and Alessandra Villa for helpful discussions and hospitality in the Molecular Dynamics group at the Rijksuniversiteit Groningen. Thanks are also due to Regione Calabria for a fellowship and to CNR (Consiglio Nazionale delle Ricerche) for financial support. M.S. thanks NWO/CW and Unilever Research Vlaardingen for their financial support. MOLMOL [46] was used for the protein displays.

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  1. Marcel Swart

    Present address: Organische en Anorganische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands

Authors and Affiliations

  1. Dipartimento di Fisica and Unità INFM, Laboratorio di Biofisica Molecolare, Università della Calabria, Ponte P. Bucci, Cubo 30C, 87030, Rende CS, Italy

    Bruno Rizzuti, Luigi Sportelli & Rita Guzzi

  2. Theoretische Chemie (MSC), Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands

    Marcel Swart

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  1. Bruno Rizzuti
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Correspondence to Rita Guzzi.

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Rizzuti, B., Swart, M., Sportelli, L. et al. Active site modeling in copper azurin molecular dynamics simulations. J Mol Model 10, 25–31 (2004). https://doi.org/10.1007/s00894-003-0165-6

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  • DOI: https://doi.org/10.1007/s00894-003-0165-6

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