Biomedical subjects

Bruno Rizzuti

Publications and source records attributed to Bruno Rizzuti.

3 recordsLinked to original sources

PubMed2006

Structural, dynamical and functional aspects of the inner motions in the blue copper protein azurin.

Molecular dynamics was applied to dissect out the internal motions of azurin, a copper protein performing electron transfer. Simulations of 16.5 ns were analyzed in search of coordinated displacements of amino acid residues that are important for the protein function. A region with high conformational instability was found in the 'southern' end of the molecule, far away from the copper site and the binding sites for the redox partners of azurin. By excluding the 'southern' region from the subsequent analysis, correlated motions were identified in the hydrophobic patch that surrounds the protein active site. The simulation results are in excellent agreement with recent NMR data on azurin in solution [A. V. Zhuravleva, D. M. Korzhnev, E. Kupce, A. S. Arseniev, M. Billeter, V. Y. Orekhov, Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures, J. Mol. Biol. 342 (2004) 1599-1611] and suggest a rationale for cooperative displacements of protein residues that are thought to be critical for the electron transfer process. A number of other structural and dynamic features of azurin are discussed in the context of the blue copper protein family and an explanation is proposed to account for the variability/conservation of some regions in the cupredoxins.

Azurin↗

PubMed2004

The early steps in the unfolding of azurin.

High-temperature molecular dynamics simulations were used to gain insight into the early steps in the unfolding pathway of azurin, a blue copper protein with a beta-barrel structure formed by two sheets arranged in a Greek key folding topology. The results reveal that unfolding of the beta-barrel in azurin is associated with dislocation of its unique alpha-helix with respect to the protein scaffold. Exposure of the hydrophobic core to solvent precedes complete disruption of secondary and tertiary structure, and modifications in the region around the active site are directly connected with this event. Denaturation of the protein initiates from the sheet coordinating the copper ion, and the other sheet maintains its topology. Results derived from the simulation were compared with experimental data obtained with different techniques, showing excellent agreement and providing a framework to understand the process of disruption and formation of the beta-barrel in azurin.

Azurin↗

PubMed2003

Active site modeling in copper azurin molecular dynamics simulations.

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 N(delta1) 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.

Azurin↗