A spectroscopic and molecular dynamics study of native and of a mutant of Xenopus laevis Cu,Zn superoxide dismutase: mechanistic consequences of replacing four charged amino acids on the 'electrostatic' loop

Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase

The enzyme Cu, Zn superoxide dismutase (Cu,Zn-SOD) is a ubiquitous oxireductase, which is responsible for the cellular defense against oxidative stress caused by the high toxicity of the superoxide radical, and has been also linked to some cases of familiar amyotrophic lateral sclerosis. In the present study a set of molecular mechanics parameters for the active site of Cu,Zn-SOD has been derived. Afterward, an extensive molecular dynamics simulation has been carried out in an aqueous environment. The obtained results shed a further light on the structural flexibility of the backbone, where the active site is nested, and the solvation shell occupancy. The relatively small backbone deviation, shown by a root-mean-square deviation below 1.0 A, confirms the accuracy of the parameters. The solvent shell analysis has shown that the first solvation shell is located at about 5 A from the copper ion, generating an empty cavity with enough space to accommodate the superoxide radical. The low residence time means that a high permutation rate of water molecules in both solvation shells is consistent with the efficiency of this catalytic mechanism. Hybrid studies using ONIOM methodologies can now be done to evaluate the mechanistic implications of the explicit inclusion of the whole system.

Structure and stability of the insulin dimer investigated by molecular dynamics simulation

Molecular dynamics simulation indicates that the dynamical behaviour of the insulin dimer is asymmetric. Atomic level knowledge of the interaction modes and protein conformation in the solvation state identifies dynamical structures, held by hydrogen bonds that stabilize, mainly in one monomer, the interaction between the chains. Dynamic cross-correlation analysis shows that the two insulin monomers behave asymmetrically and are almost independent. Solvation energy, calculated to evaluate the contribute of each interface residue to the dimer association pattern, well compares with the experimental association state found in protein mutants indicating that this parameter is an important factor to explain the association properties of mutated insulin dimers.

Single mutation induces a metal-dependent subunit association in dimeric Cu,Zn superoxide dismutase

Tryptophan 83, a residue strongly involved in the intersubunit interaction of the Cu,Zn superoxide dismutases from Photobacterium leiognathi, has been selectively mutated to phenylalanine or tyrosine. The recombinant mutant enzymes expressed in Escherichia coli were purified in two well distinct and stable forms, one dimeric and fully active and the other monomeric and devoid of metals. In agreement, in vitro experiments indicate that the removal and addition of zinc in the mutant enzymes induces monomerization and dimerization, respectively, while does not perturb the dimeric association of the native protein. This is the first unambiguous experimental proof of a direct communication between the intersubunit interface and the metal active site.

Molecular dynamics simulations of Cu,Zn superoxide dismutase: effect of temperature on dimer asymmetry

Molecular dynamics simulations of solvated dimeric Cu,Zn superoxide dismutase have been carried out at four temperatures, namely 200, 225, 250 and 300 K. Analysis of the backbone-to-backbone hydrogen bonds number indicates that the symmetry observed in the two subunits at 200 K is gradually lost by heating the system. The C(alpha) atoms displacement cross-correlation maps confirm that the asymmetric behaviour of the two subunits increases as a function of temperature. The dynamic cross-correlation of the subunits volumes indicates a fast correlation between the two subunits at 300 K, which is delayed upon lowering the simulation temperature. These results indicate that temperature plays an essential role in injecting such an asymmetry; the two subunits being asymmetric and in rapid communication at 300 K, and almost symmetric and in slow communication at lower temperatures.