Fig. 2: Molecular dynamics simulations of human Grx2 and Grx5 GSH complexes.
From: Molecular basis for the distinct functions of redox-active and FeS-transfering glutaredoxins
a, b The four most representative structures of the simulations runs of the Grx2:GSH (a) and the Grx5:GSH (b) complexes. The structures were identified with the UCSF chimera ‘Ensemble Cluster tool’ and represent 76% (Grx2:GSH) and 65% (Grx5:Grx) of all structures. c Side chain fluctuations of the residues of the loops and active sides in the Grx2:GSH complex and the Grx5:GSH complex, black squares: apo Grxs, red squares: Grx:GSH complexes. d Root mean square deviation (rmsd) of the GSH molecule bound in the complexes, black line: Grx2, red line: Grx5. e–j Distribution of distances of the indicated atom pairs over three independent simulations of 100 ns each. e–h Distances of the amino nitrogen atom of the strictly conserved lysyl residue to the thiol sulfur of the more N-terminal active site cysteinyl residue in apo Grx2 (e), apo Grx5 (f), the Grx2:GSH complex (g), and the Grx5:GSH complex (h). i, j Distances between the amino nitrogen atom of the strictly conserved lysyl residue to the thiol sulfur of the non-covalently bound GSH in the Grx2:GSH complex (e) and the Grx5:GSH complex (f). k–l Distribution of phi and psi angles of the active site seryl residue in Grx2 (black) and the respective glycyl residue in Grx5 (red) in the Ramachandran plots for the Grx:GSH complexes (k) and the apo proteins (l).
