Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase fromHaemophilus ducreyi: in silico andin vitroevidences

Abstract

X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations have been jointly applied to the study of the Cu,Zn superoxide dismutase from Haemophilus ducreyi (HdSOD) in interaction with the carbon monoxide molecule. The configurational flexibility of the Fe(II)-heme group, intercalated between the two subunits, has been sampled by MD simulations and included in the XANES data analysis without optimization in the structural parameter space. Our results provide an interpretation of the observed discrepancy in the Fe-heme distances as detected by extended X-ray absorption fine structure (EXAFS) spectroscopy and the classical XANES analysis, in which the structural parameters are optimized in a unique structure. Moreover, binding of the CO molecule to the heme induces a long range effect on the Cu,Zn active site, as evidenced by both MD simulations and in vitro experiments. MD simulation of the CO bound system, in fact, highlighted a structural rearrangement of the protein-protein hydrogen bond network in the region of the Cu,Zn active site, correlated with an increase in water accessibility at short distance from the copper atom. In line, in vitro experiments evidenced an increase of copper accessibility to a chelating agent when the CO molecule binds to the heme group, as compared to a heme deprived HdSOD. Altogether, our results support the hypothesis that the HdSOD is a heme-sensor protein, in which binding to small gaseous molecules modulates the enzyme superoxide activity as an adaptive response to the bacterial environment.

Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II)

“…MXAN analysis has already been successfully combined with MD simulations in the study of aqueous ionic solutions, 26,28,29 nonaqueous ionic solutions, 30 and, more recently, metalloproteins. 31,32 2. MATERIALS AND METHODS…”

“…To fully understand the hydration structure and dynamics of this ion, we have coupled here the MD simulations with the empirical structural models of M­(aq) 2+ that are derived from X-ray absorption spectroscopy (XAS) using the MXAN method. MXAN analysis has already been successfully combined with MD simulations in the study of aqueous ionic solutions, ,, nonaqueous ionic solutions, and, more recently, metallo-proteins. , …”

Strain-Specific Benefits of Bacillus Probiotics in Hybrid Grouper: Growth Enhancement, Metabolic Health, Immune Modulation, and Vibrio harveyi Resistance

“…Antioxidant enzymes like SOD, CAT, and GSH-Px play key roles in mitigating oxidative stress. SOD facilitates the breakdown of superoxide radicals into oxygen and hydrogen peroxide [54], while CAT decomposes hydrogen peroxide into water and oxygen [55]. GSH-Px reduces harmful peroxides to nontoxic compounds and converts hydrogen peroxide into water [56].…”

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

“…For instance, an inhibitor targeted to this cavity could disrupt binding of the auxiliary Cu, thus compromising NmSOD stability. CO or NO binding to the heme in HdSOD did in fact induce conformational rearrangements of that enzyme, including altered active-site accessibility (110). Similarly, active-site accessibility and catalysis were affected by interface substitution mutants in the P. leiognathi SOD P-class dimer (111).…”