Reactivity of Inorganic Sulfide Species toward a Heme Protein Model

Abstract

The reactivity of inorganic sulfide species toward heme peptides was explored under biorelevant conditions in order to unravel the molecular details of the reactivity of the endogenous hydrogen sulfide toward heme proteins. Unlike ferric porphyrinates, which are reduced by inorganic sulfide, some heme proteins can form stable Fe(III)-sulfide adducts. To isolate the protein factors ruling the redox chemistry, we used as a system model, the undecapeptide microperoxidase (MP11), a heme peptide derived from cytochrome c proteolysis that retains the proximal histidine bound to the Fe(III) atom. Upon addition of gaseous hydrogen sulfide (H2S) at pH 6.8, the UV-vis spectra of MP11 closely resembled those of the low-spin ferric hydroxo complex (only attained at an alkaline pH) and cysteine or alkylthiol derivatives, suggesting that the Fe(III) reduction was prevented. The low-frequency region of the resonance Raman spectrum revealed the presence of an Fe(III)-S band at 366 cm(-1) and the general features of a low-spin hexacoordinated heme. Anhydrous sodium sulfide (Na2S) was the source of sulfide of choice for the kinetic evaluation of the process. Theoretical calculations showed no distal stabilization mechanisms for bound sulfide species in MP11, highlighting a key role of the proximal histidine for the stabilization of the Fe(III)-S adducts of heme compounds devoid of distal counterparts, which is significant with regard to the biochemical reactivity of endogenous hydrogen sulfide.

Hydrogen Sulfide Oxidation by Myoglobin

“…62 This observation is in direct contrast to the demonstrated stoichiometric binding of sulfide to ferric heme in hemoglobin 10 and myoglobin (Figure 2D) under strictly anaerobic conditions, the binding of sulfide to microperoxidase 50 and to a hemoglobin model, 43 both in the absence of O 2 . The authors of the recent study used protocatechuate dioxygenase to scrub O 2 .…”

“…Microperoxidase, which also forms a low-spin ferric sulfide species, exhibits similar association (2.6 × 10 4 M −1 s −1 at pH 6.8, 25 °C) and dissociation ( k off = 5.7 ± 0.1 s −1 ) rate constants yielding a K D value of ~220 μ M. 50 Binding of sulfide to microperoxidase was only monitored under anaerobic conditions, and iron reduction was not observed.…”

Potentiation of hydrogen peroxide toxicity: From catalase inhibition to stable DNA-iron complexes

“…Indeed, the cellular systems that negate H 2 O 2 effectiveness (for example, H 2 O 2 scavengers or DNA repair pathways) could be inactivated with a different agent, to either increase the effective intracellular H 2 O 2 concentrations or to make DNA damage irreparable. In particular, catalases have heme in their active centers (37), so any simple chemical that binds heme iron tightly (NO, CN, H 2 S (47, 48)) will inhibit catalases and thus will reduce the killing concentrations of H 2 O 2 . In fact, catalases could have been the original target of the evolutionary arms race, as the cells have a second hydrogen peroxide scavenging enzyme, called alkylperoxidase, which is effective against low H 2 O 2 concentrations and that has reaction chemistry very different from the chemistry of catalase (49), meaning that the same inhibition principle will not work against both enzymes.…”

“…By inhibiting heme-containing enzymes (the preferred target of CN binding) and thus blocking respiration, CN was found to increase the intracellular pool of NADH, which would translate into a higher pool of reduced FMNs and would, therefore, elevate the pools of free soluble Fe(II) iron (101). In fact, this general scenario would work for all known H 2 O 2 potentiators, since NO, CN, H 2 S, as well as the amino acids cysteine and histidine, are all heme ligands (47, 62, 102–104). Ascorbate is the only exception in this list, but it acts as an electron donor for some heme-containing enzymes (105), and so could be considered a “transient ligand”.…”

Lessons learned about steered molecular dynamics simulations and free energy calculations

“…The change in free energy governs all chemical processes. The calculation of free energy profiles, that is, the change in free energy along a transformation or reaction coordinate, has thus been critical in understanding many complex processes such as protein–protein recognition (Gohlke, Kiel, & Case, ; Isralewitz, Baudry, Gullingsrud, Kosztin, & Schulten, 2001), drug design (Isralewitz et al., 2001; Shirts, Mobley, & Brown, ), ligand binding kinetics (Boechi et al., ; Boubeta, Bari, Estrin, & Boechi, ; Hu, Xu, & Wang, ; Selvam, Wereszczynski, & Tikhonova, ; Xiong, Crespo, Marti, Estrin, & Roitberg, ), large‐scale conformational reorganization in proteins (Bringas, Petruk, Estrin, Capece, & Martí, ; Isralewitz, Gao, & Schulten, 2001; Marsico et al., ), and in the elucidation of chemical reaction mechanisms in enzyme active sites (Bieza et al., ; Crespo, Martí, Estrin, & Roitberg, ).…”