Derivatives of cysteine related to the thiosulfate metabolism of sulfur bacteria by the multi-enzyme complex “Sox”—studied by B3LYP-PCM and G3X(MP2) calculations

Abstract

Certain sulfur bacteria oxidize thiosulfate enzymatically to sulfate, and derivatives of the amino acid cysteine play an important role as intermediates in this process. Since some of the proposed intermediates have so far been of hypothetical nature, we have investigated the structures and thermodynamic properties of more than 60 related derivatives of cysteine (CysH) by high-level quantum chemical calculations both in the gas phase and in a polarizable continuum using the PCM method to simulate an aqueous solution. Most of these molecules and anions were studied for the first time. Especially for the smaller species several conformational isomers of similar energy were identified; their relative stabilities are mainly determined by intramolecular hydrogen bonds. In contrast to the thiolate ion [Cys](-), the gaseous anions [CysS](-), [CysSO(2)](-), [CysSO(3)](-) and [CysSSO(3)](-) are most stable as zwitterions containing an NH(3) rather than an NH(2) group. This result also holds for the polarizable continuum. On the other hand, the related neutral molecules CysH, CysSH and CysSO(2)H are predicted to exist as NH(2) derivatives rather than zwitterions in the gas phase and this connectivity is predicted for CysH and CysSH also in the polarizable continuum. A model molecule of composition C(4)H(7)N(2)O(2)SH (abbreviated as RSH) simulating the structural environment of a cysteine residue within the peptide chain near the corresponding reaction center of the thiosulfate oxidizing enzyme complex "Sox" was used to elucidate the geometry of the proposed reaction intermediates as well as their thermodynamic properties. In the polarizable phase, the S-sulfonate ions [CysSO(3)](-) and [RSSO(3)](-) are predicted to react exothermically with water to the corresponding thiol and hydrogensulfate ions. These results support the proposed mechanism for enzymatic thiosulfate metabolism. Sulfur dioxide and hydrogensulfite anions are predicted to react exothermically and exergonically with thiolate and persulfide anions to give the corresponding S-sulfinate species [RSSO(2)](-) and [RSSSO(2)](-), respectively. The latter ions help to explain the inhibition of certain thiolate based enzymes by aqueous sulfite, disulfite and dithionite anions in sulfur oxidizing microorganisms.

Tailoring protein nanomechanics with chemical reactivity

“…At neutral pH, amino acids would be present in a zwitterionic NH 3 + …COO − form. However, as already observed for amino acids (including cysteine7879), the neutral tautomer NH 2 …COOH was found to be more stable in most cases. Only the inclusion of explicit water molecules would provide the necessary stabilization of the zwitterionic state by the formation of strong hydrogen bond with water80, but it is beyond the scope of the current work.…”

Structural and Mechanistic Basis for Anaerobic Ergothioneine Biosynthesis

“…A point atom refined model revealed a distance of the electron density peak centers between Cys-Sγ and the protrusion (point atom) of 2.04 Å. This distance is in good agreement with the expected length of an S–S bond (2.07 Å) . In contrast, the S–O bond of a cysteine sulfenic acid is much shorter (1.67 Å) and produced no acceptable fit upon model refinement (Figure S7).…”

“…This distance is in good agreement with the expected length of an S-S bond (2.07 Å). 30 In contrast, the S-O bond of a cysteine sulfenic acid is much shorter (1.67 Å), and produced no acceptable fit upon model refinement (Figure S7). Further evidence for the presence of a persulfide function at Cys412 was gained from anomalous diffraction data sets.…”

Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process

“…An alternative mode for attachment of sulfite to SoxYZ not involving a redox reaction is the reaction of the thiolate of the conserved SoxY-cysteine (Sox-Cys 2 ) with aqueous sulfite yielding SoxY-cysteine-Ssulfinate (SoxY-Cys-SO 2 2 ). Such a reaction is indeed feasible at the moderate pH values prevalent in the bacterial periplasm (Steudel & Steudel, 2010). However, it should be kept in mind that the reaction has so far only been shown for free cysteine and not for an active-site residue of a complex protein.…”