QM/MM (ONIOM) Study of Glycerol Binding and Hydrogen Abstraction by the Coenzyme B12-Independent Dehydratase

If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes

With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.

Glycerol as a Substrate and Inactivator of Coenzyme B12 -Dependent Diol Dehydratase

Diol dehydratase, dependent on coenzyme B₁₂ (B₁₂ -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B₁₂ -independent glycerol dehydratase (B₁₂ -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B₁₂ -dDDH and that of resistance of B₁₂ -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B₁₂ -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B₁₂ -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.

Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

Sulfur Radical-Induced Redox Modifications in Proteins: Analysis and Mechanistic Aspects

SIGNIFICANCE

The sulfur-containing amino acids cysteine (Cys) and methionine (Met) are prominent protein targets of redox modification during conditions of oxidative stress. Here, two-electron pathways have received widespread attention, in part due to their role in signaling processes. However, Cys and Met are equally prone to one-electron pathways, generating intermediary radicals and/or radial ions. These radicals/radical ions can generate various reaction products that are not commonly monitored in redox proteomic studies, but they may be relevant for the fate of proteins during oxidative stress. Recent Advances: Time-resolved kinetic studies and product analysis have expanded our mechanistic understanding of radical reaction pathways of sulfur-containing amino acids. These reactions are now studied in some detail for Met and Cys in proteins, and homocysteine (Hcy) chemically linked to proteins, and the role of protein radical reactions in physiological processes is evolving.

CRITICAL ISSUES

Radical-derived products from Cys, Hcy, and Met can react with additional amino acids in proteins, leading to secondary protein modifications, which are potentially remote from initial points of radical attack. These products may contain intra- and intermolecular cross-links, which may lead to protein aggregation. Protein sequence and conformation will have a significant impact on the formation of such products, and a thorough understanding of reaction mechanisms and specifically how protein structure influences reaction pathways will be critical for identification and characterization of novel reaction products.

FUTURE DIRECTIONS

Future studies must evaluate the biological significance of novel reaction products that are derived from radical reactions of sulfur-containing amino acids. Antioxid. Redox Signal. 26, 388-405.

Efficient poly(3-hydroxypropionate) production from glycerol using Lactobacillus reuteri and recombinant Escherichia coli harboring L. reuteri propionaldehyde dehydrogenase and Chromobacterium sp. PHA synthase genes

Poly(3-hydroxypropionate), P(3HP), is a polymer combining good biodegradability with favorable material properties. In the present study, a production system for P(3HP) was designed, comprising conversion of glycerol to 3-hydroxypropionaldehyde (3HPA) as equilibrium mixture with 3HPA-hydrate and -dimer in aqueous system (reuterin) using resting cells of native Lactobacillus reuteri in a first stage followed by transformation of the 3HPA to P(3HP) using recombinant Escherichia coli strain co-expressing highly active coenzyme A-acylating propionaldehyde dehydrogenase (PduP) from L. reuteri and polyhydroxyalkanoate synthase (PhaCcs) from Chromobacterium sp. P(3HP) content of up to 40% (w/w) cell dry weight was reached, and the yield with respect to the reuterin consumed by the cells was 78%. Short biotransformation period (4.5h), lack of additives or expensive cofactors, and use of a cheap medium for cultivation of the recombinant strain, provides a new efficient and potentially economical system for P(3HP) production.

Reversible hydrogen transfer reactions in thiyl radicals from cysteine and related molecules: absolute kinetics and equilibrium constants determined by pulse radiolysis

The mercapto group of cysteine (Cys) is a predominant target for oxidative modification, where one-electron oxidation leads to the formation of Cys thiyl radicals, CysS(•). These Cys thiyl radicals enter 1,2- and 1,3-hydrogen transfer reactions, for which rate constants are reported in this paper. The products of these 1,2- and 1,3-hydrogen transfer reactions are carbon-centered radicals at position C(3) (α-mercaptoalkyl radicals) and C(2) ((•)C(α) radicals) of Cys, respectively. Both processes can be monitored separately in Cys analogues such as cysteamine (CyaSH) and penicillamine (PenSH). At acidic pH, thiyl radicals from CyaSH permit only the 1,2-hydrogen transfer according to equilibrium 12, (+)H(3)NCH(2)CH(2)S(• )⇌ (+)H(3)NCH(2)(•)CH-SH, where rate constants for forward and reverse reaction are k(12) ≈ 10(5) s(-1) and k(-12) ≈ 1.5 × 10(5)s(-1), respectively. In contrast, only the 1,3-hydrogen transfer is possible for thiyl radicals from PenSH according to equilibrium 14, ((+)H(3)N/CO(2)H)C(α)-C(CH(3))(2)-S(•) ⇌ ((+)H(3)N/CO(2)H)(•)C(α)-C(CH(3))(2)-SH, where rate constants for the forward and the reverse reaction are k(14) = 8 × 10(4) s(-1) and k(-14) = 1.4 × 10(6) s(-1). The (•)C(α) radicals from PenSH and Cys have the additional opportunity for β-elimination of HS(•)/S(•-), which proceeds with k(39) ≈ (3 ± 1) × 10(4) s(-1) from (•)C(α) radicals from PenSH and k(-34) ≈ 5 × 10(3) s(-1) from (•)C(α) radicals from Cys. The rate constants quantified for the 1,2- and 1,3-hydrogen transfer reactions can be used as a basis to calculate similar processes for Cys thiyl radicals in proteins, where hydrogen transfer reactions, followed by the addition of oxygen, may lead to the irreversible modification of target proteins.

Cysteine residues as catalysts for covalent peptide and protein modification: a role for thiyl radicals?

Cysteine thiyl radicals engage in reversible intramolecular hydrogen-transfer reactions with amino acid residues in peptides and proteins. These reactions can be experimentally demonstrated through covalent hydrogen-deuterium exchange when experiments are carried out in (2)H2O. To this end, hydrogen-transfer reactions have been observed between cysteine thiyl radicals and glycine, alanine, serine, valine and leucine in both model peptides and a protein, insulin. The relevance of such reactions for protein oxidation under conditions of oxidative stress is discussed.