How Is a Co-Methyl Intermediate Formed in the Reaction of Cobalamin-Dependent Methionine Synthase? Theoretical Evidence for a Two-Step Methyl Cation Transfer Mechanism

Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants

Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (ε_bulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (ε_bulk^') from intrinsic KIEs on the rate-determining steps and the observed ε_bulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and S_N2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.

Reaction mechanism of the PuDddK dimethylsulfoniopropionate lyase and cofactor effects of various transition metal ions

The microbial cleavage of dimethylsulfoniopropionate (DMSP) produces volatile dimethyl sulfide (DMS) via the lyase pathway, playing a crucial role in the global sulfur cycle. Herein, the DMSP decomposition catalyzed by PuDddK (a DMSP lyase) devised with various transition metal ion cofactors are investigated using density functional calculations. The PuDddK reaction has been demonstrated to employ a concerted β-elimination mechanism, where the substrate α-proton abstraction by the deprotonated Tyr64 occurs simultaneously with the C_β-S bond cleavage and C_α = C_β double bond formation. The PuDddK enzymes with diverse divalent metal ions (Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, Zn²⁺, and Cu²⁺) incorporated prefer DMSP as a monodentate ligand. The cases of Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, and Zn²⁺ with the same 3His-1Glu ligands have close reaction energy barriers, indicating that the lyase activity may be hardly affected by the divalent transition metal type with the same ligand type and number. The coordination loss of one histidine in Cu²⁺, forming a 2His-1Glu architecture, leads to a lower activity, revealing that the 3His-1Glu ligand set used by DddK appears to be a scaffold capable of more efficiently catalyzing the DMSP decomposition. Further analysis reveals that the inactivation of Fe³⁺-dependent PuDddK is derived from an electron transfer from the Tyr64 phenolate to Fe³⁺, with the implication that the PuDddK activity may be primarily affected by the redox effects induced by a strongly oxidizing transition metal ion (like Fe³⁺).

Methyl transfer reactions catalyzed by cobalamin-dependent enzymes: Insight from molecular docking

Methyl transfer reactions, mediated by methyltransferases (MeTrs), such as methionine synthase (MetH) or monomethylamine: CoM (MtmBC), constitute one of the most important classes of vitamin B₁₂-dependent reactions. The challenge in exploring the catalytic function of MeTrs is related to their modular structure. From the crystallographic point of view, the structure of each subunit has been determined, but there is a lack of understanding of how each subunit interacts with each other. So far, theoretical studies of methyl group transfer were carried out for the structural models of the active site of each subunit. However, those studies do not include the effect of the enzymatic environment, which is crucial for a comprehensive understanding of enzyme-mediated methyl transfer reactions. Herein, to explore how two subunits interact with each other and how the methyl transfer reaction is catalyzed by MeTrs, molecular docking of the functional units of MetH and MtmBC was carried out. Along with the interactions of the functional units, the reaction coordinates, including the Co-C bond distance for methylation of cob(I)alamin (Co^ICbl) and the C-S bond distance in demethylation reaction of cob(III)alamin (Co^IIICbl), were considered. The functional groups should be arranged so that there is an appropriate distance to transfer a methyl group and present results indicate that steric interactions can limit the number of potential arrangements. This calls into question the possibility of S_N2-type mechanism previously proposed for MeTrs. Further, it leads to the conclusion that the methyl transfer reaction involves some spatial changes of modules suggesting an alternate radical-based pathway for MeTrs-mediated methyl transfer reactions. The calculations also showed that changes in torsion angles induce a change in reaction coordinates, namely Co-C and C-S bond distances, for the methylation and demethylation reactions catalyzed both by MetH and MtmBC.

Insights into the Chemical Reactivity in Acetyl-CoA Synthase

The biological synthesis of acetyl-coenzyme A (acetyl-CoA), catalyzed by acetyl-CoA synthase (ACS), is of biological significance and chemical interest acting as a source of energy and carbon. The catalyst contains an unusual hexa-metal cluster with two nickel ions and a [Fe₄S₄] cluster. DFT calculations have been performed to investigate the ACS reaction mechanism starting from three different oxidation states (+2, +1, and 0) of Ni_p, the nickel proximal to [Fe₄S₄]. The results indicate that the ACS reaction proceeds first through a methyl radical transfer from cobalamin (Cbl) to Ni_p randomly accompanying with the CO binding. After that, C-C bond formation occurs between the Ni_p-bound methyl and CO, forming Ni_p-acetyl. The substrate CoA-S^- then binds to Ni_p, allowing C-S bond formation between the Ni_p-bound acetyl and CoA-S^-. Methyl transfer is rate-limiting with a barrier of ∼14 kcal/mol, which does not depend on the presence or absence of CO. Both the Ni_p²⁺ and Ni_p¹⁺ states are chemically capable of catalyzing the ACS reaction independent of the state (+2 or +1) of the [Fe₄S₄] cluster. The [Fe₄S₄] cluster is not found to affect the steps of methyl transfer and C-C bond formation but may be involved in the C-S bond formation depending on the detailed mechanism chosen. An ACS active site containing a Ni_p(0) state could not be obtained. Optimizations always led to a Ni_p¹⁺ state coupled with [Fe₄S₄]¹⁺. The calculations show a comparable activity for Ni_p¹⁺/[Fe₄S₄]¹⁺, Ni_p¹⁺/[Fe₄S₄]²⁺, and Ni_p²⁺/[Fe₄S₄]²⁺. The results here give significant insights into the chemistry of the important ACS reaction.

An Unprecedented Ring-Contraction Mechanism in Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes

A unique member of the family of cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes, OxsB, catalyzes the ring constriction of deoxyadenosine triphosphate (dATP) to the base oxetane aldehyde phosphate, a crucial precursor for oxetanocin A (OXT-A), which is an antitumor, antiviral, and antibacterial compound. This enzyme reveals a new catalytic function for this big family that is different from the common methylation. On the basis of density functional theory calculations, a mechanism has been proposed to mainly include that the generation of 5'-deoxyadenosine radical, a hydrogen transfer forming 2'-dATP radical, and a Cbl-catalyzed ring contraction of the deoxyribose in 2'-dATP radical. The ring contraction is a concerted rearrangement step accompanied by an electron transfer from the deoxyribose hydroxyl oxygen to Co^III without any ring-opening intermediate. Co^IICbl has been ruled out as an active state. Other mechanistic characteristics are also revealed. This unprecedented non-methylation mechanism provides a new catalytic repertoire for the family of radical SAM enzymes, representing a new class of ring-contraction enzymes.

Revisiting the catalytic mechanism of Mo-Cu carbon monoxide dehydrogenase using QM/MM and DFT calculations

Previous density functional theory (DFT) studies have shown that the release of the produced carbon dioxide (CO2) from an active-site cluster is a thermodynamically or kinetically difficult step in the enzymatic carbon monoxide (CO) oxidation catalyzed by Mo-Cu carbon monoxide dehydrogenase (Mo-Cu CODH). To better understand the effect of the protein environment on this difficult CO2 release step as well as other reaction steps, we applied hybrid quantum mechanics and molecular mechanics (QM/MM) calculations to the Mo-Cu CODH enzyme. The results show that in the first step, the equatorial Mo[double bond, length as m-dash]O group in the active-site cluster attacks the nearby CO molecule bound to the Cu site. Afterward, a stable thiocarbonate intermediate is formed in which the CO2 molecule is embedded and the copper-S(μ-sulfido) bond is broken. A free CO2 molecule, i.e., the final product, is then released from the active-site cluster, not directly from the thiocarbonate intermediate but via a previously formed intermediate that also contains CO2 but retains the Cu-S(μ-sulfido) bond. In contrast to the previous DFT results, the calculated barrier for this process was low in our QM/MM calculations. An additional QM/MM analysis of the barrier height showed that the effect of the protein environment on this barrier lowering is not very large. We found that the reason for the low barrier obtained by QM/MM is that the barrier for CO2 release is already not high at the DFT level. These results allow us to conclude that the CO oxidation reaction passes through the formation of a thiocarbonate intermediate, and that the subsequent CO2 release is kinetically not difficult. Nevertheless, the protein environment has an important role to play in making the latter process thermodynamically favored. No low-barrier pathway for the product release could be obtained for the reaction of n-butylisocyanide, which is consistent with the experimental fact that n-butylisocyanide inhibits Mo-Cu CODH.

The Decarboxylation of α,β-Unsaturated Acid Catalyzed by Prenylated FMN-Dependent Ferulic Acid Decarboxylase and the Enzyme Inhibition

Ferulic acid decarboxylase (Fdc1) is able to catalyze the decarboxylation of α,β-unsaturated acids using a novel cofactor, prenylated flavin mononucleotide (PrFMN). Using density functional theory calculations, we here have investigated the Fdc1 reaction mechanism with the substrate of α-methylcinnamic acid. It is demonstrated that Fdc1 employs a 1,3-dipolar cycloaddition mechanism involving four concerted steps, where the Glu282 acts as a crucial proton donor to protonate the α carbon (C_α). The last step, the decomposition of a pyrrolidine species, is rate-limiting with an overall barrier of 18.9 kcal mol^-1. Furthermore, when α-hydroxycinnamic acid is used, the Glu282 is found to have another face to transport the hydroxyl proton to the C_β atom to promote the tautomerization from enol intermediate to ketone species leading to the inhibition of the Fdc1 enzyme. The PrFMN roles are also discussed in detail.

Intraprotein transmethylation via a CH3–Co(iii) species in myoglobin reconstituted with a cobalt corrinoid complex

A cobalt corrinoid complex bound in the myoglobin heme pocket demonstrates the formation of a CH₃–Co(iii) bond and subsequent transmethylation.

Co-C dissociation of adenosylcobalamin (coenzyme B12): role of dispersion, induction effects, solvent polarity, and relativistic and thermal corrections

Quantum-chemical cluster modeling is challenged in the limit of large, soft systems by the effects of dispersion and solvent, and well as other physical interactions. Adenosylcobalamin (AdoCbl, coenzyme B12), as one of the most complex cofactors in life, constitutes such a challenge. The cleavage of its unique organometallic Co-C bond has inspired multiple studies of this cofactor. This paper reports the fully relaxed potential energy surface of Co-C cleavage of AdoCbl, including for the first time all side-chain interactions with the dissociating Ado group. Various methods and corrections for dispersion, relativistic effects, solvent polarity, basis set superposition error, and thermal and vibrational effects were investigated, totaling more than 550 single-point energies for the large model. The results show immense variability depending on method, including solvation, functional type, and dispersion, challenging the conceived accuracy of methods used for such systems. In particular, B3LYP-D3 seems to severely underestimate the Co-C bond strength, consistent with previous results, and BP86 remains accurate for cobalamins when dispersion interactions are accounted for.

A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase

Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.

Co-C bond energies in adenosylcobinamide and methylcobinamide in the gas phase and in silico

Essential to biological activity of adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) is the Co-C bond cleavage step. Hence, we report an accurate determination of the homolytic gas-phase Co-C bond dissociation energies in the related adenosyl- and methylcobinamides (41.5 ± 1.2 and 44.6 ± 0.8 kcal/mol, respectively) utilizing an energy-resolved threshold collision-induced dissociation technique. This approach allows for benchmarking of electronic structure methods separate from (often ill-defined) solvent effects. Adequacy of various density functional theory methods has been tested with respect to the experimentally obtained values.

Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study

Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimization on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a second-sphere histidine residue in the active site of [Ni,Fe] hydrogenase, which has been shown to be very sensitive to the surroundings. We include in the QM calculations all residues within 4.5 Å of the active site, two capped residues on each side of the active-site residues, and all charged groups that are buried inside the protein, which for this enzyme includes three iron-sulfur clusters, in total, 930 atoms. These calculations are performed at the BP86/def2-SV(P) level, but the energies are then extrapolated to the B3LYP/def2-TZVP level with a smaller QM system, and zero-point energy, entropy, and thermal effects are added. We test three approaches to model the remaining atoms of the protein solvent, viz., by standard QM/MM approaches using either mechanical or electrostatic embedding or by using a continuum solvation model for the large QM systems. Quite encouragingly, the three approaches give the same results within 14 kJ/mol, and variations in the size of the QM system do not change the energies by more than 8 kJ/mol, provided that the QM/MM junctions are not moved closer to the QM system. The statistical precision for the average over 10 snapshots is 1-3 kJ/mol.

Repair of DNA Dewar photoproduct to (6-4) photoproduct in (6-4) photolyase

Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.