[NiFe], [FeFe], and [Fe] hydrogenase models from isomers

The study of hydrogenase enzymes (H₂ases) is necessary because of their importance to a future hydrogen energy economy. These enzymes come in three distinct classes: [NiFe] H₂ases, which have a propensity toward H₂ oxidation; [FeFe] H₂ases, which have a propensity toward H₂ evolution; and [Fe] H₂ases, which catalyze H^- transfer. Modeling these enzymes has so far treated them as different species, which is understandable given the different cores and ligand sets of the natural molecules. Here, we demonstrate, using x-ray analysis and nuclear magnetic resonance, infrared, Mössbauer spectroscopies, and electrochemical measurement, that the catalytic properties of all three enzymes can be mimicked with only three isomers of the same NiFe complex.

Jensen HJ, Hedegård ED. Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory

The combination of density functional theory (DFT) with a multiconfigurational wave function is an efficient way to include dynamical correlation in calculations with multiconfiguration self-consistent field wave functions.

Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site

The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H₂) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H₂ production processes.

Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy

Catalysis of H₂ production and oxidation reactions is critical in renewable energy systems based around H₂ as a clean fuel, but the present reliance on platinum-based catalysts is not sustainable. In nature, H₂ is oxidized at minimal overpotential and high turnover frequencies at [NiFe] catalytic sites in hydrogenase enzymes. Although an outline mechanism has been established for the [NiFe] hydrogenases involving heterolytic cleavage of H₂ followed by a first and then second transfer of a proton and electron away from the active site, details remain vague concerning how the proton transfers are facilitated by the protein environment close to the active site. Furthermore, although [NiFe] hydrogenases from different organisms or cellular environments share a common active site, they exhibit a broad range of catalytic characteristics indicating the importance of subtle changes in the surrounding protein in controlling their behavior. Here we review recent time-resolved infrared (IR) spectroscopic studies and IR spectroelectrochemical studies carried out in situ during electrocatalytic turnover. Additionally, we re-evaluate the significant body of IR spectroscopic data on hydrogenase active site states determined through more conventional solution studies, in order to highlight mechanistic steps that seem to apply generally across the [NiFe] hydrogenases, as well as steps which so far seem limited to specific groups of these enzymes. This analysis is intended to help focus attention on the key open questions where further work is needed to assess important aspects of proton and electron transfer in the mechanism of [NiFe] hydrogenases.

H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

CCSD(T) and DMRG-CASPT2 calculations show that H₂prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.

Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase

QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases reveal the influence of the residues in the second coordination sphere on the active site.

What is the trigger mechanism for the reversal of electron flow in oxygen-tolerant [NiFe] hydrogenases?

A new mechanistic model is developed for the sequence of events by which oxygen-tolerant [NiFe] hydrogenase enzymes respond to O₂.

The [NiFe] hydrogenases use an electron transfer relay of three FeS clusters – proximal, medial and distal – to release the electrons from the principal reaction, H₂ → 2H⁺ + 2e^–, that occurs at the Ni–Fe catalytic site. This site is normally inactivated by O₂, but the subclass of O₂-tolerant [NiFe] hydrogenases are able to counter this inactivation through the agency of an unusual and unprecedented proximal cluster, with composition [Fe₄S₃(S^cys)₆], that is able to transfer two electrons back to the Ni–Fe site and effect crucial reduction of O₂-derived species and thereby reactivate the Ni–Fe site. This proximal cluster gates both the direction and the number of electrons flowing through it, and can reverse the normal flow during O₂ attack. The unusual structures and redox potentials of the proximal cluster are known: a structural change in the proximal cluster causes changes in its electron-transfer potentials. Using protein structure analysis and density functional simulations, this paper identifies a closed protonic system comprising the proximal cluster, some contiguous residues, and a proton reservoir, and proposes that it is activated by O₂-induced conformational change at the Ni–Fe site. This change is linked to a key histidine residue which then causes protonation of the proximal cluster, and migration of this proton to a key μ₃-S atom. The resulting SH group causes the required structural change at the proximal cluster, modifying its redox potentials, and leads to the reversed electron flow back to the Ni–Fe site. This cycle is reversible, and the protons involved are independent of those used or produced in reactions at the active site. Existing experimental support for this model is cited, and new testing experiments are suggested.

Biological applications of hybrid quantum mechanics/molecular mechanics calculation

Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs) and molecular mechanics (MMs) calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD) simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the misaminoacylated tRNA(Leu), and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems.

Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site

The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.

Modulation of electronic structures of bases through DNA recognition of protein

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.

Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations

The electronic and geometric structures of the copper-binding site in a fully solvated azurin were investigated using quantum mechanics (QM) and molecular mechanics (MM) hybrid calculations. Two types of computational models were applied to evaluate the effects of the environment surrounding the active site. In model I, long-distance electrostatic interactions between QM region atoms and partial point charges of the surrounding protein moieties and solvent water were calculated in a QM Hamiltonian, for which the spin-unrestricted Hartree-Fock (UHF)/density functional theory (DFT) hybrid all-electron calculation with the B3LYP functional was adopted. In model II, the QM Hamiltonian was not allowed to be polarized by those partial point charges. Models I and II provided different descriptions of the copper coordination structure, particularly for the coordinative bonds including a large dipole. In fact, the Cu-O(Gly45) and Cu-S(Cys112) bonds are sensitive to the treatment of long-distance electrostatic interactions in the QM Hamiltonian. This suggests that biological processes occurring in the active site are regulated by the surrounding structures of protein and solvent, and therefore the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of the copper active site of metalloenzymes.