Computational Insights into the Mechanism of Nitric Oxide Generation from S-Nitrosoglutathione Catalyzed by a Copper Metal-Organic Framework.

The controlled generation of nitric oxide (NO) from endogenous sources, such as S-nitrosoglutathione (GSNO), has significant implications for biomedical implants due to the vasodilatory and other beneficial properties of NO. The water-stable metal-organic framework (MOF) Cu-1,3,5-tris[1H-1,2,3-triazol-5-yl]benzene has been shown to catalyze the production of NO and glutathione disulfide (GSSG) from GSNO in aqueous solution as well as in blood. Previous experimental work provided kinetic data for the catalysis of the 2GSNO → 2NO + GSSG reaction, leading to various proposed mechanisms. Herein, this catalytic process is examined using density functional theory. Minimal functional models of the Cu-MOF cluster and glutathione moieties are established, and three distinct catalytic mechanisms are explored. The most thermodynamically favorable mechanism studied is consistent with prior experimental findings. This mechanism involves coordination of GSNO to copper via sulfur rather than nitrogen and requires a reductive elimination that produces a Cu(I) intermediate, implicating a redox-active copper site. The experimentally observed inhibition of reactivity at high pH values is explained in terms of deprotonation of a triazole linker, which decreases the structural stability of the Cu(I) intermediate. These fundamental mechanistic insights may be generally applicable to other MOF catalysts for NO generation.

Kinetic model for reversible radical transfer in ribonucleotide reductase.

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Šthrough two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides.

Long-range electron transfer is coupled to proton transfer in a wide range of chemically and biologically important processes. Recently the proton-coupled electron transfer (PCET) rate constants for a series of biomimetic oligoproline peptides linking Ru(bpy)32+ to tyrosine were shown to exhibit a substantially shallower dependence on the number of proline spacers compared to the analogous electron transfer (ET) systems. The experiments implicated a concerted PCET mechanism involving intramolecular electron transfer from tyrosine to Ru(bpy)33+ and proton transfer from tyrosine to a hydrogen phosphate dianion. Herein these PCET systems, as well as the analogous ET systems, are studied with microsecond molecular dynamics, and the ET and PCET rate constants are calculated with the corresponding nonadiabatic theories. The molecular dynamics simulations illustrate that smaller ET donor-acceptor distances are sampled by the PCET systems than by the analogous ET systems. The shallower dependence of the PCET rate constant on the ET donor-acceptor distance is explained in terms of an additional positive, distance-dependent electrostatic term in the PCET driving force, which attenuates the rate constant at smaller distances. This electrostatic term depends on the change in the electrostatic interaction between the charges on each end of the bridge and can be modified by altering these charges. On the basis of these insights, this theory predicted a less shallow distance dependence of the PCET rate constant when imidazole rather than hydrogen phosphate serves as the proton acceptor, even though their pKa values are similar. This theoretical prediction was subsequently validated experimentally, illustrating that long-range electron transfer processes can be tuned by modifying the nature of the proton acceptor in concerted PCET processes. This level of control has broad implications for the design of more effective charge-transfer systems.

Computational Insights into Five- versus Six-Coordinate Iron Center in Ferrous Soybean Lipoxygenase.

Soybean lipoxygenase (SLO) serves as a prototype for fundamental understanding of hydrogen tunneling in enzymes. Its reactivity depends on the active site structure around a mononuclear, nonheme iron center. The available crystal structures indicate five-coordinate iron, while magnetic circular dichroism experiments suggest significant populations of both five-coordinate (5C) and six-coordinate (6C) iron in ferrous SLO. Quantum mechanical calculations of gas phase models produce only 6C geometries. Herein mixed quantum mechanical/molecular mechanical (QM/MM) calculations are employed to identify and characterize the 5C and 6C geometries. These calculations highlight the importance of the protein environment, particularly two Gln residues in a hydrogen-bonding network with Asn694, the ligand that can dissociate. This hydrogen-bonding network is similar in both geometries, but twisting of a dihedral angle in Asn694 moves its oxygen away from the iron in the 5C geometry. These insights are important for future simulations of SLO.

Theoretical Studies of Proton-Coupled Electron Transfer: Models and Concepts Relevant to Bioenergetics.

Theoretical studies of proton-coupled electron transfer (PCET) reactions for model systems provide insight into fundamental concepts relevant to bioenergetics. A dynamical theoretical formulation for vibronically nonadiabatic PCET reactions has been developed. This theory enables the calculation of rates and kinetic isotope effects, as well as the pH and temperature dependences, of PCET reactions. Methods for calculating the vibronic couplings for PCET systems have also been developed and implemented. These theoretical approaches have been applied to a wide range of PCET reactions, including tyrosyl radical generation in a tyrosine-bound rhenium polypyridyl complex, phenoxyl/phenol and benzyl/toluene self-exchange reactions, and hydrogen abstraction catalyzed by the enzyme lipoxygenase. These applications have elucidated some of the key underlying physical principles of PCET reactions. The tools and concepts derived from these theoretical studies provide the foundation for future theoretical studies of PCET in more complex bioenergetic systems such as Photosystem II.

Hydrogen bonding pathways in human dihydroorotate dehydrogenase.

Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.