Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)

Accelerated Quantum Mechanics/Molecular Mechanics Simulations via Neural Networks Incorporated with Mechanical Embedding Scheme

A powerful tool to study the mechanism of reactions in solutions or enzymes is to perform the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. However, the computational cost is too high due to the explicit electronic structure calculations at every time step of the simulation. A neural network (NN) method can accelerate the QM/MM-MD simulations, but it has long been a problem to accurately describe the QM/MM electrostatic coupling by NN in the electrostatic embedding (EE) scheme. In this work, we developed a new method to accelerate QM/MM calculations in the mechanic embedding (ME) scheme. The potentials and partial point charges of QM atoms are first learned in vacuo by the embedded atom neural networks (EANN) approach. MD simulations are then performed on this EANN/MM potential energy surface (PES) to obtain free energy (FE) profiles for reactions, in which the QM/MM electrostatic coupling is treated in the mechanic embedding (ME) scheme. Finally, a weighted thermodynamic perturbation (wTP) corrects the FE profiles in the ME scheme to the EE scheme. For two reactions in water and one in methanol, our simulations reproduced the B3LYP/MM free energy profiles within 0.5 kcal/mol with a speed-up of 30-60-fold. The results show that the strategy of combining EANN potential in the ME scheme with the wTP correction is efficient and reliable for chemical reaction simulations in liquid. Another advantage of our method is that the QM PES is independent of the MM subsystem, so it can be applied to various MM environments as demonstrated by an S_N2 reaction studied in water and methanol individually, which used the same EANN PES. The free energy profiles are in excellent accordance with the results obtained from B3LYP/MM-MD simulations. In future, this method will be applied to the reactions of enzymes and their variants.

Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one?

Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...

Isopenicillin N Synthase: Crystallographic Studies

Isopenicillin N synthase (IPNS) is a non-heme iron oxidase (NHIO) that catalyses the cyclisation of tripeptide δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) to bicyclic isopenicillin N (IPN). Over the last 25 years, crystallography has shed considerable light on the mechanism of IPNS catalysis. The first crystal structure, for apo-IPNS with Mn bound in place of Fe at the active site, reported in 1995, was also the first structure for a member of the wider NHIO family. This was followed by the anaerobic enzyme-substrate complex IPNS-Fe-ACV (1997), this complex plus nitric oxide as a surrogate for co-substrate dioxygen (1997), and an enzyme product complex (1999). Since then, crystallography has been used to probe many aspects of the IPNS reaction mechanism, by crystallising the protein with a diversity of substrate analogues and triggering the oxidative reaction by using elevated oxygen pressures to force the gaseous co-substrate throughout protein crystals and maximise synchronicity of turnover in crystallo. In this way, X-ray structures have been elucidated for a range of complexes closely related to and/or directly derived from key intermediates in the catalytic cycle, thereby answering numerous mechanistic questions that had arisen from solution-phase experiments, and posing many new ones. The results of these crystallographic studies have, in turn, informed computational experiments that have brought further insight. These combined crystallographic and computational investigations augment and extend the results of earlier spectroscopic analyses and solution phase studies of IPNS turnover, to enrich our understanding of this important protein and the wider NHIO enzyme family.

HNO to NO Conversion Mechanism with Copper Zinc Superoxide Dismutase, Comparison with Heme Protein Mediated Conversions, and the Origin of Questionable Reversibility

The interconversion of NO and HNO, via copper zinc superoxide dismutase (CuZnSOD), is important in biomedicine and for HNO detection. Many mechanistic questions, including the decades-long debate on reversibility, were resolved in this work. Calculations of various active-site and full-protein models show that the basic mechanism is proton-coupled electron transfer with a computed barrier of 10.98 kcal mol^-1 , which is in excellent agreement with experimental results (10.62 kcal mol^-1 ), and this nonheme protein-mediated reaction has many significant mechanistic differences compared with the conversions mediated by heme proteins due to geometric and electronic factors. The reasons for the irreversible nature of this conversion and models with the first thermodynamically favorable and kinetically feasible mechanism for the experimental reverse reaction were discovered. Such results are the first for nonheme enzyme mediated HNO to NO conversions, which shall facilitate other related studies and HNO probe development.

The oxygen reactivity of an artificial hydrogenase designed in a reengineered copper storage protein

The O₂ reactivity of an artificial biomolecular hydrogenase, the nickel binding protein (NBP) is investigated.

Redesign of a Copper Storage Protein into an Artificial Hydrogenase

We report the construction of an artificial hydrogenase (ArH) by reengineering a Cu storage protein (Cspl) into a Ni-binding protein (NBP) employing rational metalloprotein design. The hypothesis driven design approach involved deleting existing Cu sites of Csp1 and identification of a target tetrathiolate Ni binding site within the protein scaffold followed by repacking the hydrophobic core. Guided by modeling, the NBP was expressed and purified in high purity. NBP is a well-folded and stable construct displaying native-like unfolding behavior. Spectroscopic and computational studies indicated that the NBP bound nickel in a distorted square planar geometry that validated the design. Ni(II)-NBP is active for photo-induced H₂ evolution following a reductive quenching mechanism. Ni(II)-NBP catalyzed H⁺ reduction to H₂ gas electrochemically as well. Analysis of the catalytic voltammograms established a proton-coupled electron transfer (PCET) mechanism. Electrolysis studies confirmed H₂ evolution with quantitative Faradaic yields. Our studies demonstrate an important scope of rational metalloprotein design that allows imparting functions into protein scaffolds that have natively not evolved to possess the same function of the target metalloprotein constructs.

Dioxygen-Derived Nonheme Mononuclear FeIII(OH) Complex and Its Reactivity with Carbon Radicals

A new tetradentate, monoanionic, mixed N/O donor ligand (BNPA^Ph2O^-) with second coordination sphere H-bonding groups has been synthesized for stabilization of a terminal Fe^III(OH) complex. The complex Fe^II(BNPA^Ph2O)(OTf) (1) reacts with O₂ to give a mononuclear terminal Fe^III(OH) complex, Fe^III(OH)(BNPA^Ph2O)(OTf) (2), both of which were characterized by X-ray diffraction, electrospray ionization mass spectrometry, UV-vis, ¹H and ¹⁹F nuclear magnetic resonance, ⁵⁷Fe Mössbauer, and electron paramagnetic resonance spectroscopies. Treatment of 2 with carbon radicals (Ar₃C·) gives Ar₃COH and the Fe^II complex 1, in direct analogy with the elusive radical "rebound" process proposed for nonheme iron enzymes.

A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack

The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born-Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step-the formation of a tetrahedral, zwitterionic intermediate-is rate limiting. However, these simulations contradict another popular hypothesis that supposes that the negative charge on the intermediate is stabilized by a highly conserved asparagine (Asn79 in Ubc13). Instead, calculated reaction profiles of the N79A mutant illustrate how charge stabilization actually increases the barrier to product formation. Finally, an alternate role for Asn79 is suggested by simulations of wild-type, N79A, N79D, and H77A Ubc13: it stabilizes the motion of the electrophile prior to the reaction, positioning it for nucleophilic attack. © 2019 Wiley Periodicals, Inc.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) MbIII and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) MbIII and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The MbII-mediated reductions of nitrite to NO and structural data for the wt and mutant MbII-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

On the Difference Between Additive and Subtractive QM/MM Calculations

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.

On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase

Acireductone dioxygenase (ARD) is an intriguing enzyme from the methionine salvage pathway that is capable of catalysing two different oxidation reactions with the same substrate depending on the type of the metal ion in the active site. To date, the structural information regarding the ARD-acireductone complex is limited and possible reaction mechanisms are still under debate. The results of joint experimental and computational studies undertaken to advance knowledge about ARD are reported. The crystal structure of an ARD from Homo sapiens was determined with selenomethionine. EPR spectroscopy suggested that binding acireductone triggers one protein residue to dissociate from Fe²⁺ , which allows NO (and presumably O₂ ) to bind directly to the metal. Mössbauer spectroscopic data (interpreted with the aid of DFT calculations) was consistent with bidentate binding of acireductone to Fe²⁺ and concomitant dissociation of His88 from the metal. Major features of Fe vibrational spectra obtained for the native enzyme and upon addition of acireductone were reproduced by QM/MM calculations for the proposed models. A computational (QM/MM) study of the reaction mechanisms suggests that Fe²⁺ promotes O-O bond homolysis, which elicits cleavage of the C1-C2 bond of the substrate. Higher M³⁺ /M²⁺ redox potentials of other divalent metals do not support this pathway, and instead the reaction proceeds similarly to the key reaction step in the quercetin 2,3-dioxygenase mechanism.

Beyond ferryl-mediated hydroxylation: 40 years of the rebound mechanism and C-H activation

Since our initial report in 1976, the oxygen rebound mechanism has become the consensus mechanistic feature for an expanding variety of enzymatic C-H functionalization reactions and small molecule biomimetic catalysts. For both the biotransformations and models, an initial hydrogen atom abstraction from the substrate (R-H) by high-valent iron-oxo species (Feⁿ=O) generates a substrate radical and a reduced iron hydroxide, [Fe^n-1-OH ·R]. This caged radical pair then evolves on a complicated energy landscape through a number of reaction pathways, such as oxygen rebound to form R-OH, rebound to a non-oxygen atom affording R-X, electron transfer of the incipient radical to yield a carbocation, R⁺, desaturation to form olefins, and radical cage escape. These various flavors of the rebound process, often in competition with each other, give rise to the wide range of C-H functionalization reactions performed by iron-containing oxygenases. In this review, we first recount the history of radical rebound mechanisms, their general features, and key intermediates involved. We will discuss in detail the factors that affect the behavior of the initial caged radical pair and the lifetimes of the incipient substrate radicals. Several representative examples of enzymatic C-H transformations are selected to illustrate how the behaviors of the radical pair [Fe^n-1-OH ·R] determine the eventual reaction outcome. Finally, we discuss the powerful potential of "radical rebound" processes as a general paradigm for developing novel C-H functionalization reactions with synthetic, biomimetic catalysts. We envision that new chemistry will continue to arise by bridging enzymatic "radical rebound" with synthetic organic chemistry.

A DFT and ONIOM study of C–H hydroxylation catalyzed by nitrobenzene 1,2-dioxygenase

The DFT and ONIOM calculations show that C–H hydroxylation by nitrobenzene 1,2-dioxygenase proceeds through a HO–Fe^VO intermediate.

Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

[Recent progress in the theoretical studies of structure, function, and reaction of biological molecules]

Essential biomolecular functions often involve electron-related events such as chemical reactions and photoluminescence phenomena. Theoretical description of such electronic processes requires the use of quantum mechanics (QM), but the number of atoms that can be handled with QM is usually smaller than the number of atoms present in a single protein. A reasonable strategy is therefore to give priority to a few tens or hundreds of atoms in the system and deal with them quantum mechanically. Lower-priority atoms influence the event occurring in the higher-priority area; therefore, their effect should also be taken into account. Under these circumstances, a reasonable approach is to apply two or more different theoretical methods to differently prioritized subsystems. QM can be combined, for example, with less accurate yet much less demanding molecular mechanics (MM). Our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method allows for such hybrid calculations, and our group has been applying it to a wide range of biology-related problems. In this paper, we briefly explain the theoretical background and the procedure for the theoretical investigation of biological systems. Subsequently, we provide an overview of some of our recent studies of metalloenzymes and photobiology-related problems.