Mononuclear iron‐containing enzymes are highly versatile oxidants that often react stereospecifically and/or regioselectively with substrates. Combined experimental and computational studies on heme ...monooxygenases, nonheme iron dioxygenases and halogenases have revealed the intricate details of the second‐coordination sphere, which determine this specificity and selectivity. These second‐coordination sphere effects originate from the positioning of the substrate and oxidant, which involve the binding of the co‐factors and substrate into the active site of the protein. In addition, some enzymes affect the selectivity and reactivity through charge‐stabilization from nearby bound cations/anions, an induced electric field or through the positioning of salt bridges and hydrogen‐bonding interactions to first‐coordination sphere iron ligands and/or the substrate. Examples of all of these second‐coordination sphere effects in iron‐containing enzymes and how these influence structure and reactivity are given.
Coordination sphere effects: Metalloenzymes have important functions in chemical biology and oxygen activating ones participate in biosynthesis and biodegradation reactions in biosystems. Often these reactions are stereospecific or regioselective owing the specific long‐ or midrange interactions from the second‐coordination sphere. In this review paper an overview is given of the types of second‐coordination sphere effects in iron‐containing enzymes.
A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O‐demethylation or alternatively an acetal formation reaction. These are important reactions in ...biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)‐oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate‐binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O‐demethylation is predicted, whereas an initial hydrogen‐atom ion of the weak phenolic O‐H group would trigger a pathway leading to ring‐closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.
Using an unnatural natural product: Density functional theory calculations on a large cluster model of cytochrome P450 GcoA show that the enzyme can bind and activate lignin monomer units and convert them into hemiacetal and acetal products. Suggestions on how to bioengineer the enzyme to improve the selectivity are given.
Plants react to their environment and to management interventions by adjusting physiological functions and structure. Functional–structural plant models (FSPM), combine the representation of ...three-dimensional (3D) plant structure with selected physiological functions. An FSPM consists of an architectural part (plant structure) and a process part (plant functioning). The first deals with (i) the types of organs that are initiated and the way these are connected (topology), (ii) co-ordination in organ expansion dynamics, and (iii) geometrical variables (e.g. leaf angles, leaf curvature). The process part may include any physiological or physical process that affects plant growth and development (e.g. photosynthesis, carbon allocation). This paper addresses the following questions: (i) how are FSPM constructed, and (ii) for what purposes are they useful? Static, architectural models are distinguished from dynamic models. Static models are useful in order to study the significance of plant structure, such as light distribution in the canopy, gas exchange, remote sensing, pesticide spraying studies, and interactions between plants and biotic agents. Dynamic models serve quantitatively to integrate knowledge on plant functions and morphology as modulated by environment. Applications are in the domain of plant sciences, for example the study of plant plasticity as related to changes in the red:far red ratio of light in the canopy. With increasing availability of genetic information, FSPM will play a role in the assessment of the significance towards plant performance of variation in genetic traits across environments. In many crops, growers actively manipulate plant structure. FSPM is a promising tool to explore divergent management strategies.
•Inhibitor leaching followed by fast and effective irreversible inhibition are key criteria for active protective coatings.•BTA and 2-MBT show better intrinsic inhibition than lithium carbonate when ...studied in bulk electrolytes.•Lithium carbonate, BTA and 2-MBT demonstrated to be able to leach from an organic coating matrix.•Organic corrosion inhibitors, BTA and 2-MBT, exhibit a reversible corrosion inhibitive nature.•Lithium carbonate provides the key characteristics for active protective coatings.
Inhibitor leaching, fast, effective and irreversible passivation are essential for active protective coatings to protect aluminium alloys. This study presents the comparison of the active protective properties of lithium carbonate and two organic corrosion inhibitors, benzotriazole and 2-mercaptobenzothiazole, on aluminium alloy 2024-T3 with a special focus on the irreversibility of the inhibition. A combined approach of electrochemical measurements, optical observations, surface roughness and weight-loss measurements revealed the reversible inhibition behaviour of benzotriazole and 2-mercaptobenzothiazole on AA2024-T3. On the contrary, lithium carbonate demonstrated fast, effective and irreversible corrosion inhibition, providing the essential characteristics needed for effective active corrosion protection from coatings.
Taurine/α‐ketoglutarate dioxygenase is an important enzyme that takes part in the cysteine catabolism process in the human body and selectively hydroxylates taurine at the C1‐position. Recent ...computational studies showed that in the gas‐phase the C2−H bond of taurine is substantially weaker than the C1−H bond, yet no evidence exists of 2‐hydroxytaurine products. To this end, a detailed computational study on the selectivity patterns in TauD was performed. The calculations show that the second‐coordination sphere and the protonation states of residues play a major role in guiding the enzyme to the right selectivity. Specifically, a single proton on an active site histidine residue can change the regioselectivity of the reaction through its electrostatic perturbations in the active site and effectively changes the C1−H and C2−H bond strengths of taurine. This is further emphasized by many polar and hydrogen bonding interactions of the protein cage in TauD with the substrate and the oxidant that weaken the pro‐R C1−H bond and triggers a chemoselective reaction process. The large cluster models reproduce the experimental free energy of activation excellently.
Density functional theory calculations on large active site models of taurine/α‐ketoglutarate dioxygenase show that second‐coordination sphere effects of polar and charged amino acid residues are essential for the correct description of the regioselectivity of taurine activation by this enzyme. In particular, a charged histidine residue incurs a local electric field effect that guides the reactivity to C1‐hydroxylation.
Caffeine is a natural compound found in plant seeds that after consumption by humans effects the central nervous system as well as the cardiovascular system. In general, the cytochrome P450 enzymes ...in the liver are involved in the biodegradation of caffeine, which gives paraxanthine, theobromine and theophylline products. There has been debate for many years why multiple products are obtained and how their distributions are determined. To this end we performed a high‐level computational study using a combination of molecular dynamics and quantum mechanical approaches. A series of quantum chemical cluster models on the mechanism of caffeine activation by P450 model complexes give hydrogen atom ion barriers that predicts the correct ordering and statistical distribution of products. Our studies highlight that second‐coordination sphere effects and thermochemical properties of the substrate determine the product distributions.
DFT calculations on large P450 enzyme models reproduce experimental product distributions excellently and highlight the second coordination sphere interactions in the protein.
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all ...biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.
The do′s and don'ts of QM/MM: This manuscript gives a tutorial review on the challenges and caveats of running QM/MM calculations and explains the reader the key steps in the set‐up processes.
The nonheme iron enzyme OrfP reacts with l‐Arg selectively to form the 3R,4R‐dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure ...control. To understand the mechanisms of dioxygen activation of l‐Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3−H hydrogen atom ion. This happens despite the fact that the C3−H and C4−H bond strengths of l‐Arg are very similar. Electronic differences in the two hydrogen atom ion pathways drive the reaction with an initial C3−H activation to a low‐energy 5σ‐pathway, while substrate positioning destabilizes the C4−H ion and sends it over the higher‐lying 5π‐pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.
Density functional theory calculations on the arginine dihydroxylating dioxygenase OrfP focus on the mechanism of arginine activation. We find a selective initial C3−H oxygenation pathway followed by a second oxygenation cycle on the C4−H group. A comparison with other arginine activating enzymes highlight a tight substrate binding pocket that locks the product and enables two oxygenation cycles.
The cytochromes P450 are heme‐based mono‐oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per‐oxygenase, OleTJE, converts long‐chain fatty ...acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α‐ and β‐hydroxylation by‐products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH‐rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence‐bond models that highlight the differences in reaction mechanism.
A detailed quantum mechanics/molecular mechanics study was performed into the origins of the regioselectivity of aliphatic hydroxylation versus decarboxylation of long‐chain fatty acids. The key variables that determine the bifurcation processes were identified, and suggestions on how to bioengineer this enzyme further for optimum biofuel production are given (see scheme).
Dealloying is involved in materials science responsible for fabrication of nanoscale structures beneficially but for corrosion degradations detrimentally. Detailed understanding related to the latter ...is critical for designing corrosion-resistance alloys and dedicated inhibition systems. Thus, direct nanoscopic observations of nano-structural and compositional evolutions during the process are essential. Here using liquid phase-transmission electron microscopy (LP-TEM), for the first time, we show dynamic evolution of intricate site-specific local corrosion linked to intermetallic particles (IMPs) in aerospace aluminium alloys. To thoroughly probe degradation events, oxidation direction is controlled by purposefully masking thin specimens, allowing for observing top-view surface initiation to cross-sectional depth propagation of local degradations. Real-time capturing validated and supported by post-mortem examinations shows a dealloying-driven process that initiates at IMPs and penetrates into the depth of the alloy, establishing macroscopic corrosion pits. Besides, controversial mechanisms of noble-metal redistribution are finally elucidated.
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