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Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C4–H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C4–H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C4–H hydroxylation selectivity. Furthermore, an active site Tyr233residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome cperoxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233phenol loses a proton to the nearby Asp179residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4–H bond of the substrate and guides the selectivity to the C4-hydroxylation of the substrate.

Calmodulin (CaM) is a highly dynamic Ca2+-binding protein that exhibits large conformational changes upon binding Ca2+and target proteins. Although it is accepted that CaM exists in an equilibrium of conformational states in the absence of target protein, the physiological relevance of an elongated helical linker region in the Ca2+-replete form has been highly debated. In this study, we use PELDOR (pulsed electron–electron double resonance) EPR measurements of a doubly spin-labeled CaM variant to assess the conformational states of CaM in the apo-, Ca2+-bound, and Ca2+plus target peptide-bound states. Our findings are consistent with a three-state conformational model of CaM, showing a semi-open apo-state, a highly extended Ca2+-replete state, and a compact target protein-bound state. Molecular dynamics simulations suggest that the presence of glycerol, and potentially other molecular crowding agents, has a profound effect on the relative stability of the different conformational states. Differing experimental conditions may explain the discrepancies in the literature regarding the observed conformational state(s) of CaM, and our PELDOR measurements show good evidence for an extended conformation of Ca2+-replete CaM similar to the one observed in early X-ray crystal structures.

Metal ions are associated with a variety of proteins and play critical roles in a wide range of biochemical processes. There are multiple ways to study and quantify protein–metal ion interactions, including molecular dynamics simulations. Recently, the AMBER molecular mechanics forcefield was modified to include a 12-6-4 Lennard-Jones potential, which allows for a better description of nonbonded terms through the additional pairwise Cijcoefficients. Here, we demonstrate a method of generating Cijparameters that allows parametrization of specific metal ion-ligating groups in order to tune binding energies computed by thermodynamic integration. The new Cijcoefficients were tested on a series of chelators: ethylenediaminetetraacetic acid, nitrilotriacetic acid, egtazic acid, and the EF1 loop peptides from the proteins lanmodulin and calmodulin. The new parameters show significant improvements in computed binding energies relative to existing force fields and produce coordination numbers and ion-oxygen distances that are in good agreement with experimental values. This parametrization method should be extensible to a range of other systems and could be readily adapted to tune properties other than binding energies.

The combination of computational design and directed evolution could offer a general strategy to create enzymes with new functions. So far, this approach has delivered enzymes for a handful of model reactions. Here we show that new catalytic mechanisms can be engineered into proteins to accelerate more challenging chemical transformations. Evolutionary optimization of a primitive design afforded an efficient and enantioselective enzyme (BH32.14) for the Morita–Baylis–Hillman (MBH) reaction. BH32.14 is suitable for preparative-scale transformations, accepts a broad range of aldehyde and enone coupling partners and is able to promote selective monofunctionalizations of dialdehydes. Crystallographic, biochemical and computational studies reveal that BH32.14 operates via a sophisticated catalytic mechanism comprising a His23 nucleophile paired with a judiciously positioned Arg124. This catalytic arginine shuttles between conformational states to stabilize multiple oxyanion intermediates and serves as a genetically encoded surrogate of privileged bidentate hydrogen-bonding catalysts (for example, thioureas). This study demonstrates that elaborate catalytic devices can be built from scratch to promote demanding multi-step processes not observed in nature.

The direct C–H carboxylation of aromatic compounds is an attractive route to the corresponding carboxylic acids, but remains challenging under mild conditions. It has been proposed that the first step in anaerobic microbial degradation of recalcitrant aromatic compounds is a UbiD-mediated carboxylation. In this study, we use the UbiD enzyme ferulic acid decarboxylase (Fdc) in combination with a carboxylic acid reductase to create aromatic degradation-inspired cascade reactions, leading to efficient functionalization of styrene through CO2fixation. We reveal that rational structure-guided laboratory evolution can expand the substrate scope of Fdc, resulting in activity on a range of mono- and bicyclic aromatic compounds through a single mutation. Selected variants demonstrated 150-fold improvement in the conversion of coumarillic acid to benzofuran?+?CO2and unlocked reactivity towards naphthoic acid. Our data demonstrate that UbiD-mediated C–H activation is a versatile tool for the transformation of aryl/alkene compounds and CO2into commodity chemicals.

Protein motions and enzyme catalysis are often linked. It is hypothesized that ultrafast vibrations (femtosecond–picosecond) enhance the rate of hydride transfer catalyzed by members of the old yellow enzyme (OYE) family of ene-reductases. Here, we use time-resolved infrared (TRIR) spectroscopy in combination with stable “heavy” isotopic labeling (2H, 13C, 15N) of protein and/or cofactor to probe the vibrational energy transfer (VET) between pentaerythritol tetranitrate reductase (a member of the OYE family) and its noncovalently bound flavin mononucleotide (FMN) cofactor. We show that when the FMN cofactor is photoexcited with visible light, vibrational energy is transferred from the flavin to the surrounding protein environment on the picosecond timescale. This finding expands the scope of VET investigation in proteins, which are limited by suitable intrinsic probes, and may have implications in the understanding of the mechanism of recently discovered photoactive flavoenzymes.

The UbiD enzyme plays an important role in bacterial ubiquinone (coenzyme Q) biosynthesis. It belongs to a family of reversible decarboxylases that interconvert propenoic or aromatic acids with the corresponding alkenes or aromatic compounds using a prenylated flavin mononucleotide cofactor. This cofactor is suggested to support (de)carboxylation through a reversible 1,3-dipolar cycloaddition process. Here, we report an atomic-level description of the reaction of the UbiD-related ferulic acid decarboxylase with substituted propenoic and propiolic acids (data ranging from 1.01–1.39 Å). The enzyme is only able to couple (de)carboxylation of cinnamic acid-type compounds to reversible 1,3-dipolar cycloaddition, while the formation of dead-end prenylated flavin mononucleotide cycloadducts occurs with distinct propenoic and propiolic acids. The active site imposes considerable strain on covalent intermediates formed with cinnamic and phenylpropiolic acids. Strain reduction through mutagenesis negatively affects catalytic rates with cinnamic acid, indicating a direct link between enzyme-induced strain and catalysis that is supported by computational studies.

Conformational control limits most electron transfer (ET) reactions in biology, but we lack general insight into the extent of conformational space explored, and specifically the properties of the associated energy landscape. Here we unite electron−electron double resonance (ELDOR) studies of the diradical (disemiquinoid) form of human cytochrome P450 reductase (CPR), a nicotinamide adenine phosphate dinucleotide (NADPH)-linked diflavin oxidoreductase required for P450 enzyme reduction, with functional studies of internal ET to gain new insight into the extent and properties of the energy landscape for conformationally controlled ET. We have identified multiple conformations of disemiquinoid CPR, which point to a rugged energy landscape for conformational sampling consistent with functional analysis of ET using high-pressure stopped-flow, solvent, and temperature perturbation studies. Crystal structures of CPR have identified discrete “closed” and “open” states, but we emphasize the importance of a continuum of conformational states across the energy landscape. Within the landscape more closed states that favor internal ET are formed by nucleotide binding. Open states that enable P450 enzymes to gain access to electrons located in the FMN-domain are favored in the absence of bound coenzyme. The extent and nature of energy landscapes are therefore accessible through the integration of ELDOR spectroscopy with functional studies. We suggest this is a general approach that can be used to gain new insight into energy landscapes for biological ET mediated by conformational sampling mechanisms.

The enzyme protochlorophyllide oxidoreductase (POR) catalyses a light-dependent step in chlorophyll biosynthesis that is essential to photosynthesis and, ultimately, all life on Earth1–3. POR, which is one of three known light-dependent enzymes4,5, catalyses reduction of the photosensitizer and substrate protochlorophyllide to form the pigment chlorophyllide. Despite its biological importance, the structural basis for POR photocatalysis has remained unknown. Here we report crystal structures of cyanobacterial PORs from Thermosynechococcus elongatusand Synechocystissp. in their free forms, and in complex with the nicotinamide coenzyme. Our structural models and simulations of the ternary protochlorophyllide–NADPH–POR complex identify multiple interactions in the POR active site that are important for protochlorophyllide binding, photosensitization and photochemical conversion to chlorophyllide. We demonstrate the importance of active-site architecture and protochlorophyllide structure in driving POR photochemistry in experiments using POR variants and protochlorophyllide analogues. These studies reveal how the POR active site facilitates light-driven reduction of protochlorophyllide by localized hydride transfer from NADPH and long-range proton transfer along structurally defined proton-transfer pathways.

Abstract

Derivatives of vitamin B12are six-coordinate cobalt corrinoids found in humans, other animals, and microorganisms. By acting as enzymatic cofactors and photoreceptor chromophores, they serve vital metabolic and photoprotective functions. Depending on the context, the chemical mechanisms of the biologically active derivatives of B12—methylcobalamin (MeCbl) and 5′-deoxyadenosylcobalamin (AdoCbl)—can be very different from one another. The extent to which this chemistry is tuned by the upper axial ligand, however, is not yet clear. Here, we have used a combination of time-resolved Fourier transform-electron paramagnetic resonance (FT-EPR), magnetic field effect experiments, and spin dynamic simulations to reveal that the upper axial ligand alone only results in relatively minor changes to the photochemical spin dynamics of B12. By studying the photolysis of MeCbl, we find that, similar to AdoCbl, the initial (or “geminate”) radical pairs (RPs) are born predominantly in the singlet spin state and thus originate from singlet excited-state precursors. This is in contrast to the triplet RPs and precursors proposed previously. Unlike AdoCbl, the extent of geminate recombination is limited following MeCbl photolysis, resulting in significant distortions to the FT-EPR signal caused by polarization from spin-correlated methyl–methyl radical “f-pairs” formed following rapid diffusion. Despite the photophysical mechanism that precedes photolysis of MeCbl showing wavelength dependence, the subsequent spin dynamics appear to be largely independent of excitation wavelength, again similar to AdoCbl. Our data finally provide clarity to what in the literature to date has been a confused and contradictory picture. We conclude that, although the upper axial position of MeCbl and AdoCbl does impact their reactivity to some extent, the remarkable biochemical diversity of these fascinating molecules is most likely a result of tuning by their protein environment.

To carry out reliable and comprehensive structural investigations, the exploitation of different complementary techniques is required. Here, we report that dual triplet-spin/fluorescent labels enable the first parallel distance measurements by electron spin resonance (ESR) and Förster resonance energy transfer (FRET) on exactly the same molecules with orthogonal chromophores, allowing for direct comparison. An improved light-induced triplet–triplet electron resonance method with 2-color excitation is used, improving the signal-to-noise ratio of the data and yielding a distance distribution that provides greater insight than the single distance resulting from FRET.

Extracting kinetic parameters from DNA polymerase-catalyzed processive polymerization data using traditional initial-rate analysis has proven to be problematic for multiple reasons. The first substrate, DNA template, is a heterogeneous polymer and binds tightly to DNA polymerase. Further, the affinity and speed of incorporation of the second substrate, deoxynucleoside triphosphate (dNTP), vary greatly depending on the nature of the templating base and surrounding sequence. Here, we present a mathematical model consisting of the DNA template-binding step and a Michaelis–Menten-type nucleotide incorporation step acting on a DNA template with a finite length. The model was numerically integrated and globally fitted to experimental reaction time courses. The time courses were determined by monitoring the processive synthesis of oligonucleotides of lengths between 50 and 120 nucleotides by DNA polymerase I (Klenow fragment exo–) using the fluorophore PicoGreen. For processive polymerization, we were able to estimate an enzyme–template association rate k1of 7.4 μM–1s–1, a disassociation rate k–1of 0.07 s–1, and a Kdof 10 nM, and the steady-state parameters for correct dNTP incorporation give kcatvalues of 2.5–3.3 s–1and Kmvalues of 0.51–0.86 μM. From the analysis of time courses measured between 5 and 25 °C, an activation energy for kcatof 82 kJ mol–1was calculated, and it was found that up to 73% of Klenow fragment becomes inactivated or involved in unproductive binding at lower temperatures. Finally, a solvent deuterium kinetic isotope effect (KIE) of 3.0–3.2 was observed under processive synthesis conditions, which suggests that either the intrinsic KIE is unusually high, at least 30–40, or previous findings, showing that the phosphoryl transfer step occurs rapidly and is flanked by two slow conformational changes, need to be re-evaluated. We suggest that the numerical integration of rate equations provides a high level of flexibility and generally produces superior results compared to those of initial-rate analysis in the study of DNA polymerase kinetics and, by extension, other complex enzyme systems.

In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.

“Cohort‐ry” in motion: The chemistry following CoC bond homolysis in coenzyme B12‐dependent ethanolamine ammonia lyase is known to favor dissociation, but what of the protein contribution? Experiments reveal the radical pair reaction dynamics to be coupled to the ps–ns protein dynamics in B12photolysis. This raises the possibility of a subtle, dynamic contribution to homolysis, which acts in cohort with electrostatics and H‐abstraction from the substrate.

OBJECTIVES To investigate the perception of images of real-world scenes in patients with amblyopia and to compare their performance with that of visually normal participants by viewing conditions (monocular vs binocular) and by treatment outcomes (successfully vs unsuccessfully treated vs normal eyes). METHODS Thirty-nine healthy and 26 amblyopic individuals who had undergone previous amblyopia treatment were recruited to perform a match-to-sample task that used images of real-world scenes. Rates of correct, incorrect, and no responses and mean reaction time were recorded. RESULTS Performance during monocular viewing showed that the mean correct response rate was 59% in the amblyopic eyes, 62% in the fellow eyes, and 67% in the normal eyes (P = .008). During binocular viewing, the correct response rate remained reduced at 58% in amblyopic patients compared with 68% in participants with normal vision (P = .03). Performance by treatment outcomes showed that the mean correct response rate was 59% in the unsuccessfully treated group, 64% in the successfully treated group, and 67% in the normal group (P = .002). There was no difference in performance among amblyopia subtypes. CONCLUSIONS Real-world scene perception is impaired in amblyopia, with the poorest performance during amblyopic monocular and binocular viewing. Despite successful treatment of the amblyopic eye to normal acuity levels, perception of images in real-world scenes remains deficient in patients with a history of amblyopia.Arch Ophthalmol. 2011;129(2):176-183--

It is generally accepted that enzymes catalyze reactions by lowering the apparent activation energy by transition state stabilization or through destabilization of ground states. A more controversial proposal is that enzymes can also accelerate reactions through barrier compression—an idea that has emerged from studies of H-tunneling reactions in enzyme systems. The effects of barrier compression on classical (over-the-barrier) reactions, and the partitioning between tunneling and classical reaction paths, have largely been ignored. We performed theoretical and computational studies on the effects of barrier compression on the shape of potential energy surfaces/reaction barriers for model (malonaldehyde and methane/methyl radical anion) and enzymatic (aromatic amine dehydrogenase) proton transfer systems. In all cases, we find that barrier compression is associated with an approximately linear decrease in the activation energy. For partially nonadiabatic proton transfers, we show that barrier compression enhances, to similar extents, the rate of classical and proton tunneling reactions. Our analysis suggests that barrier compression—through fast promoting vibrations, or other means—could be a general mechanism for enhancing the rate of not only tunneling, but also classical, proton transfers in enzyme catalysis.

No Abstract

Thirty extraocular muscles (EOM) from 20 patients were evaluated by light microscopy (LM), electron microscopy (EM), and enzyme histochemistry (EZH). Twenty-one EOM were obtained from 13 patients with strabismus, 9 EOM from 4 patients undergoing eye surgery for other reasons and from 3 autopsy cases. One µm thick sections revealed marked variation in muscle fibre shape and size and in myofibrillar structure; also noted were small, hypertrophied, whorled, and ringbinden fibres. Dense and granular material in the central portion of some fibres and sarcomere disruption in 2–3 µm sections was observed. EZH revealed the absence of the classical mosaic pattern usually found in skeletal muscles. ATPase studies were inconsistent and did not correlate with the expected reciprocal activity of NAD-H diaphorase, particularly on the large fibres.

The development of human extraocular muscles (EOM) was studied in a series of fetal specimens (12–24 weeks gestation). EOM were evaluated by enzyme histochemistry (EZ) (NADH and ATPase), by differential phase contrast microscopy (DPC) and electron microscopy (EM). In the early fetus (14 weeks), there was no clear-cut sub-division into fibre types. A uniform histochemical reaction was seen with NADH while ATPase showed light and dark myotubes. Myotubes contained large central nuclei, prominent eccentric nucleoli, abundant glycogen granules, free ribosomes, numerous mitochondria, and dense and looser bundles of myofilaments. Mesenchymal cells undergoing mitosis and fibroblasts with prominent stacks of rough endoplasmic reticulum were scattered within endomysium. Mast cells with well formed cytoplasmic granules were found as early as 18–24 weeks. The same specimens by DPC showed differentiation into at least 4 different fibre types at 12 weeks. All the intramuscular nerves at 12–16 weeks were composed of unmyelinated fibres. At 18 weeks, myelinated axons were present. Morphologically immature end-plates devoid of junctional folds were found at 12 weeks. The motor innervation of some EOM appears to be derived from more than one axon (multiple innervated fibres). At 18 weeks gestational age, differentiation into fibre types became apparent by enzyme histochemistry. These histochemical and morphological findings suggest that morphologically mature endplates are not prerequisites for differentiation into muscle fibre types.

Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure–activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N–H group of the active site Trp51 of cytochrome cperoxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

Putting the squeeze on: Hydrostatic pressure causes a shortening of the chargetransfer bond in the binary complex of morphinone reductase and NADH4see diagram. Molecular dynamics simulations suggest that pressure reduces the average reaction barrier width by restricting the conformational space available to the flavin mononucleotide and NADH within the active site. The apparent rate of catalysis increases with pressure.

Bindung unter Druck: Hydrostatischer Druck staucht die Ladungstransferbindung in dem binären Komplex aus MorphinonReduktase und NADH4siehe Spektrum. Moleküldynamiksimulationen implizieren, dass die Einwirkung von Druck die Reaktionsbarriere erniedrigt, indem der dem Flavinmononucleotid und NADH zugängliche Konformationsraum innerhalb des aktiven Zentrums eingeschränkt wird. Die effektive Katalysegeschwindigkeit steigt mit zunehmendem Druck.

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