Correction: Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism – a gas-phase ab initio study

Correction for ‘Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism – a gas-phase ab initio study’ by Vivek S. Bharadwaj et al., Phys. Chem. Chem. Phys., 2015, 17, 4054–4066.

Ab initio study of the influence of resonance stabilization on intramolecular ring closure reactions of hydrocarbon radicals

The cyclization reactions of dieneyl radicals provide a low energy route to the formation of molecular weight growth products.

Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study

The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter-molecular non-covalent interactions.

Reactions of allylic radicals that impact molecular weight growth kinetics

The reactions of allylic radicals have the potential to play a critical role in molecular weight growth (MWG) kinetics during hydrocarbon oxidation and/or pyrolysis.

Speed of facial affect intensity recognition as an endophenotype of first-episode psychosis and associated limbic-cortical grey matter systems

BACKGROUND

Psychotic disorders are highly heritable such that the unaffected relatives of patients may manifest characteristics, or endophenotypes, that are more closely related to risk genes than the overt clinical condition. Facial affect processing is dependent on a distributed cortico-limbic network that is disrupted in psychosis. This study assessed facial affect processing and related brain structure as a candidate endophenotype of first-episode psychosis (FEP).

METHOD

Three samples comprising 30 FEP patients, 30 of their first-degree relatives and 31 unrelated healthy controls underwent assessment of facial affect processing and structural magnetic resonance imaging (sMRI) data. Multivariate analysis (partial least squares, PLS) was used to identify a grey matter (GM) system in which anatomical variation was associated with variation in facial affect processing speed.

RESULTS

The groups did not differ in their accuracy of facial affect intensity rating but differed significantly in speed of response, with controls responding faster than relatives, who responded faster than patients. Within the control group, variation in speed of affect processing was significantly associated with variation of GM density in amygdala, lateral temporal cortex, frontal cortex and cerebellum. However, this association between cortico-limbic GM density and speed of facial affect processing was absent in patients and their relatives.

CONCLUSIONS

Speed of facial affect processing presents as a candidate endophenotype of FEP. The normal association between speed of facial affect processing and cortico-limbic GM variation was disrupted in FEP patients and their relatives.

Induced fit and the catalytic mechanism of isocitrate dehydrogenase

NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.

Selective removal of ethylene, a deposit precursor, from a "dirty" synthesis gas stream via gas-phase partial oxidation

A fundamental issue in the gasification of biomass is that in addition to the desired synthesis gas product (a mixture of H(2) and CO), the gasifier effluent contains other undesirable products that need to be removed before any further downstream processing can occur. This work assesses the potential to selectively remove hydrocarbons from a synthesis gas stream via gas-phase partial oxidation. Specifically, the partial oxidation of methane-doped, ethylene-doped, and methane/ethylene-doped model synthesis gas mixtures has been investigated at ambient pressures over a temperature range of 760-910 degrees C and at residence times ranging from 0.4 to 2.4 s using a tubular flow reactor. For the synthesis gas mixtures that contain either methane or ethylene, the addition of oxygen substantially reduces the hydrocarbon concentration while only a small reduction in the hydrogen concentration is observed. For the synthesis gas mixtures doped with both methane and ethylene, the addition of oxygen preferentially removes ethylene while the concentrations of methane and hydrogen remain relatively unaffected. These results are compared to the predictions of a plug flow model using a reaction mechanism that is designed to describe the pyrolysis and partial oxidation of small hydrocarbon species. The agreement between the experimental observations and the model predictions is quite good, allowing us to explore the underlying chemistry that leads to the hydrocarbon selective oxidation. The implications of these results are briefly discussed in terms of using synthesis gas to produce liquid fuels and electrical power via a solid oxide fuel cell.

Hydrocarbon fuel effects in solid-oxide fuel cell operation: an experimental and modeling study of n-hexane pyrolysis

Pyrolysis experiments of n-hexane were performed and the product distribution and fuel consumption were measured as a function of temperature. The experimental temperatures ranged from 550-675 degrees C, with a pressure of approximately 1 atm, and residence times of approximately 5 s. N-Hexane was used as a model compound to represent the linear alkanes that might be found in practical hydrocarbon fuels. Under these conditions, high fuel conversion was observed at the higher temperatures and a wide range of products were formed. The experimental observations were compared to predictions from a plug-flow model using a reaction mechanism consisting of 205 species and 1403 reactions. The hydrogen abstraction and isomerization rate coefficients in this model were based on CBS-QB3 calculations. The only model modification was adjustment of the A-factor of the initiation rates to match conversion at one temperature. This model was able to successfully predict the observed trends in both product selectivities as well as fuel conversion over the temperature range. The mechanism was also used to capture the trends previously observed in n-butane pyrolysis under similar experimental conditions. Significant differences in the sensitivity coefficients for the hexane and butane systems are discussed in terms of the competition between beta-scission and isomerization of the initial radicals formed. The kinetic model predicts that n-hexane will be completely converted within 0.1 s in the higher temperature environment ( approximately 800 degrees C) of the anode channel of a solid-oxide fuel cell (SOFC). This result clearly illustrates the need to explicitly account for gas-phase reactions in SOFC models for those cases where hydrocarbons, especially those larger than methane, are fed directly to an SOFC.

Detailed Modeling of the Reaction of C2H5 + O2

Modeling of low-temperature ethane oxidation requires an accurate description of the reaction of C(2)H(5) + O(2), because its multiple reaction channels either accelerate the oxidation process via chain branching, or inhibit it by forming stable, less reactive products. We have used a steady-state chemical-activation analysis to generate pressure and temperature dependent rate coefficients for the various channels of this system. Input parameters for this analysis were obtained from ab initio calculations at the CBS-QB3 level of theory with bond-additivity corrections, followed by transition state theory calculations with Wigner tunneling corrections. The chemical-activation analysis used QRRK theory to determine k(E) and the modified strong collision (MSC) model to account for collisional deactivation. This procedure resulted in a C(2)H(5) + O(2) submechanism which was either used directly (possibly augmented with a few C(2)H(5) generating and consuming reactions) or as part of a larger extended mechanism to predict the temperature and pressure dependencies of the overall loss of ethyl and of the yields of ethylene, ethylene oxide, HO(2), and OH. A comparison of the predictions using both mechanisms allowed an assessment of the sensitivity of the experimental data to secondary reactions. Except for the time dependent OH profiles, the predictions using the extended mechanism were in good agreement with the observations. By replacing the MSC model with master equation approaches, both steady-state and time dependent, it was confirmed that the MSC assumption is adequate for the analysis of the C(2)H(5) + O(2) reaction. The good overall performance of the C(2)H(5) + O(2) submechanism developed in this study suggests that it provides a good building block for an ethane oxidation mechanism.

Nucleotide variations in the lxd region of Drosophila melanogaster: characterization of a candidate modifier of lifespan

We have investigated the structure and function of several proteins that might influence adult lifespans in Drosophila melanogaster. The present report focuses on the gene lxd ('low xanthine dehydrogenase'), which lies in a region of chromosome III identified by QTL-mapping as potentially important for lifespan. DNA sequence of a 3780 bp genomic fragment containing the lxd locus reveals differences between long-lived and control inbred lines. In order to determine the importance of nucleotide replacements, the intron/exon boundaries have been determined, based on peptide alignment and conserved amino acids. We identified four exons in the lxd coding region. The deduced amino acid sequence of exon 4 shows 46.5% identity with Escherichia coli MoaC sequences. There are eight nucleotide substitutions in exons differentiating the inbred lines, three in exon 3 and five in exon 4. One of the exon 4 substitutions has resulted in a Thr-Ile replacement at the protein surface, but not entirely solvent exposed. This substitution is potentially a modifier of lifespan via oxygen defense, but since the activities of three molybdoenzymes are unaffected in inbred lines, this possibility seems remote.

Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes

Knowledge of both prokaryotic and eukaryotic organisms is essential to the study of molecular evolution. Their common ancestry mandates that their molecular functions share many aspects of adaptation and constraint, yet their differences in size, ploidy, and structural complexity also give rise to divergent evolutionary options. We explore the interplay of adaptation, constraint, and neutrality in their evolution by the use of genetic variants to probe molecular function in context of molecular structure, metabolic organization, and phenotype-environment interactions. Case studies ranging from bacteria to butterflies, flies, and vertebrates emphasize, among other points: the importance of moving from initial recording of evolutionary pattern variation to studying the processes underlying the patterns, by experiment, reconstructive inference, or both; the complementarity, not conflict, of finding different performance and fitness impacts of natural variants in prokaryotes or eukaryotes, depending on the nature and magnitude of the variants, their locations and roles in pathways, the nature of molecular function affected, and the resulting organismal phenotype-environment interactions leading to selection or its absence; the importance of adaptive functional interaction of different kinds of variants, as in gene expression variants versus variants altering polypeptide properties, or interaction of changes in enzymes' active sites with complementary changes elsewhere that adjust catalytic function in different ways, or coadaptation of different steps' properties in pathways; the power afforded by combining structural and functional analyses of variants with study of the variants' phenotype-environment interactions to understand how molecular changes affect (or fail to affect) adaptive mechanisms "in the wild." Comparative study of prokaryotes and eukaryotes in this multifaceted way promises to deliver both new insights into evolution and a host of new and productive questions about it.

Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution

Many pathogen recognition genes, such as plant R-genes, undergo rapid adaptive evolution, providing evidence that these genes play a critical role in plant-pathogen coevolution. Surprisingly, whether rapid adaptive evolution also occurs in genes encoding other kinds of plant defense proteins is unknown. Unlike recognition proteins, plant chitinases attack pathogens directly, conferring disease resistance by degrading chitin, a component of fungal cell walls. Here, we show that nonsynonymous substitution rates in plant class I chitinase often exceed synonymous rates in the plant genus Arabis (Cruciferae) and in other dicots, indicating a succession of adaptively driven amino acid replacements. We identify individual residues that are likely subject to positive selection by using codon substitution models and determine the location of these residues on the three-dimensional structure of class I chitinase. In contrast to primate lysozymes and plant class III chitinases, structural and functional relatives of class I chitinase, the adaptive replacements of class I chitinase occur disproportionately in the active site cleft. This highly unusual pattern of replacements suggests that fungi directly defend against chitinolytic activity through enzymatic inhibition or other forms of chemical resistance and identifies target residues for manipulating chitinolytic activity. These data also provide empirical evidence that plant defense proteins not involved in pathogen recognition also evolve in a manner consistent with rapid coevolutionary interactions.

The yeast mitochondrial citrate transport protein. Probing the secondary structure of transmembrane domain iv and identification of residues that likely comprise a portion of the citrate translocation pathway

The mitochondrial citrate transport protein (CTP) has been investigated by replacing 22 consecutive residues within transmembrane domain IV, one at a time, with cysteine. A cysteine-less CTP retaining wild-type functional properties served as the starting template. The single Cys CTP variants were overexpressed in Escherichia coli, isolated, and functionally reconstituted in a liposomal system. The accessibility of each single Cys mutant to three methanethiosulfonate reagents was evaluated by determining the pseudo first order rate constants for inhibition of CTP function. These rate constants varied by seven orders of magnitude. With three independent data sets we observed peaks and troughs in the rate constant data at identical amino acid positions and a periodicity of four was observed from residues 177-193. Based on the pattern of accessibility we conclude that residues 177-193 exist as an alpha-helix. Furthermore, a water-accessible face of the helix has been defined consisting of Pro-177, Val-178, Arg-181, Gln-182, Asn-185, Gln-186, Arg-189, Leu-190, and Tyr-193, and a water-inaccessible face has been delineated consisting of Ser-179, Met-180, Ala-183, Ala-184, Ala-187, Val-188, Gly-191, and Ser-192. We infer that the water-accessible face comprises a portion of the substrate translocation pathway through the CTP, whereas the water-inaccessible surface faces the lipid bilayer.

Enzyme evolution explained (sort of)

Sites in proteins evolve at markedly different rates; some are highly conserved, others change rapidly. We have developed a maximum likelihood method to identify regions of a protein that evolve rapidly or slowly relative to the remaining structure. We also show that solvent accessibility and distance from the catalytic site are major determinants of evolutionary rate in eubacterial isocitrate dehydrogenases. These two variables account for most of the rate heterogeneity not ascribable to stochastic effects.

The applicability of SERVQUAL in different health care environments

This paper reports on a study that investigates the applicability of a modified SERVQUAL instrument as a means of measuring service quality in two types of health service environments; medical care and health care (incorporating medical, social, cognitive and emotional elements). The research confirms a four factor structure that is stable for both environments, and similar to the service quality dimensions recognised in the literature. However, the relative importance of the dimensions of quality is inconsistent for the two types of health services. These results confirm the suggestion that importance values should be part of the measurement tool. Finally, the extra diagnostic advantage achieved by the use of gap scores to measure service quality, when compared to perception only scores is demonstrated.

Carbocations in the synthesis of prostaglandins by the cyclooxygenase of PGH synthase? A radical departure!

Evidence already available is used to demonstrate that although prostaglandin G/H synthase hydroxylates arachidonic acid through radical intermediates, it effects cyclizations through a carbocation center at C-10. This is produced following migration of H to the initial radical at C-13 and a 1epsilon oxidation. Under orbital symmetry control, the cyclizations can give only the ring size and trans stereochemistry actually observed. After cyclization, the H-shift reverses to take the sequence back into current radical theory for hydroxylation at C-15. Thus 10,10-difluoroarachidonic acid cannot be cyclized, although it can be hydroxylated. Acetylation of Ser516 in the isoform synthase-2 is considered to oppose carbocation formation and/or H-migration and so prevent cyclizations while permitting hydroxylations; the associated inversion of chirality at C-15 can then readily be accommodated without the change in conformation required by other schemes. Suicide inhibition occurs when carbocations form stable bonds upon (thermal) contact with adjacent heteroatoms, etc. Because the cyclooxygenase and peroxidase functions operate simultaneously through the same heme, phenol acts as reducing cosubstrate for the cyclooxygenase, thus enabling it to promote PGG2 production and protect the enzyme from oxidative destruction.

The structural basis of molecular adaptation

The study of molecular adaptation has long been fraught with difficulties, not the least of which is identifying out of hundreds of amino acid replacements those few directly responsible for major adaptations. Six studies are used to illustrate how phylogenies, site-directed mutagenesis, and a knowledge of protein structure combine to provide much deeper insights into the adaptive process than has hitherto been possible. Ancient genes can be reconstructed, and the phenotypes can be compared to modern proteins. Out of hundreds of amino acid replacements accumulated over billions of years those few responsible for discriminating between alternative substrates are identified. An amino acid replacement of modest effect at the molecular level causes a dramatic expansion in an ecological niche. These and other topics are creating the emerging field of "paleomolecular biochemistry."

Structural constraints in protein engineering--the coenzyme specificity of Escherichia coli isocitrate dehydrogenase

In a previous study we reported on the successful inversion of coenzyme specificity in isocitrate dehydrogenase (IDH) from NADP to NAD [Chen, R., Greer, A. & Dean, A. M. (1995) A highly active decarboxylating dehydrogenase with rationally inverted coenzyme specificity, Proc. Natl Acad. Sci. USA 92, 11666-11670]. Here, we explore alternative means to generate NAD dependence in the NADP-dependent scaffold of Escherichia coli IDH. The results reveal that engineering a preference for NAD is constrained by the architecture of the IDH coenzyme binding pocket and confirms that the substituted Asp344 in the engineered enzyme is the major determinant of coenzyme specificity. Mutations in the 316-325 loop, which forms part of the coenzyme binding site, reduce activity through transmission of long-range conformational changes into the active site some 14 A distant. Conformational changes seen upon substituting Cys332-->Tyr are not directly involved with improving activity. Replacements at Cys201 reveal that subtle changes in the packing of hydrophobic residues (Met and Ile versus Leu) can elicit markedly different responses. We caution against using sequence alignments as the sole guide for mutagenesis and show how a combination of rational design of active-site residues based on X-ray structures and random substitutions at surrounding residues provides an efficient means to improve enzyme preference and catalytic efficiency towards novel substrates.