Major Role In Catalysis Research Articles

Removal of Tetracycline Hydrochloride by Photocatalysis Using Electrospun PAN Nanofibrous Membranes Coated with g-C3N4/Ti3C2/Ag3PO4.

In order to improve the photocatalytic performance of g-C3N4, the g-C3N4/Ti3C2/Ag3PO4 S-type heterojunction catalyst was prepared by electrostatic assembly method, and then the g-C3N4/Ti3C2/Ag3PO4/PAN composite nanofiber membrane was prepared by electrospinning technology. The morphology and chemical properties of the nanofiber membrane were characterized by SEM, FTIR, and XRD, and the photocatalytic degradation of tetracycline hydrochloride (TC) in water by the nanofiber membrane was investigated. The results showed that g-C3N4/Ti3C2/Ag3PO4 could be successfully loaded on PAN and uniformly distributed on the surface of composite nanofiber membrane by electrospinning technology. Increasing the amount of loading and catalyst, lowering the pH value and TC concentration of the system were conducive to the oxidation and degradation of TC. The nano-fiber catalytic membrane had been recycled five times and found to have excellent photocatalytic stability and reusability. The study of catalytic mechanism showed that h+, •OH and •O2- were produced and participated in the oxidation degradation reaction of TC, and •O2- plays a major role in catalysis. Therefore, this work provides a new insight into the construction of high-performance and high-stability photocatalytic system by electrospinning technology.

Insights of mineral catalytic effects of high ash coal on carbon conversion in fluidized bed Co-gasification through FTIR, XRD, XRF and FE-SEM

This study presents the synergy of high ash coal with different biomass when blended in different ratios for co-gasification using a fluidized bed gasifier. The moisture, CO2, oxygen, hydrogen and numerous other compounds have synergetic effects on the co-gasification because of affinity to heat and prone to reaction. The mineral constituents, discrete mineral species and ion-exchangeable elements present in coal, biomass and bottom ash residue have been identified by XRD, XRF, FTIR and SEM-EDX. The catalytic effects of mineral, major oxides, halides and chlorites content on co-gasification have been assessed. The mineral (e.g. calcite, dolomite, hematite, etc.) present in the high ash coal and biomass plays a catalytic role. Other minerals (e.g. quartz, sulfide, kaolinite and phosphates) negatively influence co-gasification and product gas composition. The positive relationship of CaO, MgO and Fe2O3 with CCE, CGE and increasing heat values also supports major oxides catalytic role. The blend of press mud and high ash coal has given better results due to more Ca, K, Mg and Na elements. SEM microphotographs reveal catalytic effects at the micro-level, indicated by the extensive cracking of hydrocarbon compounds. The empirical models proposed for estimation of catalytic effects of minerals on co-gasification.

METTL3/N6-methyladenosine/ miR-21-5p promotes obstructive renal fibrosis by regulating inflammation through SPRY1/ERK/NF-κB pathway activation.

Renal fibrosis induced by urinary tract obstruction is a common clinical occurrence; however, effective treatment is lacking, and a deeper understanding of the mechanism of renal fibrosis is needed. Previous studies have revealed that miR‐21 impacts liver and lung fibrosis progression by activating the SPRY1/ERK/NF‐kB signalling pathway. However, whether miR‐21 mediates obstructive renal fibrosis through the same signalling pathway has not been determined. Additionally, studies have shown that N6‐methyladenosine (m6A) modification‐dependent primary microRNA (pri‐microRNA) processing is essential for maturation of microRNAs, but its role in the maturation of miR‐21 in obstructive renal fibrosis has not yet been investigated in detail. To address these issues, we employed a mouse model of unilateral ureteral obstruction (UUO) in which the left ureters were ligated for 3, 7 and 14 days to simulate the fibrotic process. In vitro, human renal proximal tubular epithelial (HK‐2) cells were transfected with plasmids containing the corresponding sequence of METTL3, miR‐21‐5p mimic or miR‐21‐5p inhibitor. We found that the levels of miR‐21‐5p and m6A modification in the UUO model groups increased significantly, and as predicted, the SPRY1/ERK/NF‐kB pathway was activated by miR‐21‐5p, confirming that miR‐21‐5p plays an important role in obstructive renal fibrosis by enhancing inflammation. METTL3 was found to play a major catalytic role in m6A modification in UUO mice and drove obstructive renal fibrosis development by promoting miR‐21‐5p maturation. Our research is the first to demonstrate the role of the METTL3‐m6A‐miR‐21‐5p‐SPRY1/ERK/NF‐kB axis in obstructive renal fibrosis and provides a deeper understanding of renal fibrosis.

Amino Acid Ionic Liquids Catalyzed d-Glucosamine into Pyrazine Derivatives: Insight from NMR Spectroscopy.

Using environment-friendly catalysts to convert biomass into compounds with high values is one of the central topics of green chemistry. In this work, [Ch][Pro] (cholinium as the cation and l-proline as the anion) ionic liquid was synthesized and applied as a model catalyst in the production of deoxyfructosazine (DOF) and fructosazine (FZ) from d-glucosamine (GlcNH2). The 13C NMR chemical shift titration experiments and the diffusion-ordered NMR spectroscopy (DOSY) measurements showed that, when the [Ch][Pro] interacted with GlcNH2, the l-proline anion ([Pro]-) played a major catalytic role instead of cholinium cation ([Ch]+). The effects of the reaction temperature and the amount of [Ch][Pro] on the product yields were surveyed. The experimental results showed that the highest DOF yield (33.78%) was obtained after 30 min at 100 °C when the molar ratio of [Ch][Pro]/GlcNH2 was 1. Moreover, in situ 1H NMR and in situ 13C NMR experiments were applied to monitor the reaction process with [Ch][Pro] as the catalyst. The reactive intermediate, dihydrofructosazine, was clearly detected by these in situ techniques. Accordingly, a possible reaction pathway was proposed. By applying other amino acids as the anions, we also prepared five other [Ch][AA] ionic liquids, and they showed different catalytic activities and selectivity in the GlcNH2 self-condensation reaction.

Catalysis on Pristine 2D Materials via Dispersion and Electrostatic Interactions.

Shape complementarity between catalyst and transition state structure is one of the cornerstones of chemical catalysis. Likewise, noncovalent interactions play a major role in catalysis. It has been predicted computationally and recently confirmed experimentally [Kroeger, A. A.; Hooper, J. F.; Karton, A. ChemPhysChem, 2020, 21, 1675-1681] that pristine graphene can efficiently catalyze chemical processes via π-interactions and shape complementarity. Here we show that other two-dimensional materials with different electronic structures and chemical compositions (h-BN and graphane) can also catalyze chemical processes that proceed via planar transition state structures. These include the bowl-to-bowl inversions in corannulene and sumanene and the rotation about the C-C bond in substituted biphenyls. This catalytic activity is achieved through shape complementarity between planar nanomaterial and planar transition state structure, enabling disproportionate stabilization of the transition state structures over the nonplanar reactants and products. A DFT-based energy decomposition analysis shows that this catalytic activity is mainly driven by dispersion and electrostatic forces, which together outweigh the Pauli repulsion term. These findings enrich and expand the concept of catalysis by pristine 2D materials.

Biochemical characterization of an esterase from Clostridium acetobutylicum with novel GYSMG pentapeptide motif at the catalytic domain.

Gene CA_C0816 codes for a serine hydrolase protein from Clostridium acetobutylicum (ATCC 824) a member of hormone-sensitive lipase of lipolytic family IV. This gene was overexpressed in E. coli strain BL21and purified using Ni2+-NTA affinity chromatography. Size exclusion chromatography revealed that the protein is a dimer in solution. Optimum pH and temperature for recombinant Clostridium acetobutylicum esterase (Ca-Est) were found to be 7.0 and 60°C, respectively. This enzyme exhibited high preference for p-nitrophenyl butyrate. KM and kcat/KM of the enzyme were 24.90µM and 25.13s-1µM-1, respectively. Sequence analysis of Ca-Est predicts the presence of catalytic amino acids Ser 89, His 224, and Glu 196, presence of novel GYSMG conserved sequence (instead of GDSAG and GTSAG motif), and undescribed variation of HGSG motif. Site-directed mutagenesis confirmed that Ser 89 and His 224 play a major role in catalysis. This study reports that Ca-Est is hormone-sensitive lipase with novel GYSMG pentapeptide motif at a catalytic domain.

Study of Catalytic Combustion of Dioxins on Ce-V-Ti Catalysts Modified by Graphene Oxide in Simulating Iron Ore Sintering Flue Gas.

Ce-V-Ti and Ce-V-Ti/GO catalysts synthesized by the sol-gel method were used for the catalytic combustion of dioxins at a low temperature under simulating sintering flue gas in this paper. The catalytic mechanism of Ce-V-Ti catalysts modified with graphene oxides (GO) at a low temperature was revealed through X-ray diffractometer (XRD), Brunauer–Emmett–Teller (BET), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), H2-temperature-programmed reduction (H2-TPR) and Fourier transform infrared (FTIR). During the tests, chlorobenzene (CB) was used as a model reagent since the dioxins are poisonous. The results showed that introducing GO to Ce-V-Ti catalysts can improve the specific surface area and promote the CB adsorption on the surface of catalysts. Simultaneously, the Ce-V-Ti with 0.7 wt % GO support showed the high activity with the conversion of 60% at 100 °C and 80% at 150 °C. The adsorb ability of catalysts is strengthened by the electron interaction between GO and CB through π-π bond. In the case of Ce-V-Ti catalysts, Ce played a major catalytic role and V acted as a co-catalytic composition. After GO modification, the concentration of Ce3+ and V4+ were enlarged. The synergy between Ce3+ and V3+ played the critical role on the low-temperature performance of catalysts under sintering flue gas.

Carbon-based solid acids: a review

Green chemistry has fostered research on recyclable, insoluble and easily separable heterogeneous catalysts. Carbon materials are widely used for renewable energy and environmental studies. Here, we review the synthesis, properties and applications of carbon solid acids in the form of biomass, polymers, and carbon/silica-based catalysts. We show in particular that mesoporosity has a major role in catalysis, notably when bulk materials are transformed into valuable products.

Comparative analysis of different methods revealing the involvement of proteins during ageing of rice seeds

AbstractSeed longevity is a very important characteristic controlling seed quality. However, the mechanism underlying this characteristic is poorly understood. In this study, 'FH7185', a storable rice variety, the germination rate of which was 66.63%, much higher than the control after artificial ageing under relative humidity 88% and 42°C for 21 days. Different methods were applied to reveal the involvement of proteins during ageing of rice seeds. In total, 35 differential proteins were identified from 2D‐PAGE, and 3,719 proteins from iTRAQ analysis. A comparison of these two methods showed that not all protein types could be detected on the 2D‐PAGE gels, and the dynamic range was somewhat limited. So the comprehensive proteome map from the iTRAQ analysis was used to identify the quantitatively regulated proteins that played roles in seed longevity, and found that the most marked change was the increased abundance of many metabolic enzymes, especially the ones involved in α‐linolenic acid metabolism in the embryos during ageing. OsLOX2 and OsLOX3 had a negative effect on seed longevity, which were lower in FH7185 than the control. The dehydrogenase (LOC_Os07g44430) which played a major catalytic role in lipid peroxidation, also changed significantly during ageing. Therefore, OsLOX2, OsLOX3 and Loc_OS 07G44430 may be involved in the regulation of seed longevity with a synergistic effect.

A Model for the Origin of the First mRNAs.

I present a model for the evolution of the genetic code that seems to predict, in a totally natural way, the origin of the first mRNAs. In particular, the model--bestowing to peptidated-RNAs the major catalytic role in the phase that triggered the genetic code origin--suggests that interactions between peptidated-RNAs led to the synthesis of these ancestral catalysts. Within every group of these interactions, a pre-mRNA molecule evolved that was able to direct all interactions between peptidated-RNAs of that particular group. This represented an improvement in the coding of these interactions compared to the interaction groups that did not evolve these pre-mRNAs. This would represent a natural and intrinsic tendency. Therefore, these molecules of pre-mRNAs were positively selected because they improved the synthesis of the catalysts through this first form of coding of interactions among peptidated-RNAs. Thus, according to the model were the pairings--involving a base number greater than three (ennuplet code)-between peptidated-RNAs and pre-mRNAs that would represent the first form of the genetic code. The evolution of this ennuplet code to the triplet code might have been simply triggered by the natural tendency to make the reading module-that is the interactions between peptidated-RNAs and pre-mRNAs--of the different ennuplets to the triplet uniform, because in this way the heterogeneity existing in interactions between the aminoacylated or peptidated-RNAs and pre-mRNAs was eliminated. That is to say, there might have been the natural tendency toward the triplets because these would have made these interactions more efficient, given that the ennuplets were at least more cumbersome and therefore less economic and with an inferior adaptive value; and also because the triplets would represent the simpler choice among that available given that the doublets would have codified too few meanings and quartets instead too many. Therefore, the genetic code would result from a very long era of interactions among peptidated-RNAs under the continuous and fundamental selective pressure for improving catalysts' syntheses and thus catalysis. The model is strongly corroborated by the explanation that the tmRNA molecule (transfer-messenger RNA) would seem to be the very molecule of pre-mRNAs that the model predicts. In other words, the tmRNA would be the molecular fossil of the evolutionary stages that led to the appearance of the first mRNAs.

Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation.

The box H/ACA RNA-guided pseudouridine synthase is a complicated ribonucleoprotein enzyme that recruits substrate via both the guide RNA and the catalytic subunit Cbf5. Structural studies have revealed multiple conformations of the enzyme, but a quantitative description of the reaction pathway is still lacking. Using fluorescence correlation spectroscopy, we here measured the equilibrium dissociation constants and kinetic association and dissociation rates of substrate and product complexes mimicking various reaction intermediate states. These data support a sequential model for substrate loading and product release regulated by the thumb loop of Cbf5. The uridine substrate is first bound primarily through interaction with the guide RNA and then loaded into the active site while progressively interacted with the thumb. After modification, the subtle chemical structure change from uridine to pseudouridine at the target site triggers the release of the thumb, resulting in an intermediate complex with the product bound mainly by the guide RNA. By dissecting the role of Gar1 in individual steps of substrate turnover, we show that Gar1 plays a major role in catalysis and also accelerates product release about 2-fold. Our biophysical results integrate with previous structural knowledge into a coherent reaction pathway of H/ACA RNA-guided pseudouridylation.

Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths.

The effects of structural fluctuations, due to protein dynamics, on enzyme activity are at the heart of current debates on enzyme catalysis. There is evidence that fatty acid amide hydrolase (FAAH) is an enzyme for which reaction proceeds via a high-energy, reactive conformation, distinct from the predominant enzyme-substrate complex (Lodola et al. Biophys. J. 2007, 92, L20-22). Identifying the structural causes of differences in reactivity between conformations in such complex systems is not trivial. Here, we show that multivariate analysis of key structural parameters can identify structural determinants of barrier height by analysis of multiple reaction paths. We apply a well-tested quantum mechanics/molecular mechanics (QM/MM) method to the first step of the acylation reaction between FAAH and oleamide substrate for 36 different starting structures. Geometrical parameters (consisting of the key bond distances that change during the reaction) were collected and used for principal component analysis (PCA), partial least-squares (PLS) regression analysis, and multiple linear regression (MLR) analysis. PCA indicates that different "families" of enzyme-substrate conformations arise from QM/MM molecular dynamics simulation and that rarely sampled, catalytically significant conformational states can be identified. PLS and MLR analyses allowed the construction of linear regression models, correlating the calculated activation barriers with simple geometrical descriptors. These analyses reveal the presence of two fully independent geometrical effects, explaining 78% of the variation in the activation barrier, which are directly correlated with transition-state stabilization (playing a major role in catalysis) and substrate binding. These results highlight the power of statistical approaches of this type in identifying crucial structural features that contribute to enzyme reactivity.

Low temperature pyrolyzed cobalt tetramethoxy phenylporphyrin catalyst and its applications as an improved catalyst for metal air batteries

As an alternative catalyst to replace the expensive platinum-based catalysts for oxygen reduction reaction (ORR) in both proton exchange membrane (PEM) fuel cells and metal–air batteries, tetra methoxyphenyl porphyrin cobalt complex, CoTMPP, has drawn much attention in the areas of ORR catalyst synthesis and characterization. In the present work, CoTMPP is investigated at varying temperatures of pyrolysis, ranging from 410 to 810 °C, to determine the optimal temperature of pyrolysis to produce catalysts with desirable properties. Carbon supported pyrolyzed CoTMPP catalyst (CoTMPP/C) was assessed using X-ray diffraction and Raman, a number of varied electrochemical tests, as well as a single cell test. Through these, it has been found that the CoTMPP/C, pyrolyzed at 410 °C, demonstrates superior catalytic activity towards ORR, and has a higher fuel cell performance than the catalysts pyrolyzed at 800 °C, the industry standard pyrolysis temperature. This paper also utilizes scanning auger microscopy (SAM) to accredit the origin of the increased activity to the bond N–C(O), which plays a major role in catalysis and is decomposed at higher temperatures.

Catalytic and Noncatalytic Mechanisms in Steam Gasification of Char from the Pyrolysis of Biomass†

Steam gasification of chars from the pyrolysis of a Japanese bamboo and cedar was studied using a reactor that enabled experimental definition of the gas composition in the vicinity of gasifying char particles. Intraparticle diffusion of neither steam nor the product gases influenced the kinetics of gasification. The chars underwent noncatalytic and catalytic gasification in parallel. The noncatalytic gasification, in which kinetic parameters were successfully defined by those for the gasification of the acid-washed char, was first-order with respect to the amount of residual carbon over the entire range of char conversion. In consequence of this, contribution of the catalytic gasification was quantified as a function of the char conversion. Among the inherent alkali and alkaline earth metallic species, potassium (K) played the major catalytic role and its overall activity changed via a maximum in the course of gasification, suggesting the presence of optimum sizes of clusters or particles of K catalyst. ...

A ternary complex of hydroxycinnamoyl-CoA hydratase–lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism

HCHL (hydroxycinnamoyl-CoA hydratase-lyase) catalyses the biotransformation of feruloyl-CoA to acetyl-CoA and the important flavour-fragrance compound vanillin (4-hydroxy-3-methoxybenzaldehyde) and is exploited in whole-cell systems for the bioconversion of ferulic acid into natural equivalent vanillin. The reaction catalysed by HCHL has been thought to proceed by a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant beta-hydroxy thioester by retro-aldol reaction to yield the products. Kinetic analysis of active-site residues identified using the crystal structure of HCHL revealed that while Glu-143 was essential for activity, Ser-123 played no major role in catalysis. However, mutation of Tyr-239 to Phe greatly increased the K(M) for the substrate ferulic acid, fulfilling its anticipated role as a factor in substrate binding. Structures of WT (wild-type) HCHL and of the S123A mutant, each of which had been co-crystallized with feruloyl-CoA, reveal a subtle helix movement upon ligand binding, the consequence of which is to bring the phenolic hydroxyl of Tyr-239 into close proximity to Tyr-75 from a neighbouring subunit in order to bind the phenolic hydroxyl of the product vanillin, for which electron density was observed. The active-site residues of ligand-bound HCHL display a remarkable three-dimensional overlap with those of a structurally unrelated enzyme, vanillyl alcohol oxidase, that also recognizes p-hydroxylated aromatic substrates related to vanillin. The data both explain the observed substrate specificity of HCHL for p-hydroxylated cinnamate derivatives and illustrate a remarkable convergence of the molecular determinants of ligand recognition between the two otherwise unrelated enzymes.

Identification of Aspartic Acid and Histidine Residues Mediating the Reaction Mechanism and the Substrate Specificity of the Human UDP-glucuronosyltransferases 1A

The human UDP-glucuronosyltransferase UGT1A6 is the primary phenol-metabolizing UDP-glucuronosyltransferase isoform. It catalyzes the nucleophilic attack of phenolic xenobiotics on UDP-glucuronic acid, leading to the formation of water-soluble glucuronides. The catalytic mechanism proposed for this reaction is an acid-base mechanism that involves an aspartic/glutamic acid and/or histidine residue. Here, we investigated the role of 14 highly conserved aspartic/glutamic acid residues over the entire sequence of human UGT1A6 by site-directed mutagenesis. We showed that except for aspartic residues Asp-150 and Asp-488, the substitution of carboxylic residues by alanine led to active mutants but with decreased enzyme activity and lower affinity for acceptor and/or donor substrate. Further analysis including mutation of the corresponding residue in other UGT1A isoforms suggests that Asp-150 plays a major catalytic role. In this report we also identified a single active site residue important for glucuronidation of phenols and carboxylic acid substrates by UGT1A enzyme family. Replacing Pro-40 of UGT1A4 by histidine expanded the glucuronidation activity of the enzyme to phenolic and carboxylic compounds, therefore, leading to UGT1A3-type isoform in terms of substrate specificity. Conversely, when His-40 residue of UGT1A3 was replaced with proline, the substrate specificity shifted toward that of UGT1A4 with loss of glucuronidation of phenolic substrates. Furthermore, mutation of His-39 residue of UGT1A1 (His-40 in UGT1A4) to proline led to loss of glucuronidation of phenols but not of estrogens. This study provides a step forward to better understand the glucuronidation mechanism and substrate recognition, which is invaluable for a better prediction of drug metabolism and toxicity in human.

Influence of structural defects on the electrocatalytic activity of platinum

Structural defects play major role in catalysis and electrocatalysis. Nanocrystalline (or nanostructured) materials composed of nanometer-sized crystallites joined via grain boundaries have been recognized for their specific structure and properties, differentiating them from single crystals, coarsely grained materials or nanometer-sized supported single-grained particles (Gleiter, Nanostruct Mater 1:1–19, 1992). In this paper, we use Pt electrodes, prepared by electrodeposition on glassy carbon and gold supports, as model nanocrystalline materials to explore the influence of grain boundaries and other structural defects on electrocatalysis of CO and methanol oxidation. We build on the recently established correlations between the nanostructure (lattice parameter, grain size, and microstrains) of electrodeposited Pt and the deposition potential (Plyasova et al., Electrochim. Acta 51:4447–4488, 2006) and use the latter to obtain materials with variable density of grain boundary regions. The activity of electrodeposited Pt in the oxidation of methanol and adsorbed CO exceeds greatly that for Pt(111), polycrystalline Pt, or single-grained Pt particles. It is proposed that active sites in nanostructured Pt are located at the emergence of grain boundaries at the surface. For methanol electrooxidation, the electrodes with optimal nanostructure exhibit relatively high rates of the “direct” oxidation pathway and of the oxidation of strongly adsorbed poisoning intermediate (COads), but not-too-high methanol dehydrogenation rate constant. These electrodes exhibit an initial current increase during potentiostatic methanol oxidation explained by the COads oxidation rate constant exceeding the methanol decomposition rate constant.

The Structure of 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase Provides Insights into the Mechanism of Uric Acid Degradation

The complete degradation of uric acid to (S)-allantoin, as recently elucidated, involves three enzymatic reactions. Inactivation by pseudogenization of the genes of the pathway occurred during hominoid evolution, resulting in a high concentration of urate in the blood and susceptibility to gout. Here, we describe the 1.8A resolution crystal structure of the homodimeric 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, which catalyzes the last step in the urate degradation pathway, for both ligand-free enzyme and enzyme in complex with the substrate analogs (R)-allantoin and guanine. Each monomer comprises ten alpha-helices, grouped into two domains and assembled in a novel fold. The structure and the mutational analysis of the active site have allowed us to identify some residues that are essential for catalysis, among which His-67 and Glu-87 appear to play a particularly significant role. Glu-87 may facilitate the exit of the carboxylate group because of electrostatic repulsion that destabilizes the ground state of the substrate, whereas His-67 is likely to be involved in a protonation step leading to the stereoselective formation of the (S)-allantoin enantiomer as reaction product. The structural and functional characterization of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase can provide useful information in view of the potential use of this enzyme in the enzymatic therapy of gout.

Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions

The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate that an S(N)2-like mechanism of ThiK, with gamma-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198 are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic activity of ThiK upon mutation of Cys198 to aspartate.

Microbacterium sp. AL-210이 생산하는 levan fructotransferase의 효소활성에 중요한 아미노산의 동정

당 분해효소의 family 32 (GH32)에 속하는 <TEX>$\beta-fructofuranosidase$</TEX>는 3차구조를 근거로 볼 때 W(L/M)(C/N)DP(Q/N), FRDPK, 그리고 ECP(D/G) 부위를 포함하는 세 군데의 보전적인 영역을 가지고 있다. 이러한 <TEX>$\beta-fructofuranosidase$</TEX> family에 속하는 Microbacterium sp. AL-210 유래 levan fructotransferase (LFTase)의 보전적인 산성 아미노산들의 역할이 특정위치 돌연변이법으로 검사되었다. 각각의 돌연변이체는 대장균인 E. coli BL21 (DE3)균주에서 발현되어 대량 생산되었고, 금속 친화 크로마토그래피법과 FPLC법으로 순수 정제되었다. wild-type LFTase의 효소의 활성은 0.74 unit 인 반면 네 개의 돌연변이체인 D63A, D195N, E245A, E245D 각각은 specific activity를 측정해 본 결과 원 균주와 비교해서 약 100배 정도 감소한 효소활성을 보여 주었다. 이로써 아미노산 변형의 target이 되었던 Asp-63, Aps-195, 그리고 Glu-245가 모두 효소 활성 및 기질과의 결합에 상당히 중요한 역할을 하고 있음이 판명되었다. 이러한 세 부위의 산성 아미노산들은 inulinase, levan fructotransferase와 invertase에 모두 보전적으로 위치 하므로 이들은 <TEX>$\beta-fructofuranosidase$</TEX> family내 에서 공통된 역할을 할 것으로 사료된다. [ <TEX>$\beta$</TEX> ]-Fructofuranosidases, a family 32 of glycoside hydrolases (GH32), share three conserved domains including the W(L/M)(C/N)DP(Q/N), FRDPK, and ECP(D/G) motifs. The functional role of the conserved acidic residues within three domains of levan fructotransferase, one of the <TEX>$\beta-fructofuranosidases$</TEX>, from Microbacterium sp. AL-210 was studied by site-directed mutagenesis. Each mutant was overexpressed in E. coli BL21(DE3) and purified by using Hi-Trap chelating affinity chromatography and fast performance liquid chromatography. Substitution of Asp-63 by Ala, Asp-195 by Asn, and Glu-245 by Ala and Asp decreased the enzyme activity by approximately 100-fold compared to the wild-type enzyme. This result indicates that three acidic residues Asp-63, Asp-195, and Glu-245 play a major role in catalysis. Since the three acidic residues are present in a conserved position in inulinase, levanase, levanfructotransferase, and invertase, they are likely to have a common functional role as nucleophile, transition state stabilizer, and general acid in <TEX>$\beta-fructofuranosidases$</TEX>.