Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites

Abietadiene synthase (AS) catalyzes two sequential, mechanistically distinct cyclizations in the conversion of geranylgeranyl diphosphate to a mixture of abietadiene double bond isomers as the initial step of resin acid biosynthesis in grand fir (Abies grandis). The first reaction converts geranylgeranyl diphosphate to the stable bicyclic intermediate (+)-copalyl diphosphate via protonation-initiated cyclization. In the second reaction, diphosphate ester ionization-initiated cyclization generates the tricyclic perhydrophenanthrene-type backbone, and is directly coupled to a 1,2-methyl migration that generates the C13 isopropyl group characteristic of the abietane family of diterpenes. Using the transition-state analogue inhibitor 14,15-dihydro-15-azageranylgeranyl diphosphate, it was demonstrated that each reaction of abietadiene synthase is carried out at a distinct active site. Mutations in two aspartate-rich motifs specifically delete one or the other activity and the location of these motifs suggests that the two active sites reside in separate domains. These mutants effectively complement each other, suggesting that the copalyl diphosphate intermediate diffuses between the two active sites in this monomeric enzyme. Free copalyl diphosphate was detected in steady-state kinetic reactions, thus conclusively demonstrating a free diffusion transfer mechanism. In addition, both mutant enzymes enhance the activity of wild-type abietadiene synthase with geranylgeranyl diphosphate as substrate. The implications of these results for the kinetic mechanism of abietadiene synthase are discussed.     

多相催化剂活性位点的配位环境及其对催化性能的影响

多相催化技术在化工产业中一直发挥着重要作用,近年来也被广泛应用于燃料电池、绿色化学、纳米技术、生物技术等新兴领域.其中,金属催化剂在加氢、氧化、氢甲酰化、偶联等多种反应中表现出较高的催化效率.然而社会发展对金属催化剂的效率提出了更高的要求,针对特定反应,开发兼具高活性、高选择性和优良稳定性的理想催化剂一直是学术界和工业...     

Mitochondria from cultured cells derived from normal and thiamine-responsive megaloblastic anemia individuals efficiently import thiamine diphosphate

Background

Within the family of green fluorescent protein (GFP) homologs, one can mark two main groups, specifically, fluorescent proteins (FPs) and non-fluorescent or chromoproteins (CPs). Structural background of differences between FPs and CPs are poorly understood to date.

Results

Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595) from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP) were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield (< 0.001). These spectral characteristics allow one to regard DsRed-NF as a true chromoprotein.

Conclusions

We located a novel point in asCP sequence (position 165) mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed.     

Modeling chemical transformations at the active sites of cholinesterases by quantum-based simulations

The significance of the quantum-mechanical–molecular-mechanical (QM/MM) method in modeling chemical transformations at the active sites of cholinesterases is discussed. Diverse versions of the QM/MM approach are applied to understand the molecular mechanisms of the reactivation reaction of butyrylcholinesterase phosphorylated by the catalytic serine residue.     

Fast grain boundary diffusion and surface exchange reactions at active surface sites of polycrystalline materials

Analytical solutions to the diffusion equations for fast grain boundary diffusion and surface exchange reactions at active surface sites are derived. The microstructure of the polycrystalline sample of finite thickness is modelled by parallel grain boundaries. The ratio between the surface exchange coefficient and the diffusion coefficient for the grain boundaries is assumed to be greater than or equal to that for the bulk. The analytical solutions allow the calculation of diffusion profiles for thin films. Special emphasis is laid on a detailed analysis of the time dependence of the total amount of diffusant exchanged between the constant diffusion source (e.g. gas phase) and the polycrystalline sample (e.g. oxide ceramics) which corresponds to relaxation curves obtained from, e.g., oxygen exchange measurements. The calculated relaxation curves refer to Harrison's type-A kinetics where homogeneous medium solutions are satisfactorily applicable, introducing effective kinetic parameters. Apart from expressions for the effective diffusion coefficient analogous relations for the effective surface exchange coefficient are proposed, depending on the microstructure of the polycrystalline material and the corresponding kinetic parameters of bulk and grain boundary regions, respectively.     

The nature of active sites and stereospecificity of their action in diene polymerization catalysed by chromium-containing systems

A study has been made of the nature of active sites, stereospecificity of their action and the regularities of diene polymerization catalysed by chromium-containing systems. All possible polymer structures with high stereospecificity can be produced for butadiene and isoprene with π-allyl chromium compounds. Tris-π-allyl chromium produces polybutadiene predominantly of 1,2-units. Cis-polybutadiene is formed when the electronegative group (Cl^?, CCl₃COO^?) is substituted for one or two π-allyl groups in Tris-allyl chromium or in the catalytic system (π-C₃H₅)₃CrAl₂O₃. A catalyst obtained through interaction of (π-C₃H₅)₃Cr with silica-alumina or silica gel produces 1,4-trans-polybutadiene and 1,4-trans-polyisoprene. The rate of butadiene polymerization in the presence of Tris-π-allyl chromium is given by k[Cr]², and in polymerization of isoprene with the catalytic system (π-C₃H₅)₃Cr-silica-alumina, by k[Cr].[M]². Polymerization of dienes catalysed by (π-C₃H₅)₃Cr-silica-alumina system or supported chromium oxide catalyst proceeds according to a type of living system. A study was made of copolymerization of butadiene and isoprene in the presence of supported chromium oxide catalyst and with that produced by the reaction of (π-C₃H₅)₃Cr with silica-alumina. The constants of copolymerization for the systems were equal. A conclusion has been drawn regarding the similar mechanisms for diene polymerization under the action of supported chromium oxide catalyst or of catalyst formed in the reaction of (π-C₃H₅)₃Cr with silica-alumina or silica gel.     

Synthesis of chemically active polymeric fibers bearing sulfo and carboxy groups

A chemically active material bearing two types of acid groups, strongly acidic sulfo groups and weakly acidic carboxy groups, was prepared by radiation-induced graft copolymerization of two kinds of monomers, acrylic acid and sodium styrenesulfonate, onto polypropylene fibers. The main parameters affecting the graft copolymerization are considered.     

Rapid screening by MALDI-TOF mass spectrometry to probe binding specificity at enzyme active sites

The binding affinity of aspartate decarboxylase has been probed using MALDI-TOF spectrometry; adducts formed covalently in the active site were detected by MALDI-TOF mass spectrometry after incubation of the enzyme with a range of potential ligands in the presence of NaCNBH3; this has highighted key structural features which will aid design of potential inhibitors.     

Quantum mechanical design of enzyme active sites

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.     

Comparing interfacial cation hydration at catalytic active sites and spectator sites on gold electrodes: understanding structure sensitive CO2 reduction kinetics

Hydrated cations present in the electrochemical double layer (EDL) are known to play a crucial role in electrocatalytic CO₂ reduction (CO₂R), and numerous studies have attempted to explain how the cation effect contributes to the complex CO₂R mechanism. CO₂R is a structure sensitive reaction, indicating that a small fraction of total surface sites may account for the majority of catalytic turnover. Despite intense interest in specific cation effects, probing site-specific, cation-dependent solvation structures remains a significant challenge. In this work, CO adsorbed on Au is used as a vibrational Stark reporter to indirectly probe solvation structure using vibrational sum frequency generation (VSFG) spectroscopy. Two modes corresponding to atop adsorption of CO are observed with unique frequency shifts and potential-dependent intensity profiles, corresponding to direct adsorption of CO to inactive surface sites, and in situ generated CO produced at catalytic active sites. Analysis of the cation-dependent Stark tuning slopes for each of these species provides estimates of the hydrated cation radius upon adsorption to active and inactive sites on the Au electrode. While cations are found to retain their bulk hydration shell upon adsorption at inactive sites, catalytic active sites are characterized by a single layer of water between the Au surface and the electrolyte cation. We propose that the drastic increase in catalytic performance at active sites stems from this unique solvation structure at the Au/electrolyte interface. Building on this evidence of a site-specific EDL structure will be critical to understand the connection between cation-dependent interfacial solvation and CO₂R performance.

Site-specific vibrational probes were used to elucidate the interfacial solvation structure between catalytic active sites and inactive sites on a Au electrode to reveal a unique, opposing cation-dependent double layer structure at active sites.     

Structure-based drug design: exploring the proper filling of apolar pockets at enzyme active sites

The proper filling of apolar pockets at enzyme active sites is central for increasing binding activity and selectivity of hits and leads in medicinal chemistry. In our structure-based design approach toward the generation of potent enzyme inhibitors, we encountered a variety of challenges in gaining suitable binding affinity from the occupation of such pockets. We summarize them here for the first time. A fluorine scan of tricyclic thrombin inhibitors led to the discovery of favorable orthogonal dipolar C-F...CO interactions. Efficient cation-pi interactions were established in the S4 pocket of factor Xa, another serine protease from the blood coagulation cascade. Changing from mono- to bisubstrate inhibitors of catechol O-methyltransferase, a target in the L-Dopa-based treatment of Parkinson's disease, enabled the full exploitation of a previously unexplored hydrophobic pocket. Conformational preorganization of a pocket at an enzyme active site is crucial for harvesting binding affinity. This is demonstrated for two enzymes from the nonmevalonate pathway of isoprenoid biosynthesis, IspE and IspF, which are pursued as antimalarial targets. Disrupting crystallographically defined water networks on the way into a pocket might cost all of the binding free enthalpy gained from its occupation, as revealed in studies with tRNA-guanine transglycosylase, a target against shigellosis. Investigations of the active site of plasmepsin II, another antimalarial target, showed that principles for proper apolar cavity filling, originally developed for synthetic host-guest systems, are also applicable to enzyme environments.     

Self-assembled and self-sorted array of chemically active beads for analytical and biochemical screening

A technique for generating a general screening platform consisting of dots of immobilized beads on silicon has been developed via self-sorting and -assembly of different kinds of beads. The dots are defined by a teflon-like film, which due to its hydrophobic characteristics also prevents cross-contamination of liquid from different dots. To enable functionalization of individual dots with different target molecules simultaneously a new way of microcontact printing has been explored where different target solutions are printed in parallel using one stamp. In order to show that this platform can be designed for both biochemical assays and organic chemistry, streptavidin-, amino- and hydroxy-functionalized beads have been self-sorted and -assembled both on separate and common platforms. The self-sorting and -arrangement are based on surface chemistry only, which has not previously been reported. Beads of different sizes and material have successfully been immobilized in line patterns as narrow as 5 mum. Besides silicon, quartz and polyethylene have also been used as substrates.     

Synthesis of nitric oxide reductase active site models bearing key components at both distal and proximal sites

Porphyrins 1ab and 2ab were successfully synthesized from cis-alpha2-bisimidazole-beta-imidazole-tail porphyrins and two newly synthesized imidazole pickets containing an aliphatic ester chain following a [2+1] approach. The four compounds possess a distal trisimidazole set, a distal carboxylic acid, and a proximal imidazole, which constitute all the key features of the coordination environment of the active site in Bacterial Nitric Oxide Reductase (NOR) and make them the closest synthetic NOR model ligands to date.     

Kinetic and thermodynamic study of a chemically modified highly active xylanase fromScopulariopsis sp

The amino groups of purified least acidic xylanase (LAX) isomer and carboxyl groups of purified highly acidic xylanase (HAX) isomer fromScopulariopsis sp. were chemically modified, resulting in charge neutralization and reversal. Modification of the second amino group was accompanied by the complete loss of enzyme activity in both the absence and presence of xylose. Multiple alignments of family 10 and 11 xylanases revealed that there is a pair of fully conserved Lys residues only in family 10 members. Xylanase structures from family 10 members showed that one of the conserved Lys residues is found near the active-site cleft that makes an H-bond with the substrate. The LAX and HAX isoenzymes in which one amino and three to four carboxyl groups were modified were subjected to kinetic and thermodynamic characterization. There were no differences in pH optima between the native and modified HAX, but there was a broadening of pH optimum toward the alkaline range for charge-neutralized LAX and a double pH optimum for charge-reversed LAX. TheV _max/K _m of both modified LAX and HAX decreased relative to the native species. The thermodynamics of xylan hydrolysis showed that the decrease in the catalytic activity of modified LAX enzymes was entropically driven. When compared with native enzyme, the thermostabilities of modified LAX enzymes increased in the presence and decreased in the absence of substrate. The thermodynamics of kinetic stability for modified LAX enzymes revealed that this increase in thermolability was owing to the decrease in ΔH# with a concomitant increase in ΔS# compared with native LAX. The thermostabilities of all the modified HAX species decreased except that of charge-neutralized HAX, whose half-life significantly increased in 50% (v/v) aqueous dioxan. These results suggest that the altered properties of the modified enzymes were a result of the conformational changes brought about by chemical modification. An erratum to this article is available at .