Specificity of action of piperidylcholine derivatives as substrates of cholinesterases of various origin

The review deals with study of enzymologic properties of a novel highly specific acetylcholinesterase substrate, N-(β-acetoxyethyl) piperidinium iodomethylate (“piperidylcholine”), and its 30 derivatives that were tested as effectors of cholinesterases of mammals and various species of Pacific squids. It was proven for the first time that responsible for specificity of action was structure of cyclic ammonium grouping of the alcohol part of molecule of the ester substrate. Analysis of specificity is performed based on enzymatic hydrolysis parameters—activity of catalytic center of cholinesterases and bimolecular constant of the reaction rate that are determined at optimal and low substrate concentrations. Among the specially synthesized group of thioester compounds there is revealed one more highly specific acetylcholinesterase substrate—N-(β-acetoxyethyl) piperidinium.     

Isolation of alcohol dehydrogenases from germinating seeds of pea,broad-bean,lentil and kidney-bean

The maximum of alcohol dehydrogenase (ADH) activity of germinating pea and broad-bean seeds sediments from 40 to 60% ammonium sulfate saturation, from lentil and kidney-bean seeds between 40 and 50%. This operation increased the specific activity of ADH preparations roughly tenfold. Chromatography on DEAE-eellulose and gel filtration increased the activity of the resulting preparation when compared with the initial preparation 178 times with pea, 334 times with broad-bean, 122 times with lentil and 77 times with kidney-bean. The ADHs resemble each other in coenzyme specificity: the reaction rate with NAD is one hundred times greater than with NADP. The substrate specificity is quite wide: besides ethanol, these enzymes oxidize 2-propene-l-ol (actually faster than ethanol), 2-butene-l-ol (at the rate of one half t h a t of ethanol) and butanol (even more slowly). In general, saturated alcohol analogues are oxidized more slowly than unsaturated ones. Methanol is a substrate for the enzym from pea only. The ADHs of the plants studied did not oxidize diols, sugar alcohols and cyclic alcohols. The enzyme from pea has the widest substrate specificity oxidizing isobutanol, phenylalcohol and mercaptoethanol. ADHs, which are widely encountered in plants, resemble each other to a certain degree — they have identical coenzymes, equal K_m values and equal values of the pH optimum, they differ in the purification process and in substrate specificity.     

Thermodynamic secrets of multidrug resistance: A new take on transport mechanisms of secondary active antiporters

Multidrug resistance (MDR) presents a growing challenge to global public health. Drug extrusion transporters play a critical part in MDR; thus, their mechanisms of substrate recognition are being studied in great detail. In this work, we review common structural features of key transporters involved in MDR. Based on our membrane potential‐driving hypothesis, we propose a general energy‐coupling mechanism for secondary‐active antiporters. This putative mechanism provides a common framework for understanding poly‐specificity of most—if not all—MDR transporters.     

Glucose transporters: physiological and pathological roles

Glucose is a primary energy source for most cells and an important substrate for many biochemical reactions. As glucose is a need of each and every cell of the body, so are the glucose transporters. Consequently, all cells express these important proteins on their surface. In recent years developments in genetics have shed new light on the types and physiology of various glucose transporters, of which there are two main types—sodium–glucose linked transporters (SGLTs) and facilitated diffusion glucose transporters (GLUT)—which can be divided into many more subclasses. Transporters differ in terms of their substrate specificity, distribution and regulatory mechanisms. Glucose transporters have also received much attention as therapeutic targets for various diseases. In this review, we attempt to present a simplified view of this complex topic which may be of interest to researchers involved in biochemical and pharmacological research.     

The structure of a GH149 β-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-β-(1 → 3)-glucose (laminaribiose) phosphorylase

Glycoside phosphorylases (GPs) with specificity for β-(1 → 3)-gluco-oligosaccharides are potential candidate biocatalysts for oligosaccharide synthesis. GPs with this linkage specificity are found in two families thus far—glycoside hydrolase family 94 (GH94) and the recently discovered glycoside hydrolase family 149 (GH149). Previously, we reported a crystallographic study of a GH94 laminaribiose phosphorylase with specificity for disaccharides, providing insight into the enzyme's ability to recognize its' sugar substrate/product. In contrast to GH94, characterized GH149 enzymes were shown to have more flexible chain length specificity, with preference for substrate/product with higher degree of polymerization. In order to advance understanding of the specificity of GH149 enzymes, we herein solved X-ray crystallographic structures of GH149 enzyme Pro_7066 in the absence of substrate and in complex with laminarihexaose (G6). The overall domain organization of Pro_7066 is very similar to that of GH94 family enzymes. However, two additional domains flanking its catalytic domain were found only in the GH149 enzyme. Unexpectedly, the G6 complex structure revealed an oligosaccharide surface binding site remote from the catalytic site, which, we suggest, may be associated with substrate targeting. As such, this study reports the first structure of a GH149 phosphorylase enzyme acting on β-(1 → 3)-gluco-oligosaccharides and identifies structural elements that may be involved in defining the specificity of the GH149 enzymes.     

Partial purification and characterization of sorbitol dehydrogenase from rat brain.

Abstract— Sorbitol dehydrogenase (EC 1.1.1.14) was isolated and purified 700-fold from rat brain. Most substrate specificities and properties are similar to those reported for sorbitol dehydrogenase from other mammalian tissues; however, the substrate specificity of this brain enzyme does not conform to the d -cis 2,4 dihydroxy configuration. The physiological substrate for sorbitol dehydrogenase is probably sorbitol. The isolation of sorbitol dehydrogenase from rat brain tissue is confirmation that (1) all the constituents of the sorbitol (polyol) pathway are present in the brain and that (2) fructose synthesis from glucose in this tissue proceeds via the intermediate formation of sorbitol.     

Using substrate engineering to harness enzymatic promiscuity and expand biological catalysis

Despite their unparalleled catalytic prowess and environmental compatibility, enzymes have yet to see widespread application in synthetic chemistry. This lack of application and the resulting underuse of their enormous potential stems not only from a wariness about aqueous biological catalysis on the part of the typical synthetic chemist but also from limitations on enzyme applicability that arise from the high degree of substrate specificity possessed by most enzymes. This latter perceived limitation is being successfully challenged through rational protein engineering and directed evolution efforts to alter substrate specificity. However, such programs require considerable effort to establish. Here we report an alternative strategy for expanding the substrate specificity, and therefore the synthetic utility, of a given enzyme through a process of "substrate engineering". The attachment of a readily removable functional group to an alternative glycosyltransferase substrate induces a productive binding mode, facilitating rational control of substrate specificity and regioselectivity using wild-type enzymes.     

Designing the substrate specificity of d-hydantoinase using a rational approach

Enzymes that exhibit superior catalytic activity, stability and substrate specificity are highly desirable for industrial applications. These goals prompted the designed substrate specificity of Bacillus stearothermophilus d-hydantoinase toward the target substrate hydroxyphenylhydantoin (HPH). Positions crucial to substrate specificity were selected using structural and mechanistic information on the structural loops at the active site. The size and hydrophobicity of the involved amino acids were rationally changed, and the substrate specificities of the designed d-Hyd mutants were investigated. As a result, M63I/F159S exhibited about 200-fold higher specificity for HPH than the wild-type enzyme. Systematic mutational analysis and computational modeling also supported the rationale used in the design.     

Improved substrate specificity of water-soluble pyrroloquinoline quinone glucose dehydrogenase by a peptide ligand

A new approach in altering the substrate specificity of enzyme is proposed using glucose dehydrogenase, with pyrroroquinoine quinone (PQQGDH) as co-factor, as the model. This approach is based on the selection of random peptide phage displayed library. Using an M13 phage-display random peptide library, we have selected peptide ligands. Among the peptide ligands, a 7-mer peptide, composed of Thr-Thr-Ala-Thr-Glu-Tyr-Ser, caused PQQGDH substrate specificity to decrease significantly toward disaccharides, such as maltose and lactose, while a smaller effect was observed toward glucose. Consequently, this peptide narrowed the substrate specificity of PQQGDH, without a significant loss of the enzyme activity.     

Substrate Specificity of Cholinesterases in Various Representatives of the Animal Kingdom

This review summarizes the literature data as well as experimental results obtained at our Institute over a period of 50 years on the substrate specificity of cholinesterases–acetylcholine acetylhydrolases (EC 3.1.1.7) and acylcholine acylhydrolases (EC 3.1.1.8). The parameters of enzymatic hydrolysis of oxo- and thiocholine and β-methylcholine esters in different organs and tissues were analyzed in 66 animal species including 22 chordate, 20 insect, 1 mite, 17 mollusk, 4 nematode, and 2 flatworm species. Our substrate specificity studies and extensive data on the inhibitory specificity obtained using irreversible organophosphorous inhibitors and reversible effectors unequivocally indicate that the cholinesterase family is characterized by a clear-cut species and tissue specificity.     

Changing the substrate specificity of creatine kinase from creatine to glycocyamine: evidence for a highly evolved active site

Eight variants of creatine kinase were created to switch the substrate specificity from creatine to glycocyamine using a rational design approach. Changes to creatine kinase involved altering several residues on the flexible loops that fold over the bound substrates including a chimeric replacement of the guanidino specificity loop from glycocyamine kinase into creatine kinase. A maximal 2,000-fold change in substrate specificity was obtained as measured by a ratio of enzymatic efficiency (k(cat)/K(M).K(d)) for creatine vs. glycocyamine. In all cases, a change in specificity was accompanied by a large drop in enzymatic efficiency. This data, combined with evidence from other studies, indicate that substrate specificity in the phosphagen kinase family is obtained by precise alignment of substrates in the active site to maximize k(cat)/K(M).K(d) as opposed to selective molecular recognition of one guanidino substrate over another. A model for the evolution of the dimeric forms of phosphagen kinases is proposed in which these enzymes radiated from a common ancestor that may have possessed a level of catalytic promiscuity. As mutational events occurred leading to greater degrees of substrate specificity, the dimeric phosphagen kinases became evolutionary separated such that the substrate specificity could not be interchanged by a small number of mutations.     

Substrate specificity of haloalkane dehalogenases

An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.     

Substrate specificity of protein kinases and computational prediction of substrates

To ensure signalling fidelity, kinases must act only on a defined subset of cellular targets. Appreciating the basis for this substrate specificity is essential for understanding the role of an individual protein kinase in a particular cellular process. The specificity in the cell is determined by a combination of "peptide specificity" of the kinase (the molecular recognition of the sequence surrounding the phosphorylation site), substrate recruitment and phosphatase activity. Peptide specificity plays a crucial role and depends on the complementarity between the kinase and the substrate and therefore on their three-dimensional structures. Methods for experimental identification of kinase substrates and characterization of specificity are expensive and laborious, therefore, computational approaches are being developed to reduce the amount of experimental work required in substrate identification. We discuss the structural basis of substrate specificity of protein kinases and review the experimental and computational methods used to obtain specificity information.     

Molecular characteristics of transporters of C<Subscript>4</Subscript>-dicarboxylates and mechanism of translocation

An important role in cell metabolism is played by transport of C₄-dicarboxylates (C₄-DCB). Specifically, they are intermediates of the citrate cycle. Transport of succinate across the mitochondrial membrane provides correlation between metabolism in peroxysomes and in mitochondria. There is known transport of C₄-DCB across all kinds of energy-transforming membranes of the animal, plant, fungal, and bacterial cells. This review summarizes molecular characteristics of the C₄-DCB transporters. Of particular interest are primary structures for the transporters with the known kinetic mechanism and kinetic transport parameters. For each studied group of organisms, the number of transmembrane segments in the carried molecule or the character of specificity does not correlate with the certain transport mechanism—antiport, symport with proton or symport with cation. The review describes perspective methodical approaches allowing association of peculiarities of structure with transport mechanism for individual transporters, preparation of functional hybrid transporters—“protein chimeras,” scanning of transporter transmembrane segments with aid of essential acids, probing of the transporter active center with aid of alkyl and acyl substrate derivatives used to obtain the “lipophilic profile” of the channel of the C₄-DCB transporter. It is recommended to use these approaches to one transporter that has small sizes and large substrate specificity.     

Identification and analysis of residues contained on β → α loops of the dual‐substrate (βα)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity

A good model to experimentally explore evolutionary hypothesis related to enzyme function is the ancient‐like dual‐substrate (βα)₈ phosphoribosyl isomerase A (PriA), which takes part in both histidine and tryptophan biosynthesis in Streptomyces coelicolor and related organisms. In this study, we determined the Michaelis–Menten enzyme kinetics for both isomerase activities in wild‐type PriA from S. coelicolor and in selected single‐residue monofunctional mutants, identified after Escherichia coli in vivo complementation experiments. Structural and functional analyses of a hitherto unnoticed residue contained on the functionally important β → α loop 5, namely, Arg¹³⁹, which was postulated on structural grounds to be important for the dual‐substrate specificity of PriA, is presented for the first time. Indeed, enzyme kinetics analyses done on the mutant variants PriA_Ser⁸¹Thr and PriA_Arg¹³⁹Asn showed that these residues, which are contained on β → α loops and in close proximity to the N‐terminal phosphate‐binding site, are essential solely for the phosphoribosyl anthranilate isomerase activity of PriA. Moreover, analysis of the X‐ray crystallographic structure of PriA_Arg¹³⁹Asn elucidated at 1.95 Å herein strongly implicates the occurrence of conformational changes in this β → α loop as a major structural feature related to the evolution of the dual‐substrate specificity of PriA. It is suggested that PriA has evolved by tuning a fine energetic balance that allows the sufficient degree of structural flexibility needed for accommodating two topologically dissimilar substrates—within a bifunctional and thus highly constrained active site—without compromising its structural stability.     

Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and 440 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function.     

Role of the active site residues arginine-216 and arginine-237 in the substrate specificity of mammalian <Emphasis Type="SmallCaps">d</Emphasis>-aspartate oxidase

d-Aspartate oxidase (DDO) and d-amino acid oxidase (DAO) are flavin adenine dinucleotide-containing flavoproteins that catalyze the oxidative deamination of d-amino acids. Unlike DAO, which acts on several neutral and basic d-amino acids, DDO is highly specific for acidic d-amino acids. Based on molecular modeling and simulated annealing docking analyses, a recombinant mouse DDO carrying two substitutions (Arg-216 to Leu and Arg-237 to Tyr) was generated (R216L-R237Y variant). This variant and two previously constructed single-point mutants of mouse DDO (R216L and R237Y variants) were characterized to investigate the role of Arg-216 and Arg-237 in the substrate specificity of mouse DDO. The R216L-R237Y and R216L variants acquired a broad specificity for several neutral and basic d-amino acids, and showed a considerable decrease in activity against acidic d-amino acids. The R237Y variant, however, did not show any additional specificity for neutral or basic d-amino acids and its activity against acidic d-amino acids was greatly reduced. The kinetic properties of these variants indicated that the Arg-216 residue is important for the catalytic activity and substrate specificity of mouse DDO. However, Arg-237 is, apparently, only marginally involved in substrate recognition, but is important for catalytic activity. Notably, the substrate specificity of the R216L-R237Y variant differed significantly from that of the R216L variant, suggesting that Arg-237 has subsidiary effects on substrate specificity. Additional experiments using several DDO and DAO inhibitors also suggested the involvement of Arg-216 in the substrate specificity and catalytic activity of mouse DDO and that Arg-237 is possibly involved in substrate recognition by this enzyme. Collectively, these results indicate that Arg-216 and Arg-237 play crucial and subsidiary role(s), respectively, in the substrate specificity of mouse DDO.     

Arg305 of Streptomyces L-glutamate oxidase plays a crucial role for substrate recognition

Recently, we have solved the crystal structure of L-glutamate oxidase (LGOX) from Streptomyces sp. X-119-6 (PDB code: 2E1M), the substrate specificity of which is strict toward L-glutamate. By a docking simulation using L-glutamate and structure of LGOX, we selected three residues, Arg305, His312, and Trp564 as candidates of the residues associating with recognition of L-glutamate. The activity of LGOX toward L-glutamate was significantly reduced by substitution of selected residues with Ala. However, the enzyme, Arg305 of which was substituted with Ala, exhibited catalytic activity toward various L-amino acids. To investigate the role of Arg305 in substrate specificity, we constructed Arg305 variants of LGOX. In all mutants, the substrate specificity of LGOX was markedly changed by the mutation. The results of kinetics and pH dependence on activity indicate that Arg305 of LGOX is associated with the interaction of enzyme and side chain of substrate.     

Enzymologic characteristics of monoamine oxidase from liver of the skipjack tuna Katsuwonus pelamis

Substrate and inhibitory specificity of mitochondrial monoamine oxidase (MAO) from liver of skipjack tuna Katsuwonus pelamis was studied. The results of substrate—inhibitory analysis with application of chlorgilin and deprenyl might be indirect proofs of existence of one molecular MAO form in the tuna liver. Studied enzyme, as liver MAO of terrestrial mammals, deaminates tyramine, tryptamine, dopamine, serotonin, noradrenalin, benzylamine, β-phenylethylamine, N-methylhistamine and does not deaminate histamine, is not suppressed by 10 mM semicarbazide. Takrin, acriflavin, proflavin, acridine orange and pyronine G were established to be irreversible inhibitors of middle strength in respect to MAO of tuna liver. The specificity of inhibitors action upon deamination of various substrates was equal.     

基于水分控制的切花百合生长预测模型

光合作用与干物质生产是观赏植物外观品质形成的基础。水分是影响植物光合作用与干物质生产的重要因子。为定量研究水分对切花百合光合作用与干物质生产的影响,以切花百合品种‘索邦’(Lilium‘Sorbonne’)为试验材料,于2009年3月至2010年1月在南京的连栋温室内开展了不同定植期和不同水分处理的栽培试验,以基于光温的温室花卉生长动态预测模型为基础,定量分析了不同定植期和不同水分处理条件下切花百合叶面积指数、光合速率和干物质生产的动态影响,并确定了切花百合正常生长的临界基质水势,建立了基质水势对切花百合光合速率和干物质生产影响的动态预测模型。结果表明,本文所建模型对切花百合叶片最大总光合速率和植株总干质量的预测效果较好,模型对叶面积指数、叶片最大总光合速率和植株干物质量的预测值与实测值之间的决定系数(r2)分别为0.97,0.96,0.94,相对根均方差(rRMSE)分别为7.12%、4.37%、11.14%。该模型能较好地预测水分对切花百合叶片最大总光合速率和植株总干质量的动态影响,可为进一步优化切花百合生产的水分管理提供决策支持。