Catalytic coupling of the active sites in acetyl-CoA synthase, a bifunctional CO-channeling enzyme.

Acetogenic bacteria contain acetyl-CoA synthase (ACS), an enzyme with two distinct nickel-iron-sulfur active sites connected by a tunnel through which CO migrates. One site reduces CO2 to CO, while the other synthesizes acetyl-CoA from CO, CoA, and the methyl group of another protein (CH3-CP). Rapid binding of CO2 and a two-electron reduction activates ACS. When CoA and CH3-CP bind ACS, CO is rerouted through the tunnel to the synthase site, and kinetic parameters at the reductase site are altered. Under these conditions, the rates of CO2 reduction and acetyl-CoA synthesis are synchronized by an ordered catalytic mechanism.     

Determinants of variation in serum paraoxonase enzyme activity in baboons

Paraoxonase (PON), an HDL-associated enzyme, is one of many circulating antioxidants thought to play a vital protective role. To better understand the determinants of quantitative variation in serum PON activity, we assayed PON in samples from 611 pedigreed baboons fed three diets. PON was measured enzymatically; the main determinant of variation was genetic and consisted of at least three components: two loci detected by linkage analyses and a residual polygenic component. Multipoint linkage analyses gave peak log of the odds (LOD) scores on the baboon homolog of human chromosome 7q21-22 (near PON1, the structural gene) of 9.1 on the low-cholesterol, high-fat diet and 4.1 on the high-cholesterol, high-fat diet (genome-wide P values were 1 x 10(-8) and 0.0018, respectively). Surprisingly, a second locus on the baboon homolog of human chromosome 12q13 gave a LOD score of 2.9 on the high-cholesterol, high-fat diet (genome-wide P value was 0.032). We identified several significant covariates, including age, sex, diet, and apolipoprotein A-I concentrations. We estimate that 53% of total trait variation in baboons is explained by genes and 17% by covariates, thus accounting for approximately 70% of total variation in baboon PON. Although the generation of free radicals is influenced primarily by environmental factors, our findings suggest strong genetic regulation of one component in the antioxidant defense system that plays a major role in susceptibility to atherosclerosis.     

Plasticity of enzyme active sites

The expectation is that any similarity in reaction chemistry shared by enzyme homologues is mediated by common functional groups conserved through evolution. However, detailed enzyme studies have revealed the flexibility of many active sites, in that different functional groups, unconserved with respect to position in the primary sequence, mediate the same mechanistic role. Nevertheless, the catalytic atoms might be spatially equivalent. More rarely, the active sites have completely different locations in the protein scaffold. This variability could result from: (1) the hopping of functional groups from one position to another to optimize catalysis; (2) the independent specialization of a low-activity primordial enzyme in different phylogenetic lineages; (3) functional convergence after evolutionary divergence; or (4) circular permutation events.     

活性部位的柔性

比较酶在变性过程中构象和活力变化,发现在活性完全丧失时尚无可察 觉的整体构象变化。排除变性剂抑制和寡聚酶解聚等可能性之后,提出了酶活性部位柔性假说。随后用多种实验方法直接证实了活性部位的构象变化先于分子整体构象变化,并与活性丧失同步,根据催化过程中活性部位构旬变化,以及限制活性部位构象变化对酶活性的影响,提出了酶活性部位柔性为酶充分表现其催化活性所必需的设想。     

Calculating pKa values in enzyme active sites

The ionization properties of the active-site residues in enzymes are of considerable interest in the study of the catalytic mechanisms of enzymes. Knowledge of these ionization constants (pKa values) often allows the researcher to identify the proton donor and the catalytic nucleophile in the reaction mechanism of the enzyme. Estimates of protein residue pKa values can be obtained by applying pKa calculation algorithms to protein X-ray structures. We show that pKa values accurate enough for identifying the proton donor in an enzyme active site can be calculated by considering in detail only the active-site residues and their immediate electrostatic interaction partners, thus allowing for a large decrease in calculation time. More specifically we omit the calculation of site-site interaction energies, and the calculation of desolvation and background interaction energies for a large number of pairs of titratable groups. The method presented here is well suited to be applied on a genomic scale, and can be implemented in most pKa calculation algorithms to give significant reductions in calculation time with little or no impact on the accuracy of the results. The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts.     

Analysis of catalytic residues in enzyme active sites

We present an analysis of the residues directly involved in catalysis in 178 enzyme active sites. Specific criteria were derived to define a catalytic residue, and used to create a catalytic residue dataset, which was then analysed in terms of properties including secondary structure, solvent accessibility, flexibility, conservation, quaternary structure and function. The results indicate the dominance of a small set of amino acid residues in catalysis and give a picture of a general active site environment. It is hoped that this information will provide a better understanding of the molecular mechanisms involved in catalysis and a heuristic basis for predicting catalytic residues in enzymes of unknown function.     

Baculovirus-mediated expression and purification of human serum paraoxonase 1A

Human paraoxonase 1 (hPON1) is a lipid-associated enzyme transported on HDL. There is considerable interest in hPON1 because of its putative antioxidative/antiatherogenic properties. We have created a recombinant baculovirus (BV) to generate hPON1A in large quantities for structure-function studies and here describe the method for production and isolation of the enzyme. A high level of recombinant hPON1 type A (rPON1A) was produced by Hi-5 insect cells (40 mg/l); a fraction ( approximately 10 mg/l) was secreted into the cell culture medium, but the majority ( approximately 30 mg/l) remained associated with the host insect cells. Cell-associated rPON1A was purified by detergent extraction (Tergitol NP-10) followed by three simple chromatography steps (DEAE-Sepharose, Sephacryl S-200, and concanavalin A). The purified enzyme bound to concanavalin A and was converted to a lower molecular mass by endoglycosidase H digestion, suggesting that rPON1A contained high-mannose N-glycan chains. There was a significant decrease in arylesterase activity (>99%) concomitant with enzymatic deglycosylation. rPON1A was dependent on Ca(2+) for arylesterase activity, exhibiting kinetic parameters similar to native hPON1A (K(m) = 3.8 +/- 2.1 vs. 3.7 +/- 2.0 mM and V(max) = 1,305 +/- 668 vs. 1,361 +/- 591 U/mg protein, rPON1A and hPON1A, respectively). Both rPON1A and hPON1A efficiently inhibited lipoxygenase-mediated peroxidation of phospholipid. In contrast to the arylesterase activity, which was sensitive to endoglycosidase H treatment, enzymatic deglycosylation did not inhibit the antioxidant activity of rPON1A. In conclusion, our BV-mediated PON1A expression system appears ideally suited for the production of relatively large quantities of rPON1A for structure-function studies.     

Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites

An important goal of structural genomics is to complete the structural analysis of all the enzymes in metabolic pathways and to understand the structural similarities and differences. A preliminary glimpse of this type of analysis was achieved before structural genomics efforts with the glycolytic pathway and efforts are underway for many other pathways, including that of catecholamine metabolism. Structural enzymology necessitates a complete structural characterization, even for highly homologous proteins (greater than 80% sequence homology), as every active site has distinct structural features and it is these active site differences that distinguish one enzyme from another. Short cuts with homology modeling cannot be taken with our current knowledge base. Each enzyme structure in a pathway needs to be determined, including structures containing bound substrates, cofactors, products and transition state analogs, in order to obtain a complete structural and functional understanding of pathway-related enzymes.     

Catalytic sites of medicinal leech enzyme destabilase-lysozyme (mlDL): Structure-function relationship

Based on the three-dimensional model of the bifunctional enzyme destabilase-lysozyme of the medicinal leech (mlDL) in complex with trimer of N-acetylglucosamine (NAG)₃ by site-directed mutagenesis method, the functional role of the group of amino acids (Glu14, Asp26, Ser29, Ser31, Lys38, His92) in manifestation of lysozyme (glycosidase, muramidase) and isopeptidase activities has been investigated by site-directed mutagenesis. The results obtained go well with hypothesis, that lysozyme active site of mlDL includes catalytic Glu14 and Asp26 residues, and isopeptidase site functions as Ser/Lys catalytic dyad presented by catalytic residues Ser29 and Lys38. Thus, among the invertebrate lysozymes, mlDL presents the first example of a bifunctional enzyme with identified position of the isopeptidase active site and localization of the corresponding catalytic residues.     

Deconstructing the DGAT1 enzyme: Binding sites and substrate interactions

Diacylglycerol acyltransferase 1 (DGAT1) is a microsomal membrane enzyme responsible for the final step in the synthesis of triacylglycerides. Although DGATs from a wide range of organisms have nearly identical sequences, there is little structural information available for these enzymes. The substrate binding sites of DGAT1 are predicted to be in its large luminal extramembranous loop and to include common motifs with acyl-CoA cholesterol acyltransferase enzymes and the diacylglycerol binding domain found in protein kinases.     

Functional conservation of the active sites of human and Drosophila angiotensin I-converting enzyme

Human somatic angiotensin I-converting enzyme (sACE) has two active sites present in two homologous protein domains, resulting from a tandem gene duplication. It has been proposed that the N- and C-terminal active sites can have specific in vivo roles. In Drosophila melanogaster, Ance and Acercode for two ACE-like single-domain proteins, also predicted to have distinct physiological roles. We have investigated the relationship of Ance and Acer to the N- and C-domains of human sACE by genomic sequence analysis and by using domain-selective inhibitors, including RXP 407, a selective inhibitor of the human N-domain. These phosphinic peptides were potent inhibitors of Acer, but not of Ance. We conclude that the active sites of the N-domain and of Acer share structural features that permit the binding of the unusual RXP407 inhibitor and the hydrolysis of a broader range of peptide structures. In comparison, Ance, like the human C-domain of ACE, displays greater inhibitor selectivity. From the analysis of the published sequence of the Adh region of Drosophila chromosome 2, which carries Ance, Acer, and four additional ACE-like genes, we also suggest that this functional conservation is reflected in an ancestral gene structure identifiable in both protostome and deuterostome lineages and that the duplication seen in vertebrate genomes predates the divergence of these lineages. The conservation of ACE enzymes with distinct active sites in the evolution of both vertebrate and invertebrate species provides further evidence that these two kinds of active sites have different physiological functions.     

Impacts of some antibiotics on human serum paraoxonase 1 activity

Some enzymes are known to be drug target inhibitions of which can be critical for organisms. PON has a critical role to prevent atherogenesis by inhibiting lipid peroxidation. It is well known that paraoxonase 1 (PON1) plays an important function on high-density lipoprotein (HDL) structure to prevent lipid oxidation not only of low-density lipoprotein, but also of HDL itself. We investigated in vitro effects of some medical drugs on PON1 activity from human serum. K_i constants for oxytetracycline hydrochloride, netilmycin sulfate, lincomycin hydrochloride, clindamycin phosphate, and streptomycin sulfate were found as 0.2, 3.73, 18.30, 35.80, and 56.30 mM, respectively. Our results indicate that these commonly used drugs inhibit the activity of the enzyme at very low doses with different inhibition mechanisms.     

A novel approach to predict active sites of enzyme molecules

Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. Proteins 2004. © 2004 Wiley-Liss, Inc.     

Oligomeric states of the detergent-solubilized human serum paraoxonase (PON1)

Human plasma paraoxonase (HuPON1) is a high density lipoprotein (HDL)-bound enzyme exhibiting antiatherogenic properties. The molecular basis for the binding specificity of HuPON1 to HDL has not been established. Isolation of HuPON1 from HDL requires the use of detergents. We have determined the activity, dispersity, and oligomeric states of HuPON1 in solutions containing mild detergents using nondenaturing electrophoresis, size exclusion chromatography, and cross-linking. HuPON1 was active whatever its oligomeric state. In nonmicellar solutions, HuPON1 was polydisperse. In contrast, HuPON1 exhibited apparent homogeneity in micellar solutions, except with CHAPS. The enzyme apparent hydrodynamic radius varied with the type of detergent and protein concentration. In C(12)E(8) micellar solutions, from sedimentation velocity, equilibrium analytical ultracentrifugation, and radioactive detergent binding, HuPON1 was described as monomers and dimers in equilibrium. A decrease of the detergent concentration shifted this equilibrium toward the formation of dimers. About 100 detergent molecules were associated per monomer and dimer. The assembly of amphiphilic molecules, phospholipids in vivo, in sufficiently large aggregates could be a prerequisite for anchoring of HuPON1 and then allowing stabilization of the enzyme activity. Changes of HDL size and shape could strongly affect the binding affinity and stability of HuPON1 and result in reduced antioxidative capacity of the lipoprotein.     

Flexibility analysis of enzyme active sites by crystallographic temperature factors

Protein flexibility is inherent to protein structural behavior. Experimental evidence for protein flexibility is extensive both in solution and in the solid state. A major question is whether the flexibility observed in enzymes is simply an inherent property of proteins that must always be borne in mind or is essential for catalysis or substrate binding. The temperature factors or B-values, as determined crystallographically, are linearly related to the mean square displacement of an atom and give an indication of atomic flexibility in the crystalline state. In this paper, we describe the frequency distributions of the normalized B-factor (B'-factor) for the active site and non-active site residues in the selected 69 apo-enzymes. This analysis was performed over the entire sequences and for different structural subsets defined by the three-dimensional structure of proteins, as alpha-helices, beta-structures and coil conformation and buried and non-buried residues. The results show that in all cases, the active site residues predominantly occur in region of low B'-factor and the non-active site residues have a tendency to exist in the high B'-factor region. This observation suggests that the active site residues, in general, are less flexible than the non-active site residues and therefore the vibrational and the fast collective motions of the C(alpha) atoms of proteins appear not to have clear biological significance.     

Effects of caloric restriction and gender on rat serum paraoxonase 1 activity

Paraoxonase 1 (PON1) associates to specific high-density lipoproteins (HDLs)--those containing apolipoprotein A-I (apoA-I) and apolipoprotein J (apoJ)--and is largely responsible for their antiatherogenic properties. Caloric restriction (CR) has been shown to reduce major atherosclerotic risk factors. The aims of this work were to study PON1 activity response to CR (40% over 14 weeks) and to elucidate whether there are adaptive differences related to gender. Serum and liver paraoxonase and arylesterase activities, serum triglyceride, total and HDL cholesterol concentrations, serum PON1, apoA-I and apoJ contents and liver PON1 mRNA levels were measured. No effects of CR or gender were observed in triglyceride, total cholesterol concentration and PON1 mRNA levels. HDL cholesterol was higher in female rats than in male rats and increased with CR only in the latter animals. Serum PON1 activities tended to be higher in female rats and dropped with CR, with females showing the biggest decrease. Serum PON1 content was higher in female rats and decreased in both genders with CR, whereas apoA-I and apoJ contents, which were higher in female rats too, decreased only in the former animals, accounting for the high PON1 activity decrease observed in these animals. In conclusion, the short-term CR-associated reduction of serum PON1 activity and PON1, apoA-I and apoJ levels points toward a reduced stability of HDL-PON1 complexes and/or HDL particle levels responsible for PON1 transport and function in the blood. Moreover, the variations in PON1 activity and apolipoprotein levels show gender-related differences that are indicative of a different adaptive strategy of male and female rats when faced with a period of food restriction.     

VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results

Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown. In this study, we created a transition state model for VX hydrolysis (VX(ts)) in water using quantum mechanical/molecular mechanical simulations, and docked the transition state model to 22 experimentally characterized HuPON1 variants using AutoDock Vina. The HuPON1-VX(ts) complexes were grouped by reaction mechanism using a novel clustering procedure. The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX. The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results. The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.     

Reproductive versatility in legumes: the case of amphicarpy in Trifolium polymorphum

Amphicarpy is a fascinating reproductive strategy, defined as fruit produced both below the soil surface and as aerial fruit on the same plant. Trifolium polymorphum is a grassland species subject to herbivory that combines amphicarpy with vegetative reproduction through stolons. Underground flowers have been described as obligate autogamous and aerial ones as self‐compatible allogamous, with aerial floral traits favouring cross‐pollination. In the present work we performed different pollination treatments on aerial flowers to analyse rates of pollen tube development and offspring fitness, measured as fruit set, seed production and germination percentage. This last variable was compared to that of seeds produced underground. No significant differences were found between fruit set in self‐ and cross‐pollinations. Seed production was higher in self‐pollinations, which is consistent with the higher rate of pollen tube development observed in self‐crosses. Spontaneous self‐pollination is limited in aerial flowers; thus pollen transfer by means of a vector is required even within the same flower. Germination tests showed that aerial seeds produced after self‐ and cross‐pollination did not differ in fitness, but underground seeds had higher germination percentage than aerial ones. Thus, we conclude that T. polymorphum has a mixed mating system. In grasslands with heavy grazing pressure, clonal propagation and underground seed production ensure persistence in the field. An intermediate level of selfing in aerial flowers ensures offspring, but morphological (herkogamy) and functional (dicogamy) floral traits maintain a window to incorporate genetic variability, allowing the species to tolerate temporal and spatial pressures.