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1.
Bacillus subtilisin has been a popular model protein for engineering altered substrate specificity. Although some studies have succeeded in increasing the specificity of subtilisin, they also demonstrate that high specificity is difficult to achieve solely by engineering selective substrate binding. In this paper, we analyze the structure and transient state kinetic behavior of Sbt160, a subtilisin engineered to strongly prefer substrates with phenylalanine or tyrosine at the P4 position. As in previous studies, we measure improvements in substrate affinity and overall specificity. Structural analysis of an inactive version of Sbt160 in complex with its cognate substrate reveals improved interactions at the S4 subsite with a P4 tyrosine. Comparison of transient state kinetic behavior against an optimal sequence (DFKAM) and a similar, but suboptimal, sequence (DVRAF) reveals the kinetic and thermodynamic basis for increased specificity, as well as the limitations of this approach. While highly selective substrate binding is achieved in Sbt160, several factors cause sequence specificity to fall short of that observed with natural processing subtilisins. First, for substrate sequences which are nearly optimal, the acylation reaction becomes faster than substrate dissociation. As a result, the level of discrimination among these substrates diminishes due to the coupling between substrate binding and the first chemical step (acylation). Second, although Sbt160 has 24-fold higher substrate affinity for the optimal substrate DFKAM than for DVRAF, the increased substrate binding energy is not translated into improved transition state stabilization of the acylation reaction. Finally, as interactions at subsites become stronger, the rate-determining step in peptide hydrolysis changes from acylation to product release. Thus, the release of the product becomes sluggish and leads to a low k(cat) for the reaction. This also leads to strong product inhibition of substrate turnover as the reaction progresses. The structural and kinetic analysis reveals that differences in the binding modes at subsites for substrates, transition states, and products are subtle and difficult to manipulate via straightforward protein engineering. These findings suggest several new strategies for engineering highly sequence selective enzymes. 相似文献
2.
Activated Lactococcus lactis beta-phosphoglucomutase (betaPGM) catalyzes the conversion of beta-d-glucose 1-phosphate (betaG1P) derived from maltose to beta-d-glucose 6-phosphate (G6P). Activation requires Mg(2+) binding and phosphorylation of the active site residue Asp8. Initial velocity techniques were used to define the steady-state kinetic constants k(cat) = 177 +/- 9 s(-)(1), K(m) = 49 +/- 4 microM for the substrate betaG1P and K(m) = 6.5 +/- 0.7 microM for the activator beta-d-glucose 1,6-bisphosphate (betaG1,6bisP). The observed transient accumulation of [(14)C]betaG1,6bisP (12% at approximately 0.1 s) in the single turnover reaction carried out with excess betaPGM (40 microM) and limiting [(14)C]betaG1P (5 microM) and betaG1,6bisP (5 microM) supported the role of betaG1,6bisP as a reaction intermediate in the conversion of the betaG1P to G6P. Single turnover reactions of [(14)C]betaG1,6bisP with excess betaPGM were carried out to demonstrate that phosphoryl transfer rather than ligand binding is rate-limiting and to show that the betaG1,6bisP binds to the active site in two different orientations (one positioning the C(1)phosphoryl group for reaction with Asp8, and the other orientation positioning the C(6)phosphoryl group for reaction with Asp8) with roughly the same efficiency. Single turnover reactions carried out with betaPGM, [(14)C]betaG1P, and unlabeled betaG1,6bisP demonstrated complete exchange of label to the betaG1,6bisP during the catalytic cycle. Thus, the reorientation of the betaG1,6bisP intermediate that is required to complete the catalytic cycle occurs by diffusion into solvent followed by binding in the opposite orientation. Published X-ray structures of betaG1P suggest that the reorientation and phosphoryl transfer from betaG1,6bisP occur by conformational cycling of the enzyme between the active site open and closed forms via cap domain movement. Last, the equilibrium ratio of betaG1,6bisP to betaG1P plus G6P was examined to evidence a significant stabilization of betaPGM aspartyl phosphate. 相似文献
3.
We present the structures of bovine catalase in its native form and complexed with ammonia and nitric oxide, obtained by X-ray crystallography. Using the NO generator 1-(N,N-diethylamino)diazen-1-ium-1,2-diolate, we were able to generate sufficiently high NO concentrations within the catalase crystals that substantial occupation was observed despite a high dissociation rate. Nitric oxide seems to be slightly bent from the heme normal that may indicate some iron(II) character in the formally ferric catalase. Microspectrophotometric investigations inline with the synchrotron X-ray beam reveal photoreduction of the central heme iron. In the cases of the native and ammonia-complexed catalase, reduction is accompanied by a relaxation phase. This is likely not the case for the catalase NO complex. The kinetics of binding of NO to catalase were investigated using NO photolyzed from N,N'-bis(carboxymethyl)-N,N'-dinitroso-p-phenylenediamine using an assay that combines catalase with myoglobin binding kinetics. The off rate is 1.5 s(-1). Implications for catalase function are discussed. 相似文献
4.
5.
Natural substrates and analogs rapidly diffuse through crystals of pig heart mitochondrial aspartate aminotransferase and react at the active sites causing spectral changes that can be measured by single-crystal microspectrophotometry. Dissociation constants for natural substrates and rate constants of transamination for slowly reacting substrates have been determined. A comparison between the data obtained in the crystal and in solution shows that the crystalline enzyme is catalytically competent and that events occurring in the crystal essentially parallel those occurring in solution, even though minor differences have been detected. 相似文献
6.
Yuan Guo Panjie Zhao Wenhao Zhang Xiaolong Li Xiwen Chen 《Bioscience, biotechnology, and biochemistry》2016,80(7):1336-1343
To improve the catalytic activity of atrazine chlorohydrolase (AtzA), amino acid residues involved in substrate binding (Gln71) and catalytic efficiency (Val12, Ile393, and Leu395) were targeted to generate site-saturation mutagenesis libraries. Seventeen variants were obtained through Haematococcus pluvialis-based screening, and their specific activities were 1.2–5.2-fold higher than that of the wild type. For these variants, Gln71 tended to be substituted by hydrophobic amino acids, Ile393 and Leu395 by polar ones, especially arginine, and Val12 by alanine, respectively. Q71R and Q71M significantly decreased the Km by enlarging the substrate-entry channel and affecting N-ethyl binding. Mutations at sites 393 and 395 significantly increased the kcat/Km, probably by improving the stability of the dual β-sheet domain and the whole enzyme, owing to hydrogen bond formation. In addition, the contradictory relationship between the substrate affinity improvement by Gln71 mutation and the catalytic efficiency improvement by the dual β-sheet domain modification was discussed. 相似文献
7.
Biotin carboxylase was purified from Escherichia coli by a new procedure, and its steady-state kinetic parameters were examined. MgATP and bicarbonate add to the enzyme randomly, followed by addition of biotin. Both bicarbonate and MgATP add in rapid equilibrium. A catalytic base with a pK of 6.6 is observed in V/K profiles. Inactivation studies also revealed a sulfhydryl group in the active site that is essential for catalysis. It is proposed that the acid-base catalysts are necessary for the tautomerization of biotin, which presumably enhances its nucleophilicity toward the carboxyl group donor. A second enzymic group with a pK of 6.6, whose role is unknown, is seen in Vmax profiles. The pH profiles for the biotin carboxylase catalyzed phosphorylation of ADP by carbamoyl phosphate have the same shape as the profiles for the forward reaction, which demonstrates that the enzymic bases assume the same protonation states for catalysis of transphosphorylation in either direction. The lack of reactivity of thionucleotide analogues of ATP when Mg is used as the divalent metal ion suggests that both metal ions required for reaction coordinate to the nucleotide. The second metal ion appears to be absolutely required for reaction and not merely an activator of the reaction. Characterization of a bicabonate-dependent biotin-independent ATPase activity strongly suggests that carboxylation proceeds via a carboxyphosphate intermediate. 相似文献
8.
For a full understanding of an enzyme reaction pathway, one must identify the reaction intermediates and obtain their structures and rates of interconversion. It is impossible to obtain all this information under normal conditions. An approach is to work suboptimally, in particular at subzero temperatures. This is cryoenzymology, an approach that implies both kinetic and structural measurements on enzyme systems below 0°C. To work below 0°C one must add an antifreeze so cryoenzymology means perturbation by two agents: temperature and antifreeze, usually an organic solvent. Certain precautions are needed with these agents, which we will discuss here. In particular, we discuss the importance of choosing the right solvent: this requires extensive exploratory studies but it is the key for the successful practice of cryoenzymology. Each system has its particularities and its own ‘good’ solvent. Cryoenzymology is not only a way of reducing reaction rates, it is also a way of perturbing one's system. Thus, it is a method that allows for the accumulation of intermediates that cannot be observed under normal conditions by slowing down their kinetics of formation, by changes in rate limiting steps or by shifts in equilibria. We illustrate the usefulness of cryoenzymology by myosin and actomyosin ATPases and by creatine, arginine and 3-phosphoglycerate kinases. We also discuss recent results obtained by X-ray crystallography. 相似文献
9.
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein–double-stranded DNA and protein–single-stranded DNA complexes. The interface properties of the protein–RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein–RNA and protein–DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein–RNA complexes, backbone contacts were more dominant in the protein–DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level. 相似文献
10.
A kinetic study of acetaminophen oxidation by tyrosinase in the presence of a physiological nucleophilic agent such as the amino acid L-proline is performed in the present paper. The o-quinone product of the catalytic activity, 4-acetamido-o-benzoquinone, becomes unstable through the chemical addition of L-proline, in competition with the nucleophilic addition of hydroxide ion from water. In both cases, the catechol intermediate, 3(')-hydroxyacetaminophen, is generated, as can be demonstrated by liquid chromatography. When the effect of the presence of the nucleophilic agent on the time course of the enzymatic reaction was kinetically analyzed, it was seen to decrease the duration of the lag period and increase the steady-state rate. Rate constants for the reaction of 4-acetamido-o-benzoquinone with water and L-proline were also determined. The results obtained in this paper open a new possibility to acetaminophen toxicity, that has been attributed hitherto to its corresponding p-quinone, N-acetyl-p-benzoquinone imine. 相似文献
11.
Membrane cycling and macrovacuolation under the influence of cytochalasin: kinetic and morphometric studies 总被引:1,自引:0,他引:1
Fibroblasts exposed to higher doses of cytochalasin accumulate very big discrete endoplasmic vacuoles, the membrane of which is derived by internalization of plasmalemma. Morphometry confirms that the amount of surface interiorized is equal to the difference between the original cell surface area (before CD) and the reduced surface area measurable after CD-induced rounding. Correspondingly, there is a nearly two-fold increase in the activity of the ectoenzyme 5'-nucleotidase (a marker for plasma membrane) internally within the cytoplasm, after treatment with CD. Macrovacuolation increases cell volume by approximately 30%. Surface membrane is internalized as micropinocytotic vesicles at a rate measurable by the accumulation of HRP, a marker of fluid-phase pinocytosis. Uptake of HRP is shown to be enhanced at all times during exposure to CD, and is balanced by accelerated exocytic recycling of membrane except during a phase (approximately 4-8 hr) in which pinocytic uptake exceeds exocytosis. Vesicular membrane accumulated intracellularly in this period is retained in the endoplasm, and by successive fusions forms vacuoles in close approximation to microfilament aggregates. Once established, this new macrovacuolar membrane compartment is in dynamic equilibrium with the cell surface, and its membrane is cycled like the plasma membrane, in a mutual exchange of pinosomes between the several vacuoles and the cell surface. In drug-free medium vacuole membrane apparently reverts to the surface by pinocytotic recycling, and the cells recover normal characteristics 4-6 hr after withdrawal of cytochalasin. 相似文献
12.
A simple and rapid method for the purification of glutathione S-transferase is described. The physical and kinetic properties of purified enzyme are reported. The protein is constituted of two identical subunits with a total molecular weight of 46,000 daltons. The isoelectric focusing of crude cytosol or purified preparation gives a single peak of activity with a pI of 7.1. The kinetic analysis shows a relatively strict substrate specificity. Only 1-chloro-2,4-dinitrobenzene is conjugated to reduced glutathione at an appreciable rate. The peroxidase activity of the enzyme with respect to cumene hydroperoxide as substrate is negligible. Hemin and bilirubin are competitive inhibitors of catalytic activity. 相似文献
13.
The pyrolysis kinetics of tobacco rob (TR) was investigated using thermogravimetric analysis (TGA) under inert atmosphere, adding chemicals (dolomite and NiO) as catalysts by catalytic-mixing method. The TGA results showed that mass loss and mass loss rates were affected by catalysts. The conversion rates increased while the activation energy decreased. Moreover, the thermal decomposition behaviors of TR were studied in the fixed-bed reactor using dolomite and NiO/γ-Al2O3 as catalysts by catalyst-bed method. A series of experiments had been performed to explore the effects of catalysts, and reaction temperature on the composition and yield of fuel gas. The experiments demonstrated that the catalysts had a high activity of cracking tar and hydrocarbons, as well as yielding a high fuel gas production. For both methods, dolomite and NiO revealed better catalytic performance as a view of enhancing conversion rates and increasing product gas yield. 相似文献
14.
Tomsic J Vitali LA Daviter T Savelsbergh A Spurio R Striebeck P Wintermeyer W Rodnina MV Gualerzi CO 《The EMBO journal》2000,19(9):2127-2136
Binding of the 50S ribosomal subunit to the 30S initiation complex and the subsequent transition from the initiation to the elongation phase up to the synthesis of the first peptide bond represent crucial steps in the translation pathway. The reactions that characterize these transitions were analyzed by quench-flow and fluorescence stopped-flow kinetic techniques. IF2-dependent GTP hydrolysis was fast (30/s) followed by slow P(i) release from the complex (1.5/s). The latter step was rate limiting for subsequent A-site binding of EF-Tu small middle dotGTP small middle dotPhe-tRNA(Phe) ternary complex. Most of the elemental rate constants of A-site binding were similar to those measured on poly(U), with the notable exception of the formation of the first peptide bond which occurred at a rate of 0.2/s. Omission of GTP or its replacement with GDP had no effect, indicating that neither the adjustment of fMet-tRNA(fMet) in the P site nor the release of IF2 from the ribosome required GTP hydrolysis. 相似文献
15.
De Simone G Mandrich L Menchise V Giordano V Febbraio F Rossi M Pedone C Manco G 《The Journal of biological chemistry》2004,279(8):6815-6823
The reaction mechanism of the esterase 2 (EST2) from Alicyclobacillus acidocaldarius was studied at the kinetic and structural level to shed light on the mechanism of activity and substrate specificity increase previously observed in its double mutant M211S/R215L. In particular, the values of kinetic constants (k1, k(-1), k2, and k3) along with activation energies (E1, E(-1), E2, and E3) were measured for wild type and mutant enzyme. The previously suggested substrate-induced switch in the reaction mechanism from kcat=k3 with a short acyl chain substrate (p-nitrophenyl hexanoate) to kcat=k2 with a long acyl chain substrate (p-nitrophenyl dodecanoate) was validated. The inhibition afforded by an irreversible inhibitor (1-hexadecanesulfonyl chloride), structurally related to p-nitrophenyl dodecanoate, was studied by kinetic analysis. Moreover the three-dimensional structure of the double mutant bound to this inhibitor was determined, providing essential information on the enzyme mechanism. In fact, structural analysis explained the observed substrate-induced switch because of an inversion in the binding mode of the long acyl chain derivatives with respect to the acyl- and alcohol-binding sites. 相似文献
16.
The crystal structure of EcoRV endonuclease bound to non-cognate DNA at 2.0 angstroms resolution shows that very small structural adaptations are sufficient to ensure the extreme sequence specificity characteristic of restriction enzymes. EcoRV bends its specific GATATC site sharply by 50 degrees into the major groove at the center TA step, generating unusual base-base interactions along each individual DNA strand. In the symmetric non-cognate complex bound to GAATTC, the center step bend is relaxed to avoid steric hindrance caused by the different placement of the exocyclic thymine methyl groups. The decreased base-pair unstacking in turn leads to small conformational rearrangements in the sugar-phosphate backbone, sufficient to destabilize binding of crucial divalent metal ions in the active site. A second crystal structure of EcoRV bound to the base-analog GAAUTC site shows that the 50 degrees center-step bend of the DNA is restored. However, while divalent metals bind at high occupancy in this structure, one metal ion shifts away from binding at the scissile DNA phosphate to a position near the 3'-adjacent phosphate group. This may explain why the 10(4)-fold attenuated cleavage efficiency toward GAATTC is reconstituted by less than tenfold toward GAAUTC. Examination of DNA binding and bending by equilibrium and stopped-flow florescence quenching and fluorescence resonance energy transfer (FRET) methods demonstrates that the capacity of EcoRV to bend the GAATTC non-cognate site is severely limited, but that full bending of GAAUTC is achieved at only a threefold reduced rate compared with the cognate complex. Together, the structural and biochemical data demonstrate the existence of distinct mechanisms for ensuring specificity at the bending and catalytic steps, respectively. The limited conformational rearrangements observed in the EcoRV non-cognate complex provide a sharp contrast to the extensive structural changes found in a non-cognate BamHI-DNA crystal structure, thus demonstrating a diversity of mechanisms by which restriction enzymes are able to achieve specificity. 相似文献
17.
Li C Montgomery MG Mohammed F Li JJ Wood SP Bugg TD 《Journal of molecular biology》2005,346(1):241-251
C-C hydrolase MhpC (2-hydroxy-6-keto-nona-1,9-dioic acid 5,6-hydrolase) from Escherichia coli catalyses the hydrolytic C-C cleavage of the meta-ring fission product on the phenylpropionic acid catabolic pathway. The crystal structure of E. coli MhpC has revealed a number of active-site amino acid residues that may participate in catalysis. Site-directed mutants of His263, Ser110, His114, and Ser40 have been analysed using steady-state and stopped-flow kinetics. Mutants H263A, S110A and S110G show 10(4)-fold reduced catalytic efficiency, but still retain catalytic activity for C-C cleavage. Two distinct steps are observed by stopped-flow UV/Vis spectrophotometry, corresponding to ketonisation and C-C cleavage: H263A exhibits very slow ketonisation and C-C cleavage, whereas S110A and S110G exhibit fast ketonisation, an intermediate phase, and slow C-C cleavage. H114A shows only twofold-reduced catalytic efficiency, ruling out a catalytic role, but shows a fivefold-reduced K(M) for the natural substrate, and an ability to process an aryl-containing substrate, implying a role for His114 in positioning of the substrate. S40A shows only twofold-reduced catalytic efficiency, but shows a very fast (500 s(-1)) interconversion of dienol (317 nm) to dienolate (394 nm) forms of the substrate, indicating that the enzyme accepts the dienol form of the substrate. These data imply that His263 is responsible for both ketonisation of the substrate and for deprotonation of water for C-C cleavage, a novel catalytic role in a serine hydrolase. Ser110 has an important but non-essential role in catalysis, which appears not to be to act as a nucleophile. A catalytic mechanism is proposed involving stabilisation of reactive intermediates and activation of a nucleophilic water molecule by Ser110. 相似文献
18.
(4-Hydroxyphenyl)pyruvate dioxygenase (HPPD) incorporates both atoms of molecular oxygen into 4-hydroxyphenylpyruvate (HPP) to form homogentisate (HG). This reaction has direct relevance in both medicine and agriculture. In humans, the specific inhibition of HPPD alleviates the symptoms of diseases that arise from tyrosine catabolism defects. However, in plants, the inhibition of HPPD bleaches, stunts, and ultimately kills the organism. The reason for this is that in mammalian metabolism the product HG does not feed into other pathways, whereas in plants it is the precursor for the redox active portion of tocopherols and plastoquinones. There are a number of commercially available herbicides that directly target the inhibition of the HPPD reaction. Plant HPPD however is largely uncharacterized in terms of its catalysis and inhibition reactions. In this study, we examine the catalysis and inhibition of HPPD from Arabidopsis thaliana (AtHPPD). We have expressed AtHPPD and purified the enzyme to high specific activity. This form of HPPD accumulates two transient species in single turnover reactions with the native substrate HPP. These transients appear to be equivalent to intermediates I and III observed in the enzyme from Streptomyces (Johnson-Winters et al. (2005), Biochemistry, 44, 7189-7199). The first intermediate is a relatively strongly absorbing species with maxima at 380 and 490 nm. This species decays to a second intermediate that is fluorescent and has been assigned as the complex of the enzyme with the product, HG. The decay of this intermediate is rate-determining in multiple turnover reactions. The reaction of the enzyme with the analogue of the substrate, phenylpyruvate (PPA), is noncatalytic. A single turnover reaction is observed with this ligand that renders the enzyme oxidized to the ferric form, consumes a stoichiometric amount of dioxygen, and yields 66% phenylacetate as a product. Additional absorbance features at 365 and 670 nm accumulate during inactivation and give the inactivated enzyme a green color but has the same molecular mass as the active enzyme as determined by mass spectrometry. 相似文献
19.
To provide data for fatigue life prediction and testing of structural components in off-road bicycles, the objective of the research described herein was to quantify the loads input to an off-road bicycle as a result of surface-induced loads. A fully instrumented test bicycle was equipped with dynamometers at the pedals, handlebars, and hubs to measure all in-plane structural loads acting through points of contact between the bicycle and both the rider and the ground. A portable data acquisition system carried by the standing rider allowed, for the first time, this loading information to be collected during extended off-road testing. In all, seven experienced riders rode a downhill trial test section with the test bicycle in both front-suspension and full-suspension configurations. The load histories were used quantitatively to describe the load components through the computation of means, standard deviations, amplitude probability density functions, and power spectral density functions. For the standing position, the coefficients of variation for the load components normal to the ground were greater than 1.2 for handlebar forces and 0.3 and 0.5-0.6 for the pedal and hub forces, respectively. Thus, the relative contribution of the dynamic loading was much greater than the static loading at the handlebars but less so at the pedals and hubs. As indicated by the rainflow count, high amplitude loading was developed approaching 3 and 5 times the weight of the test subjects at the front and rear wheels, respectively. The power spectral densities showed that energy was concentrated in the band 0-50 Hz. Through stress computations and knowledge of material properties, the data can be used analytically to predict the fatigue life of important structural components such as those for steering. The data can also be used to develop a fatigue testing protocol for verifying analytical predictions of fatigue life. 相似文献
20.
Coupling between carbon cycling and climate in a high-elevation,subalpine forest: a model-data fusion analysis 总被引:7,自引:0,他引:7
Fundamental questions exist about the effects of climate on terrestrial net ecosystem CO2 exchange (NEE), despite a rapidly growing body of flux observations. One strategy to clarify ecosystem climate–carbon interactions
is to partition NEE into its component fluxes, gross ecosystem CO2 exchange (GEE) and ecosystem respiration (R
E), and evaluate the responses to climate of each component flux. We separated observed NEE into optimized estimates of GEE
and R
E using an ecosystem process model combined with 6 years of continuous flux data from the Niwot Ridge AmeriFlux site. In order
to gain further insight into the processes underlying NEE, we partitioned R
E into its components: heterotrophic (R
H) and autotrophic (R
A) respiration. We were successful in separating GEE and R
E, but less successful in accurately partitioning R
E into R
A and R
H. Our failure in the latter was due to a lack of adequate contrasts in the assimilated data set to distinguish between R
A and R
H. We performed most model runs at a twice-daily time step. Optimizing on daily-aggregated data severely degraded the model’s
ability to separate GEE and R
E. However, we gained little benefit from using a half-hourly time step. The model-data fusion showed that most of the interannual
variability in NEE was due to variability in GEE, and not R
E. In contrast to several previous studies in other ecosystems, we found that longer growing seasons at Niwot Ridge were correlated
with less net CO2 uptake, due to a decrease of available snow-melt water during the late springtime photosynthetic period. Warmer springtime
temperatures resulted in increased net CO2 uptake only if adequate moisture was available; when warmer springtime conditions led into mid-summer drought, the annual
net uptake declined. 相似文献