Multi-isomorphous replacement phasing of the earthworm fibrinolytic enzyme component A from Eisenia fetida

Thrombosis is one of the most widely occurring diseases in modern life, which often causes disability and death. Fibrinolytic enzymes degrade fibrin, the major protein component of blood clots, and eventually lead to thrombolysis. Medications using fibrinolytic enzymes are the most effective methods used in the treatment of thrombosis. A variety of fibrinolytic enzymes, such as tPA, uPA, and streptokinase, have been extensively studied and used as thrombolytic agents in clinic. However, thes…     

Multi-isomorphous replacement phasing of the earthworm fibrinolytic enzyme component A from <Emphasis Type="Italic">Eisenia fetida</Emphasis>

Earthworm fibrinolytic enzyme component A (EFEa) from Eisenia fetida, a protein functioning not only as a direct fibrinolytic enzyme, but also as a plasminogen activator, has been crystallized in P212121 space group with 3 proteinmolecules per asymmetric unit. Four heavy atom derivatives were prepared using a mother liquor containing 1.4 mol@L-1 Li2SO4 and 0.1 mol@L-1 MOPS buffer (pH7.2) and used to solve the protein's diffraction phase. The heavy atom binding sites in the derivative crystals were determined using difference Patterson and difference Fourier methods and were refined in combination to yield the initial protein's structure phase at 0.25 nm resolution. The non-crystallographic symmetryrelationship of the three independent protein molecules in the asymmetric unit was determined using the correlative heavy atom sites and used for the averagingof the initial electron density. As a result, the electron density was significantly improved, providing a solid foundation for subsequent structure determination.     

Catalytic activities of dismution reactions of Cu(bpy)Br2 compound and its derivatives as SOD mimics: A theoretical study

The systematical investigations on the catalytic mechanisms of dismutation reactions for the superoxide dismutase (SOD) mimics of Cu(bpy)Br₂ and its derivatives Cu(L¹)Br₂ and Cu(L²)Br₂ (bpy=2,2’- dipyridyl, L¹=5,5’- di[1- (triethylammonio)methyl]- 2,2’- dipyridyl cation and L²=5,5’- di [1- (tributylammonio)methyl]- 2,2’- dipyridyl cation) have been carried out by the DFT/UB3LYP method. The catalytic reaction for each of these compounds is confirmed to be a redox cycle consisting of two half-reactions. In the first half-reaction, a proton is transferred from hydroperoxide neutral radical (·OOH) to one nitrogen atom of pyridinic ring with Cu(II) being reduced to Cu(I) in the meantime. In the second half-reaction, the proton is transferred back to another hydroperoxide radical (·OOH) to form hydrogen peroxide molecule, oxidizing Cu(I) back to its initial state. Our results show that the first half-reaction for all reactions is the rate-controlling step with the forward barrier values of 6.61, 4.84, 3.79 kcal·mol⁻¹ for Cu(bpy)Br₂, Cu(L¹)Br₂, and Cu(L²)Br₂, respectively. Consequently, the SOD-like activities of the three mimics are in the order of Cu(bpy)Br₂ < Cu(L¹)Br₂ < Cu(L²)Br₂. The effect factors on the SOD-like activity for the studied compounds have also been discussed.     

Twinning in crystals of human skeletal muscle d-glyceraldehyde-3-phosphate dehydrogenase

The coenzyme-bound form of human skeletal muscle d-glyceraldehyde-3-phosphate dehydrogenase has been shown to crystallize in the space group C2 and not C222₁ as previously reported. The unit cell contains two tetrameric molecules with the dimer of molecular weight 72,000 as the crystallographic asymmetric unit. The recorded X-ray intensity distribution clearly indicates the presence of non-crystallographic 2-fold axes perpendicular to the crystallographic 2-fold axis showing that the subunits are arranged with near perfect 222 symmetry.Isomorphous derivatives of the enzyme have been prepared and the heavy atom positions defined in complete agreement with the C2 space group assignment. Further confirmation that the space group is C2 and not C222₁ comes from the 3.5 Å resolution electron density map of the human enzyme, which appears almost identical to that of the lobster holo-enzyme where no such space group ambiguity exists.     

Purification and characterization of a membrane-bound hydrogenase from Sporomusa sphaeroides involved in energy-transducing electron transport

Hydrogenase was solubilized from the cytoplasmic membrane fraction of betaine-grown Sporomusa sphaeroides, and the enzyme was purified under oxic conditions. The oxygen-sensitive enzyme was partially reactivated under reducing conditions, resulting in a maximal activity of 19.8 μmol H₂ oxidized min^–1 (mg protein)^–1 with benzyl viologen as electron acceptor and an apparent K _m value for H₂ of 341 μM. The molecular mass of the native protein estimated by native PAGE and gel filtration was 122 and 130 kDa, respectively. SDS-PAGE revealed two polypeptides with molecular masses of 65 and 37 kDa, present in a 1:1 ratio. The native protein contained 15.6 ± 1.7 mol Fe, 11.4 ± 1.4 mol S^2–, and 0.6 mol Ni per mol enzyme. The hydrogenase coupled with viologen dyes, but not with other various artificial electron carriers, FAD, FMN, or NAD(P)⁺. The amino acid sequence of the N-termini of the subunits showed a high degree of similarity to eubacterial membrane-bound uptake hydrogenases. Washed membranes catalyzed a H₂-dependent cytochrome b reduction at a rate of 0.18 nmol min^–1 (mg protein)^–1. Received: 7 September 1995 / Accepted: 4 December 1995     

Methyl-detected ‘out-and-back’ NMR experiments for simultaneous assignments of Alaβ and Ileγ2 methyl groups in large proteins

A set of sensitive methyl-detected ‘out-and-back’ NMR experiments for simultaneous assignments of Alaβ and Ileγ2 methyl positions in large proteins is described. The developed methodology is applied to an 82-kDa enzyme Malate Synthase G. Complete alanine β and isoleucine γ2 ¹H–¹³C methyl chemical shift assignments could be obtained from the set of new methyl-detected ‘out-and-back’ 3D experiments. The described methodology for methyl assignments should be applicable to protein molecules within approximately 100-kDa molecular weight range irrespective of the labeling strategy chosen to produce selectively protonated Alaβ and Ileγ2 ¹³CH₃ sites on a deuterated background.     

Phenoxyl-copper(II) complexes: models for the active site of galactose oxidase

 The reaction of the macrocycles 1,4,7-tris (3,5-di-tert-butyl-2-hydroxy-benzyl)-1,4,7-triazacyclononane, L¹H₃, or 1,4,7-tris(3-tert-butyl-5-methoxy-2-hydroxy-benzyl)-1,4,7-triazacyclononane, L²H₃, with Cu(ClO₄)₂·6H₂O in methanol (in the presence of Et₃N) affords the green complexes [Cu^II(L¹H)] (1), [Cu^II(L²H)]·CH₃OH (2) and (in the presence of HClO₄) [Cu^II(L¹H₂)](ClO₄) (3) and [Cu^II(L²H₂)] (ClO₄) (4). The Cu^II ions in these complexes are five-coordinate (square-base pyramidal), and each contains a dangling, uncoordinated pendent arm (phenol). Complexes 1 and 2 contain two equatorially coordinated phenolato ligands, whereas in 3 and 4 one of these is protonated, affording a coordinated phenol. Electrochemically, these complexes can be oxidized by one electron, generating the phenoxyl-copper(II) species [Cu^II(L¹H)]^+ ·, [Cu(L²H)]^+ ·, [Cu^II(L¹H₂)]^2+ ·, and [Cu^II(L²H₂)]^2+ ·, all of which are EPR-silent. These species are excellent models for the active form of the enzyme galactose oxidase (GO). Their spectroscopic features (UV-VIS, resonance Raman) are very similar to those reported for GO and unambiguously show that the complexes are phenoxyl-copper(II) rather than phenolato-copper(III) species. Received: 10 February 1997 / Accepted: 7 April 1997     

Effect of Mg2+ on the Structure and Function of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Mg²⁺ in various concentrations was added to purified Rubisco in vitro to gain insight into the mechanism of molecular interactions between Mg²⁺ and Rubisco. The enzyme activity assays showed that the reaction between Rubisco and Mg²⁺ was two order, which means that the enhancement of Rubisco activity was accelerated by low concentration of Mg²⁺ and slowed by high concentration of Mg²⁺. The kinetics constant (K _m) and V _max was 1.91 μM and 1.13 μmol CO₂ mg⁻¹ protein∙min⁻¹, respectively, at a low concentration of Mg²⁺, and 3.45 μM and 0.32 μmol CO₂∙mg⁻¹ protein∙min⁻¹, respectively, at a high concentration of Mg²⁺. By UV absorption and fluorescence spectroscopy assays, the Mg²⁺ was determined to be directly bound to Rubisco; the binding site of Mg²⁺ to Rubisco was 0.275, the binding constants (K _A) of the binding site were 6.33 × 10⁴ and 5.5 × 10⁴ l·mol⁻¹. Based on the analysis of the circular dichroism (CD) spectra, it was concluded that the binding of Mg²⁺ did not alter the secondary structure of Rubisco, suggesting that the observed enhancement of Rubisco carboxylase activity was caused by a subtle structural change in the active site through the formation of the complex with Mg²⁺.     

INORGANIC CARBON ACQUISITION BY CHRYSOPHYTES1

Twelve species, representing 12 families of the chrysophytes sensu lato, were tested for their ability to take up inorganic carbon. Using the pH‐drift technique, CO₂ compensation points generally varied between 1 and 20 μmol · L^?1 with a mean concentration of 5 μmol · L^?1. Neither pH nor alkalinity affected the CO₂ compensation point. The concentration of oxygen had a relatively minor effect on CO₂‐uptake kinetics, and the mean CO₂ compensation point calculated from the kinetic curves was 3.6 μmol · L^?1 at 10–15 kPa starting oxygen partial pressure and 3.8 μmol · L^?1 at atmospheric starting oxygen partial pressure (21 kPa). Similarly, uptake kinetics were not affected by alkalinity, and hence concentration of bicarbonate. Membrane inlet mass spectrometry (MIMS) in the presence and absence of acetazolamide suggested that external carbonic anhydrase in Dinobryon sertularia Ehrenb. and Synura petersenii Korschikov was either very low or absent. Rates of net HCO₃^? uptake were very low (～5% of oxygen evolution) using MIMS and decreased rather than increased with increasing HCO₃^? concentration, suggesting that it was not a real uptake. The CO₂ compensation points determined by MIMS for CO₂ uptake and oxygen evolution were similar to those determined in pH‐drift and were >1 μmol · L^?1. Overall, the results suggest that chrysophytes as a group lack a carbon‐concentrating mechanism (CCM), or an ability to make use of bicarbonate as an alternative source of inorganic carbon. The possible evolutionary and ecological consequences of this are briefly discussed.     

ACCLIMATION OF NITRATE UPTAKE BY PHYTOPLANKTON TO HIGH SUBSTRATE LEVELS1

A literature review of data on nitrate uptake by phytoplankton suggests that nitrate levels above 20 μmol N·L^?1 generally stimulated uptake rates in cultured unicellular algae and natural phytoplankton communities. This phenomenon indicates that phytoplankton cells acclimate to elevated nitrate levels by increasing their uptake capacity in a range of concentrations previously considered to be saturating. Cyanobacteria and flagellates were found to present a considerable capacity for acclimation, with low (0.1–2 μmol N·L^?1) half‐saturation values (K_s) at low (5–20 μmol N·L^?1) substrate levels and high (1–80 μmol N·L^?1) K_s values at high (30–100 μmol N·L^?1) substrate levels. However, some diatom genera (Rhizosolenia, Skeletonema, Thalassiosira) also appeared to possess a low affinity nitrate uptake system (K_s between 18 and 120 μmol N·L^?1), which can help resolve the paradox of their presence in enriched seas. It follows that present models of nitrate uptake can severely underestimate the effects of high nitrate concentrations on phytoplankton dynamics and development. A more adequate approach would be to consider the possibility of multiphasic uptake involving several phase transitions as nitrate concentrations increased. Because it is a nonlinear phenomenon featuring strong thresholds, this effect appears to override that of other variables, such as irradiance, temperature, and cell size. Within the present context of eutrophication and for a range of concentrations that is becoming more and more ecologically relevant, equations are tentatively presented as a first approach to estimate K_s from ambient nitrate concentrations.     

Irradiance influences tea leaf (<Emphasis Type="Italic">Camellia sinensis</Emphasis> L.) photosynthesis and transpiration

Rates of net photosynthesis (P _N) and transpiration (E), and leaf temperature (T_L) of maintenance leaves of tea under plucking were affected by photosynthetic photon flux densities (PPFD) of 200–2 200 μmol m⁻² s⁻¹. P _N gradually increased with the increase of PPFD from 200 to 1 200 μmol m⁻² s⁻¹ and thereafter sharply declined. Maximum P _N was 13.95 μmol m⁻² s⁻¹ at 1 200 μmol m⁻² s⁻¹ PPFD. There was no significant variation of P _N among PPFD at 1 400–1 800 μmol m⁻² s⁻¹. Significant drop of P _N occurred at 2 000 μmol m⁻² s⁻¹. PPFD at 2 200 μmol m⁻² s⁻¹ reduced photosynthesis to 6.92 μmol m⁻² s⁻¹. PPFD had a strong correlation with T_L and E. Both T_L and E linearly increased from 200 to 2 200 μmol m⁻² s⁻¹ PPFD. T_L and E were highly correlated. The optimum T_L for maximum P _N was 26.0 °C after which P _N declined significantly. E had a positive correlation with P _N.     

Microsolvation of aminoethanol: a study using DFT combined with QTAIM

The microsolvation of aminoethanol (AE) with one, two, three or four water molecules was investigated using a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen-bonding characteristics of AE–(H₂O) _n (n = 1–4) complexes. The results showed that AE tends to break its intramolecular OH^AE···N^AE hydrogen bond (H-bond) upon microsolvation and form intermolecular H-bonds with water molecules, while complexes that retain the intramolecular OH^AE···N^AE H-bond show reduced stabilities. The intermolecular H-bond that forms between the nitrogen atom of AE and the hydroxyl of a water molecule is the strongest one for the most stable AE–(H₂O) _n (n = 1–4) complexes, and as n increases from 1 to 4 they grow stronger. The partial covalent character of this H-bond was confirmed by QTAIM analyses. Many-body interaction analysis showed that the relaxation energies and two- and three-body energies make significant contributions to the binding energies of the complexes.     

钙素对彩叶玉簪光合作用和保护酶活性的影响

该文以彩叶玉簪为材料,研究了不同钙素水平对玉簪叶片光合作用和保护酶活性的影响。结果表明:随着钙素水平的提高,彩叶玉簪叶片的净光合速率(Pn)、气孔导度(Gs)、胞间CO_2浓度(Ci)、蒸腾速率(Tr)和最大光化学效率(F_v/F_m)均呈单峰曲线,最高峰值出现在Ca~(2+)90 mg·L~(-1)时;电子传递速率(ETR)的变化也呈单峰曲线,峰值出现在Ca~(2+)50 mg·L~(-1)时;初始荧光(F_0)和最大荧光(F_m)值在0~360 mg·L~(-1)钙素水平下呈先升高后下降再升高的趋势,最大值均出现在90 mg·L~(-1)时;Pn和Gs值的变化与Ci值成正相关。同时叶片中过氧化物酶(POD)、过氧化氢酶(CAT)的活性及丙二醛(MDA)、可溶性蛋白质(SP)含量均表现为单谷曲线,在Ca~(2+)90 mg·L~(-1)时达最小值。超氧化物歧化酶(SOD)活性呈现持续下降趋势。综上所述,彩叶玉簪Pn下降主要由气孔引起,叶面喷施90 mg·L~(-1)的Ca~(2+)可增强彩叶玉簪光合作用,降低保护酶活性。     

Non-crystallographic symmetry in the crystal dimer of wheat germ agglutinin

Three isomorphous heavy atom derivatives of wheat germ agglutinin crystals, KAu(CN)₂, K₂Pt(NH₃)₂(NO)₂ and mersalyl, have been examined at high resolution. Heavy atom sites were located from difference Patterson maps in three dimensions at 2.15 Å resolution for the gold and platinum derivatives and with less certainty in the centrosymmetric [010] projection for the mersalyl derivative. These sites are distributed in the crystallographic asymmetric unit such that one half of them can be related to the other half by a 180 ° rotation about an axis parallel to a, and an additional translation of about 6.35 Å along that axis. It is suggested that the two subunits of the wheat germ agglutinin dimer, which represent the asymmetric unit of the C2 unit cell, are related by the same symmetry axis, causing heterologous subunit contacts due to the 6.35 Å translation of one relative to the other subunit.     

Acclimation of photosynthetic capacity to irradiance in tree canopies in relation to leaf nitrogen concentration and leaf mass per unit area

The observation of acclimation in leaf photosynthetic capacity to differences in growth irradiance has been widely used as support for a hypothesis that enables a simplification of some soil‐vegetation‐atmosphere transfer (SVAT) photosynthesis models. The acclimation hypothesis requires that relative leaf nitrogen concentration declines with relative irradiance from the top of a canopy to the bottom, in 1 : 1 proportion. In combination with a light transmission model it enables a simple estimate of the vertical profile in leaf nitrogen concentration (which is assumed to determine maximum carboxylation capacity), and in combination with estimates of the fraction of absorbed radiation it also leads to simple ‘big‐leaf’ analytical solutions for canopy photosynthesis. We tested how forests deviate from this condition in five tree canopies, including four broadleaf stands, and one needle‐leaf stand: a mixed‐species tropical rain forest, oak (Quercus petraea (Matt.) Liebl), birch (Betula pendula Roth), beech (Fagus sylvatica L.) and Sitka spruce (Picea sitchensis (Bong.) Carr). Each canopy was studied when fully developed (mid‐to‐late summer for temperate stands). Irradiance (Q, µmol m^?2 s^?1) was measured for 20 d using quantum sensors placed throughout the vertical canopy profile. Measurements were made to obtain parameters from leaves adjacent to the radiation sensors: maximum carboxylation and electron transfer capacity (V_a, J_a, µmol m^?2 s^?1), day respiration (R_da, µmol m^?2 s^?1), leaf nitrogen concentration (N_m, mg g^?1) and leaf mass per unit area (L_a, g m^?2). Relative to upper‐canopy values, V_a declined linearly in 1 : 1 proportion with N_a. Relative V_a also declined linearly with relative Q, but with a significant intercept at zero irradiance (P < 0·01). This intercept was strongly related to L_a of the lowest leaves in each canopy (P < 0·01, r² = 0·98, n= 5). For each canopy, daily lnQ was also linearly related with lnV_a(P < 0·05), and the intercept was correlated with the value for photosynthetic capacity per unit nitrogen (PUN: V_a/N_a, µmol g^?1 s^?1) of the lowest leaves in each canopy (P < 0·05). V_a was linearly related with L_a and N_a(P < 0·01), but the slope of the V_a : N_a relationship varied widely among sites. Hence, whilst there was a unique V_a : N_a ratio in each stand, acclimation in V_a to Q varied predictably with L_a of the lowest leaves in each canopy. The specific leaf area, L_m(cm² g^?1), of the canopy‐bottom foliage was also found to predict carboxylation capacity (expressed on a mass basis; V_m, µmol g^?1 s^?1) at all sites (P < 0·01). These results invalidate the hypothesis of full acclimation to irradiance, but suggest that L_a and L_m of the most light‐limited leaves in a canopy are widely applicable indicators of the distribution of photosynthetic capacity with height in forests.     

EFFECTS OF EXTERNAL INORGANIC NITROGEN CONCENTRATION ON METABOLISM,GROWTH AND ACTIVITIES OF KEY CARBON AND NITROGEN ASSIMILATORY ENZYMES OF LAMINARIA SACCHARINA (PHAEOPHYCEAE) IN CULTURE1

The growth rate of Laminaria saccharina (L.) Lamour. is dependent on inorganic nitrogen in culture. Growth rates were saturated between 5 and 10 μmol · L^?1 nitrate. The activities of ribulose-1,5 bisphosphate carboxylase, phosphoenolpyruvate carboxykinase, mannitol-1-phosphate dehydrogenase, nitrate reductase and glutamine synthetase also varied with the concentration of inorganic nitrogen in the medium. All enzyme activities were lowest at 2.5 μmol · L^?1 nitrate (the lowest concentration used) increasing to a maximum activity between 10 and 30 μmol · L^?1 nitrate. Most enzyme activities followed a hyperbolic curve resembling those described by the Michaelis-Menten equation, with different half-saturation constants.     

Zn、B配施对鸡血藤黄酮类化合物积累的影响

为探讨Zn、B配施对鸡血藤(Spatholobus suberectus)黄酮类化合物积累的影响,采用营养液叶面喷施,对其总黄酮含量、可溶性蛋白质和PAL活性的变化进行研究。结果表明,Zn、B配施的鸡血藤总黄酮含量、可溶性蛋白质含量、PAL活性增加,其中施用50 mg L–1 Zn SO4+10 mg L–1 Na_2B_4O_7·10H_2O鸡血藤的可溶性蛋白质含量最高,达0.89%;施用25 mg L–1Zn SO4+50 mg L–1 Na2B4O7·10H2O鸡血藤的总黄酮含量和PAL活性最高,分别为4.65%、29.47 U g–1min–1。因此,合理配施Zn、B能促进鸡血藤黄酮类化合物的积累。     

Immediate response of Chara braunii exposed to zinc and hydrogen peroxide

The immediate effect of zinc (Zn) and hydrogen peroxide (H₂O₂) in Chara braunii was analyzed in short-time exposure experiments. The exposure concentrations were 12.3, 18.4, and 24.5 μmol L^?1 H₂O₂, 12, 60, and 120 mg L^?1 Zn, and 12.3 μmol L^?1 H₂O₂ + 12 mg L^?1 Zn, 12.3 μmol L^?1 H₂O₂ + 60 mg L^?1 Zn, and 18.4 μmol L^?1 H₂O₂ + 12 mg L^?1 Zn. The stress response of C. braunii was analyzed by measuring photosynthetic photosystem II activity, chlorophyll a and b and carotenoid contents, the H₂O₂ concentration, and antioxidant enzyme activities of ascorbic peroxidase, catalase, and guaiacol peroxidase. The short-term addition of Zn reduced pigment contents in C. braunii. Chlorophyll a and b and carotenoid contents in H₂O₂-exposed C. braunii were as high as in control plants. Photosynthesis was reduced in H₂O₂-treated C. braunii and the short-term addition of Zn did not affect the electron transport rate. H₂O₂ concentration and antioxidant enzyme activities in C. braunii were not significantly different between control and exposed plants. Trends of enzymatic adaptation were described: the H₂O₂-induced stress response was characterized by increased antioxidant enzyme activities, whereas Zn inactivated catalase in C. braunii.     

Purification and properties of the H2-oxidizing (uptake) hydrogenase of the N2-fixing anaerobe Clostridium pasteurianum W5

Clostridium pasteurianum has two distinct hydrogenases, the bidirectional hydrogenase and the H₂-oxidizing (uptake) hydrogenase. The H₂-oxidizing hydrogenase has been purified (up to 970-fold) to a specific activity of 17,600 μmol H₂ oxidized/min·mg protein (5 mM methylene blue) or 3.5 μmol H₂ produced/min·mg protein (1 mM methyl viologen). The uptake hydrogenase has a M_r of 53,000 (one polypeptide chain). Depending upon how protein was measured, the Fe and S⁼ contents (gatom/mol) were 4.7 and 5.2 (by the dye-binding assay) or 7.2 and 8.0 (by the Lowry method). Both reduced and oxidized forms of the enzyme gave electron paramagnetic resonance signals. The activation energy for H₂-production and H₂-oxidation by the uptake hydrogenase was 59.1 and 31.2 kJ/mol, respectively. In the exponential phase of growth, the ratio of uptake hydrogenase/bidirectional hydrogenase in NH₃-grown cells was much lower than that in N₂-fixing cells.