Fractal structure and conformational entropy of protein chain

The structures of 25 proteins arbitrarily chosen are investigated by fractal geometry, and their fractal dimensions (D_f) and conformational entropies S(N₀) are calculated by Havlin—Ben Avraham and Monte Carlo method, respectively. Comparison of the D_f and S(N₀) gives the relation: D_f = 1.532 - 3.00 × 10⁻⁴ S(N₀). The entropy data obtained by Monte Carlo method for the chain of random self-avoiding walks confirm the prediction of renormalization group: S(N₀) = 1.544N₀ + 0.1667 In N₀ + 0.1570 where N₀ is the number of residues in a protein chain. Both the D_f and S(N₀) reflect the conformational properties of a protein molecular chain. The idea resulting from the present communication suggests that the thermodynamic behaviours of proteins may be related to multifractals.     

Redox state of the partially reduced cytochrome aa3-cyanide complex

The low-spin ferric cyanide complex of beef heart cytochrome aa₃ can be partially reduced by stoichiometric additions of ferrous cytochrome c or by similar additions of N,N,N′,N′-tetramethyl-p-phenylene diamine. In both cases the initial ratio of cytochrome c oxidized: cytochrome a reduced or Wurster's Blue: cytochrome a reduced approximates the value 2. It is concluded that the binding of a single HCN prevents the reduction of both cytochrome a₃ and its associated EPR-invisible Cu atom.     

Dihydroxamic acid complexes of iron (III): ligand pKa and coordinated water hydrolysis constants

A series of dihydroxamic acid ligands of the formula [RN(OH)C(O)]₂(CH₂)_n, (n = 2, 4, 6, 7, 8; R = CH₃, H) has been studied in 2.0 M aqueous sodium perchlorate at 25.0 °C. These ligands may be considered as synthetic analogs to the siderophore rhodotorulic acid. Acid dissociation constants (pK_a) have been determined for the ligands and for N-methylacetohydroxamic acid (NMHA). The pK_a1 and pK_a2 values are: n = 2, R = CH₃ (8.72, 9.37); N = 4, R = CH₃ (8.79, 9.37); N = 6, R = CH₃; N = 7, R = CH₃ (8.95, 9.47); N = 8, R = CH₃ (8.93, 9.45); N = 8, R = H (9.05, 9.58). Equilibrium constants for the hydrolysis of coordinated water (log K) have been estimated for the 1:1 feeric complexes of the ligands n = 2, 4, 8; R = CH₃. The N = 8 ligand forms a monomeric complex with Fe(III) while the n = 2 and 4 ligands form dimeric complexes. For hydrolysis of the n = 8 monomeric complex, log K₁ = −6.36 and log K₂ = −9.84. Analysis of the spectrophotometric data for the dimeric complexes indicates deprotonation of all four coordinated waters. The successive hydrolysis constants, log K_1–4, for the dimeric complexes are as follows: n = 2 (−6.37, −5.77, −10.73, −11.8); n = 4 (−5.54, −5.07, −11.57, −10.17). The log K₂ values for the dimers are unexpectedly high, higher in fact than log K₁, inconsistent with the formation of simple ternary hydroxo complexes. A scheme is proposed for the hydrolysis of the ferric dihydroxamate dimers, which includes the possible formation of μ-hydroxo and μ-oxo bridges.     

Biochemical and biophysical studies on cytochrome aa3 VIII. Effect of cyanide on the catalytic activity

1. 1. Cyanide inhibits the catalytic activity of cytochrome aa₃ in both polarographic and spectrophotometric assay systems with an apparent velocity constant of 4·10³ M⁻¹·s⁻¹ and a K_i that varies from 0.1 to 1.0 μM at 22 °C, pH 7·3.

2. 2. When cyanide is added to the ascorbate-cytochrome c-cytochromeaa₃−O₂ system a biphasic reduction of cytochrome c occurs corresponding to an initial K_i of 0.8 μM and a final K_i of about 0.1 μM for the cytochrome aa₃−cyanide reaction.

3. 3. The inhibited species (a²+a₃³⁺HCN) is formed when a²⁺a₃³⁺ reacts with HCN, when a²⁺a₃²⁺HCN reacts with oxygen, or when a³⁺a₃³⁺HCN (cyano-cytochrome aa₃) is reduced. Cyanide dissociates from a²⁺a₃³⁺HCN at a rate of 2·10⁻³ s⁻¹ at 22 °C, pH 7.3.

4. 4. The results are interpreted in terms of a scheme in which one mole of cyanide binds more tightly and more rapidly to a²⁺a₃³⁺ than to a³⁺a₃³⁺.

H NMR study of the interaction of N,N′,N″-triacetyl chitotriose with Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus

The interaction between Ac-AMP2, a lectin-like small protein with antimicrobial and antifungal activity isolated from Amaranthus caudatus, and N,N′,N″-triacetyl chitotriose was studied using ¹H NMR spectroscopy. Changes in chemical shift and line width upon increasing concentration of N,N′,N″-triacetyl chitotriose to Ac-AMP2 solutions at pH 6.9 and 2.4 were used to determine the interaction site and the association constant K_a. The most pronounced shifts occur mainly in the C-terminal half of the sequence. They involve the aromatic residues Phe¹⁸, Tyr²⁰ and Tyr²⁷ together with their surrounding residues, as well as the N-terminal Val-Gly-Glu segment. Several NOEs between Ac-AMP2 and the N,N′,N″-triacetyl chitotriose resonances are reported.     

Studies of the cation complexing ability of crowns Part I. Synthesis, characterization and crystal structure of diazacrowns and their barium complexes

A number of N,N′-bis(4-substituted phenyl)-1,7-diaza-12-crown-4 and N,N′-bis(4-substituted phenyl)-1, 10-diaza-18-crown-6 (where the substituents are OCH₃, CH₃, H, Cl, respectively) have been prepared by cyclization reaction of a ditosylate with the appropriately substituted diol. These new macrocyclic ligands have been characterized by means of elemental analysis, IR, ¹H NMR and MS spectra. The crystal structures of N,N′-bis(4-chlorophenyl)-1,10-diaza-18-crown-6 (21) and its complex with barium thiocyanate Ba(SCN)₂ (22) have been determined by single crystal X-ray diffraction. The crystallographic data are as follows: 21: C₂₄H₃₂Cl₂N₂O₄, orthorhombic, P2₁2₁2₁, A=4.852(1), B=11.989(2), C=41.231(8) Å, V=2398.7(8) ų, Z=4; 22: C₂₆H₃₂Cl₂N₄O₄S₂Ba, monoclinic, P2₁/c, A=8.801(2), B=11.653(9), C=15.756(6) Å, ß=105.96(3)°, V=1553.7(14) ų, Z=2. In the complex, the Ba atom is eight-coordinate (O(1), O(2), O(1)′, O(2)′, N(1), N(1)′, N(21), N(21)′) to form a distorted D_6h geometry with the Ba atom at the center of crystallographic symmetry.     

The radiosensitivity of spermatogonial stem cells in C3H/101 F1 hybrid mice

The radiosensitivity of spermatogonial stem cells of C3H/HeH × 101/H F₁ hybrid mice was determined by counting undifferentiated spermatogonia at 10 days after X-irradiation. During the spermatogenic cycle, differences in radiosensitivity were found, which were correlated with the proliferative activity of the spermatogonial stem cells. In stage VIII_irr, during quiescence, the spermatogonial stem cells were most radiosensitive with a D₀ of 1.4 Gy. In stages XI_irr−V_irr, when the cells were proliferatively active, the D₀ was about 2.6 Gy. Based on the D₀ values for sensitive and resistant spermatogonia and on the D₀ for the total population, a ratio of 45:55% of sensitive to resistant spermatogonial stem cells was estimated for cell killing.

When the present data were compared with data on translocation induction obtained in mice of the same genotype, a close fit was obtained when the translocation yield (Y; in % abnormal cells) after a radiation dose D was described by Y = e^τD, with τ = 1 for the sensitive and τ = 0.1 for the resistant spermatogonial stem cells, with a maximal e^τD of 100.     

Hydrogen bonding in nucleosides and nucleotides

An analysis of the hydrogen bonding in 76 nucleoside and 11 nucleotide crystal structures shows that the hydrogen bond lengths fall into well-defined categories according to the nature of the donor or acceptor groups. The shortest bonds are those involving P---OH or O=P groups. For donor groups, the sequence in bond lengths is

P—OH<C—OH< N−H<O_w(H)—H<N(H)—H<C−H

There are ten examples of two centre

H—H…O

bonds, which are comparable in length with P---OH …O bonds. The acceptor seqeunce is

O=P<OH₂<OH₂<O=CO(H)C<N N(H₂)C<Cl^…<O<S=C

The number of three-centre bonds, about 24%, is comparable to that observed in the carbohydrates and the amino acids. Most hydrogen bonds are involved in short finite chains. Only in the nucleotides are cyclic hydrogen bonding schemes observed.     

N-Ethylmaleimide inhibition of the catalytic activities of the Dunaliella salina coupling factor 1 (CF1) and the restoration of the inhibition of the CF1 ATPase activity by N-ethylmaleimide

The sensitivity of the catalytic activities of the D. salina chloroplast coupling factor 1 (CF₁) to chemical modification by N-ethylmaleimide has been investigated. (i) When D. salina thylakoid membranes are treated with N-ethylmaleimide, both photophosphorylation and the inducible CF₁ ATPase activity are partially (approx. 60%) inhibited. The inhibition of both activities does not require the presence of a proton-motive force, and the inhibition of photophosphorylation is directly related to the N-ethylmaleimide-covalent modification of CF₁ as shown by (a) the time-course for the inhibition and (b) the maximal extent of inhibition. (ii) Treatment of the purified, latent, D. salina CF₁ with low concentrations of N-ethylmaleimide also results in the partial (approx. 60%) inhibition of the inducible ATPase activity (I₅₀ ≈ 50 μM). The inhibition does not require the presence of the chemical modifier during the activation of the enzyme. (iii) N-ethylmaleimide-induced inhibition of the ATPase activity of either membrane-bound or solubilized CF₁ is partially reversed by either (a) prolonged incubation at low concentrations of N-ethylmaleimide or (b) short incubation times at high concentrations of N-ethylmaleimide. The results are interpreted as indicating multiple binding sites on the D. salina CF₁ that have different rates of reactivity with N-ethylmaleimide. Those sites (or site) that react rapidly with N-ethylmaleimide cause(s) an inhibition of both ATP synthase and ATPase activities, whereas those sites (or site) that react more slowly partially restore(s) the original-ATPase activity. The effects of N-ethylmaleimide on the catalytic activity of D. salina CF₁ are probably mediated by N-ethylmaleimide-induced conformational changes of the enzyme.     

枫香叶斑病病原菌

从福建多地采集了55份感染叶斑病的枫香植物病样,包含叶片、叶柄、枝条和树皮。通过分离纯化得到了12个类拟盘多毛孢属真菌菌株,综合形态特征以及3个基因(ITS、β-tubulin和tef1)的分子系统发育分析结果,分别鉴定为Neopestalotiopsis cocoes、N. chrysea、Pestalotiopsis neglecta和P. neolitseae,均为枫香上首次报道,其中N. cocoes在国内首次被发现。通过柯赫氏法则验证,发现N. cocoes能够侵染叶片、叶柄和枝条,N. chrysea能侵染叶片和枝条,P. neglecta能侵染叶柄和枝条,而P. neolitseae不能侵染枫香植物组织。     

No association between N7-methyldeoxyguanosine and 8-oxodeoxyguanosine levels in human lymphocyte DNA

To examine associations between two different classes of DNA damage that can occur through endogenous processes or exogenous exposures such as smoking, N7-methyldeoxyguanosine (N7-MedG) and 8-oxodeoxyguanosine (8-oxodG) levels were measured in lymphocyte DNA from 22 bronchoscopy patients. 8-OxodG and N7-MedG was detected in 100% and 91% of samples, respectively with 8-oxodG levels being approx 20 times higher (mean 8.39 ± 3.57 8-oxodG/10⁶dG versus 0.41 ± 0.33 N7-MedG/10⁶ dG) which provides an indication of the relative importance of the agents that induce oxidative DNA damage or alkylation damage. The sources of these genotoxic lesions remain to be established but N7-MedG and 8-oxodG levels were not correlated (r² < 0.01) suggesting that there is no association between alkylating agent and reactive oxygen species exposure, their metabolism and/or the DNA repair processes that can remove this DNA damage.     

Characterization of purified cytochrome c1 from Rhodobacter sphaeroides R-26

Cytochrome c₁ from a photosynthetic bacterium Rhodobacter sphaeroides R-26 has been purified to homogeneity. The purified protein contains 30 nmol heme per mg protein, has an isoelectric point of 5.7, and is soluble in aqueous solution in the absence of detergents. The apparent molecular weight of this protein is about 150 000, determined by Bio Gel A-0.5 m column chromatography; a minimum molecular weight of 30 000 is obtained by sodium dodecylsulfate polyacrylamide gel electrophoresis. The absorption spectrum of this cytochrome is similar to that of mammalian cytochrome c₁, but the amino acid composition and circular dichroism spectral characteristics are different. The heme moiety of cytochrome c₁ is more exposed than is that of mammalian cytochrome c₁, but less exposed than that of cytochrome c₂. Ferricytochrome c₁ undergoes photoreduction upon illumination with light under anaerobic conditions. Such photoreduction is completely abolished when p-chloromercuriphenylsulfonate is added to ferricytochrome c₁, suggesting that the sulfhydryl groups of cytochrome c₁ are the electron donors for photoreduction. Purified cytochrome c₁ contains 3 ± 0.1 mol of the p-chloromercuriphenylsulfonate titratable sulfhydryl groups per mol of protein. In contrast to mammalian cytochrome c₁, the bacterial protein does not form a stable complex with cytochrome c₂ or with mammalian cytochrome c at low ionic strength. Electron transfer between bacterial ferrocytochrome c₁ and bacterial ferricytochrome c₂, and between bacterial ferrocytochrome c₁ and mammalian ferricytochrome c proceeds rapidly with equilibrium constants of 49 and 3.5, respectively. The midpoint potential of purified cytochrome c₁ is calculated to be 228 mV, which is identical to that of mammalian cytochrome c₁.     

Variations and interrelationships of foliar hydraulic and photosynthetic traits for Larix gmelinii

Aims Variations and potential trade-offs of leaf hydraulic and photosynthetic traits are essential for assessing and predicting the effect of climate change on tree survival, growth and distribution. Our aims were to examine variations and interrelationships of leaf hydraulic and photosynthetic traits in response to changes in site conditions for Dahurian larch (Larix gmelinii)—a dominant tree species in Chinese boreal forests.Methods This study was conducted at the Maoershan Forest Ecosystem Research Station. A transect of 27 year-old Dahurian larch plantation was established that consisted of five plots extending from the valley to the ridge of a slope. The predawn leaf water potential (Ψ_pre), area- and mass-based leaf hydraulic conductance (K_area and K_mass, respectively), resistance to embolism capacity (P₅₀), leaf mass per area (LMA), net photosynthetic rate (A), and leaf nitrogen content (N) were measured in August 2016.Important findings The Ψ_pre, K_area, K_mass, P₅₀, A, LMA, and N all varied significantly among the plots (p < 0.05), indicating significant intra-specific variations in these traits in response to the changes in site conditions. The P₅₀ was significantly (p < 0.05) correlated with Ψ_pre, K_area or K_mass, suggesting that a trade-off between hydraulic efficiency and safety exist within the species to some degree. There were significant (p < 0.05) pairwise correlations between A, LMA, and N. Nevertheless, there was no significant (p < 0.05) correlation between the measured photosynthetic traits and hydraulic traits. We concluded that the intra-specific variations and multiple interrelationships of the leaf hydraulic and photosynthetic traits for the larch reflect the plasticity of its leaf traits and strategies of its survival and growth as a result of its acclimation to diverse site conditions.     

Cytochrome b(5) coexpression increases the CYP2E1-dependent mutagenicity of dialkylnitrosamines in methyltransferase-deficient strains of Salmonella typhimurium.

Addition of cytochrome b₅ to recombinant cytochrome P450 2E1 systems has been shown to enhance the metabolism of dialkylnitrosamines in vitro. To determine if this effect could be observed with recombinant expression systems in vivo, we have constructed mutagenicity tester strains that coexpress full-length human cytochrome P450 2E1 (CYP2E1), rat cytochrome P450 reductase, and human cytochrome b₅ in Salmonella typhimurium lacking ogt and ada methyltransferases (YG7104, ogt⁻; and YG7108, ogt⁻, ada⁻). These new recombinant strains exhibit a four- to five-fold greater mutagenic response to dimethylnitrosamine, diethylnitrosamine, and dipropylnitrosamine than strains that contain only CYP2E1 and reductase, and are over 100-fold more sensitive to nitrosamines than the parental strains in the presence of an exogenous activating system (S9 fraction). The four-fold increase in mutagenicity in the presence of cytochrome b₅ was consistent with increasing alkyl chain length up to dibutylnitrosamine, which was poorly activated by CYP2E1. The greatest enhancement was obtained with a tricistronic construct in which the b₅ cDNA preceded the P450 and reductase cDNAs; placing the b₅ cDNA after the reductase cDNA was substantially less effective. These new, highly sensitive strains may prove useful in the detection of nitrosamine contamination of food and environmental samples.     

Cytochrome c1 and b-type cytochrome with two heme centers in the photosynthetic membranes from Rhodopseudomonas palustris

The photosynthetic membranes from Rhodopseudomonas palustris contained one species of membrane-bound c-type cytochrome, presumably cytochrome c₁, and a b-type cytochrome with two heme centers. The molecular weight and midpoint potential of cytochrome c₁ were 30000 and 275 mV, respectively. The peak of the reduced-minus-oxidized difference spectrum of cytochrome c₁ was at 552 nm. Molecular weight of the b-type cytochrome was 32000 and the cytochrome had two midpoint potentials of 60 mV and −55 mV. The peaks of the reduced-minus-oxidized difference spectra of the high and low midpoint potential heme centers were at 560 and 562 nm, respectively. These results suggested that there was a cytochrome b-c₁ complex in Rps. palustris.     

Mitochondrial cytochrome components of Paragonimus adult worms

The cytochrome components of adult Paragonimus miyazakii mitochondria were investigated by polyacrylamide gel electrophoresis. The mitochondria were found to contain cytochromes b, c₁, c and aa₃. Two types of mitochondria, lightweight mitochondria (LWMt) and heavyweight mitochondria (HWMt), were obtained by centrifugation from the mitochondrial fraction of the adult Paragonimus ohirai. The succinate-reduced and oxidized difference spectrum of LWMt and HWMt at −196°C revealed that both mitochondria contained at least functional levels of cytochromes b, c₁, c and a low value of aa₃. Although succinate-reduced cytochromes of LWMt reoxidized in the presence of air, those of HWMt did so only minimally.     

Physiological electron donors to the photochemical reaction center of Rhodobacter capsulatus

The nature and number of physiological electron donors to the photochemical reaction center of Rhodobacter capsulatus have been probed by deleting the genes for cytochromes c₁ and b of the cytochrome bc₁ complex, alone or in combination with deletion of the gene for cytochrome c₂. Deletion of cytochrome c₁ renders the organism incapable of photosynthetic growth, regardless of the presence or absence of cytochrome c₂, because in the absence of the bc₁ complex there is no cyclic electron transfer, nor any alternative source of electrons to rereduce the photochemically oxidized reaction center. While cytochrome c₂ is capable of reducing the reaction center, there appears no alternative route for its rereduction other than the bc₁ complex. The deletion of cytochromes c₁ and c₂ reveals previously unrecognized membrane-bound and soluble high potential c-type cytochromes, with E_m7 = + 312 mV and E_m6.5 = +316 mV, respectively. These cytochromes do not donate electrons to the reaction center, and their roles are unknown.     

Solvent extraction of divalent palladium and platinum from aqueous solutions of their chloro complexes using an N,N-dimethyldithiocarbamoylethoxy substituted calix[4]arene

The compound 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetra-(2-bromoethoxy)calix[4]arene has been prepared by first converting 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetra-(2-hydroxyethoxy)calix[4]arene into the tosylate, and then to the product by reaction with LiBr. The compound crystallizes in the trigonal space group P3₂21 with A = 13.160(2), C = 25.595(6) Å, A = 90.00(2), β = 90.00(1), γ = 120.000(9)⁰, Z = 3, _calc = 1.40 g cm⁻³. The final R value for 2391 unique reflections was 0.061. The compound reacts with excess sodium N,N-dimethyldithiocarbamate to give 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetra-(2-N,N-dimethyldithiocarbamoylethoxy)calix[4]arene. This compound is an effective extractant for transferring palladium(II) from an aqueous to a chloroform phase. No extraction of PtCl₄²⁻ is observed under thermal conditions. Under photochemical conditions using a mixture of PtCl₄²⁻ and PtCl₆²⁻, extraction of platinum into the chloroform layer is observed. An explanation for this observation is given.     

油蒿资源利用效率在生长季的相对变化及对环境因子的响应

为了探明西北半干旱区典型沙生植物油蒿(Artemisia ordosica)叶水平资源利用效率的相对变化及对环境因子的响应机制, 该研究于2018年5-10月, 使用LI-6400XT便携式光合仪测定了毛乌素沙地油蒿叶片的净光合速率(P_n)、蒸腾速率(E)、叶表面光合有效辐射(PAR_l)、叶表面温度(T_l)、叶表面相对湿度(RH_l), 在实验室计算叶片单位面积氮含量(N_area), 分析了叶片氮利用效率(NUE)、水分利用效率(WUE)、光利用效率(LUE)与环境因子之间的关系及NUE、WUE、LUE之间的相对变化。研究结果表明, 在充足且稳定光强下油蒿的P_n主要受温度的影响, NUE、WUE与VPD_l、T_l之间具有显著负相关关系, NUE、WUE与LUE间为正相关关系, NUE、WUE和LUE最大值分别发生在5、7和9月, 分别为9.43 μmol CO₂·g^-1·s^-1、3.86 mmol·mol^-1、0.04 mol·mol^-1, 资源利用效率的变化主要受P_n的影响。温度通过影响植物N分配来改变P_n, 进而影响着资源利用效率, WUE与LUE显著正相关, 对构建荒漠区生态系统能量交换过程模型有重要意义。     

Rhodobacter capsulatus MT113: A single mutation results in the absence of c-type cytochromes and in the absence of the cytochrome bc1 complex

MT113, a nonphotosynthetic mutant of Rhodobacter capsulatus previously characterized as lacking cytochrome c₂ is shown to lack also cytochrome c₁, the Rieske iron-sulfur cluster and the antimycin sensitive semiquinone Q_c, all components of the cytochrome bc₁ complex. Although MT113 contained b-type cytochromes and other iron-sulfur clusters at nearly wild-type level, it lacks c-type cytochromes. Based on antibody detection, c₂ apoprotein was absent in MT113, however the apoproteins corresponding to the cytochromes b and c₁ and the Rieske iron-sulfur cluster were present in reduced amounts. Genetic analysis indicated that the lesion appears to be due to a single mutation which is not localized in the structural genes of cytochrome c₂ or the bc₁ complex. These data taken together suggest that the pleiotropic mutation in MT113 might be related to the biosynthesis of c-type cytochromes.