Two different ways that hydrogen ions are involved in the thermodynamics and rapid-equilibrium kinetics of the enzymatic catalysis of S=P and S+H2O=P

Hydrogen ions are involved in two different ways in the thermodynamics and rapid-equilibrium kinetics of enzyme-catalyzed reactions. The two ways are through pKs and through the production or consumption of hydrogen ions in the mechanism. These ways are examined for the catalyzed reactions S=P and S+H2O=P. Since the apparent equilibrium constant K' can be calculated from the kinetic parameters by use of the Haldane equation, the treatment of the effects of pH must be consistent in thermodynamics and kinetics. This leads to a new kind of Haldane equation that involves 10(pH) or 10(-pH) in addition to the kinetic parameters when hydrogen ions are produced or consumed. These concepts are applicable to more complicated reactions and rate equations. Derivations of equations for calculating these two types of pH effects are discussed in thermodynamics and rapid-equilibrium kinetics. A computer program is used to make four plots of apparent equilibrium constants and changes in the binding of hydrogen ions in the catalyzed reaction.     

Synthesis and structural study of variously oxidized diastereomeric 5'-dimethoxytrityl-thymidine-3'-O-[O-(2-cyanoethyl)-N,N-diisopropyl]-phosphoramidite derivatives. Comparison of the effects of the P=O, P=S, and P=Se functions on the NMR spectral and chromatographic properties

R(P)- and S(P)-diastereomers of 5'-dimethoxytrityl-thymidine-3'-O-[O-(2-cyanoethyl)-N,N-diisopropyl]-phosphoramidite (T-CED) were separated by silica gel chromatography. Oxidation of both isomers with H(2)O(2), elemental sulfur and selenium, respectively, resulted in the corresponding oxidized analogues in nearly quantitative yields. All reactions were found to proceed with retention of P-configuration. This was confirmed by thorough NMR analysis which, in addition, aimed to study the spectral properties of the diastereomers with special respect to differences in the heteroatom effect of the O, S and Se atoms, double-bonded to the phosphorus, on the vicinal carbon-phosphorus couplings. It was found that the changes in the DeltaJ (=(3)J(P,C4') - (3)J(P,C2')) values were basically induced by the electronegativity of the heteroatoms, rather than differences in the rotational preferences about the C3'-O3' bond. The impact of the benzene solvent on the above couplings is also discussed. The effect of these heteroatoms on the chromatographic (normal and reverse phase HPLC) behavior of the compounds was also investigated and the reverse phase HPLC profiles showed an unambiguous correlation between the electronegativity of the heteroatoms and the chromatographic mobility of the analogues.     

Highly purified cytochrome P-448 and P=450 from rat liver microsomes.

Cytochrome P-448 from 3-methylcholanthrene-treated rats has been purified to a specific content of greater than 20 nmoles/mg protein, and cytochrome P-450 from phenobarbital-treated rats to greater than 17 nmoles/mg protein. Both cytochromes are catalytically active when reconstituted with lipid and NADPH-cytochrome c reductase and exhibit differential substrate specificities for benzphetamine and benzo[a]pyrene. Cytochrome P-448 has a minimum molecular weight of approximately 53,000, and cytochrome P-450, 48,000 by SDS polyacrylamide gel electrophoresis.     

Role of the scaffolding protein in P22 procapsid size determination suggested by T = 4 and T = 7 procapsid structures.

Assembly of bacteriophage P22 procapsids requires the participation of approximately 300 molecules of scaffolding protein in addition to the 420 coat protein subunits. In the absence of the scaffolding, the P22 coat protein can assemble both wild-type-size and smaller size closed capsids. Both sizes of procapsid assembled in the absence of the scaffolding protein have been studied by electron cryomicroscopy. These structural studies show that the larger capsids have T = 7 icosahedral lattices and appear the same as wild-type procapsids. The smaller capsids possess T = 4 icosahedral symmetry. The two procapsids consist of very similar penton and hexon clusters, except for an increased curvature present in the T = 4 hexon. In particular, the pronounced skewing of the hexons is conserved in both sizes of capsid. The T = 7 procapsid has a local non-icosahedral twofold axis in the center of the hexon and thus contains four unique quasi-equivalent coat protein conformations that are the same as those in the T = 4 procapsid. Models of how the scaffolding protein may direct these four coat subunit types into a T = 7 rather than a T = 4 procapsid are presented.     

Adaptive significance and possible origin of B-chromosomes in Picea Glauca (moench.) voss = P.canadensis B.S.P

The karyotype (2n = 24 + 1B) was detected in 8 trees of Picea glauca (Moench.) Voss. = P. canadensis B.S.P., and the karyotype (2n = 24) was detected in 2 trees of spruce from the same stand in the centre of Voronezh. The majority of seeds, collected from these trees, were empty. From 150 selected seeds, which were full, four plantlets were obtained. One of them died, another one had no mitotic figures, and the third and fourth plantlets had karyotypes (2n = 24 + 1B, and 2n = 24, respectively). A possible mechanism of formation of B-chromosomes and their adaptive role are discussed.     

Different responses to changes in phosphorus,P, among lakes. A study of slopes in chl-a = f(P) graphs

The least squares estimator of a linear regression coefficient _L will give an overall expression for the change in with x. In fresh water ecology, however, subgroups, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiuaSGaci% 4Aaaaa!37BE!\[P\operatorname{k}\], of a parent population may have slopes which differ from the overall slope, _L. By constructing frequency histograms for the set of angles: Arctang % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaci4uaSGaam% yAaiaadQgaaaa!38AE!\[\operatorname{S} ij\],% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaci4uaSGaam% yAaiaadQgaaaa!38AE!\[\operatorname{S} ij\]= para sa y and x% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaaiikaiaadM% faliaadMgakiabgkHiTiaadMfaliaadQgakiaacMcacaGGVaGaaiik% aiaadIhaliaadMgakiabgkHiTiaadIhaliaadQgakiaacMcaaaa!42F0!\[(Yi - Yj)/(xi - xj)\], i < j, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiEaSGaam% yAaOGaeyiyIKRaamiEaSGaamOAaaaa!3BAB!\[xi \ne xj\], peaks in the distribution may be identified and related to ecological phenomenon. To identify peaks we fit Gaussian distributions to the frequency histograms. For a set consisting of 142 observations of chlorophyll-a and total phosphorus (nutrient) concentrations (TP) from 16 lakes we found four Gaussian peaks corresponding to four subgroups, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiuaSGaci% 4Aaaaa!37BE!\[P\operatorname{k}\]k = 1,4. One group identified a response of chl-a to changes in TP which correspond approximately to the average slope found by least square regression (the slope was 0.49). The second group consisted of steeper response than the average (1.28). A third group showed that there is an enhanced proportion of cases where chl-a does not respond to TP (zero slope, all the three deep lakes > 10 m, included in the date set contributed to this group). The size of the last group, spanning a wide range of slopes, suggested that about 30% of the inter annual changes in chl-a is unrelated to TP. The results are compared to result obtained by simple least squares regression and to the Theil non-parametric slope estimator.     

Effect of chronic hypoxia (Fi02 = 0.06 - Fi02 = 0.08) on mouse liver cytochrome P450 and b5 content]

During a eight days period of chronic hypoxia (FiO2 : 0,06) the cytochrome P 450 content of mice'liver decreases the 1st day, increases the 2nd and the 3rd day and decreases again and remains at a low levels. During a 13 days period of chronic hypoxia (FiO2 = 0,08) the P 450 level remains inchanged during 5 days. It decreases after until the 13teen day. G6Pase, an endoplasmic reticulum enzyme marker is quite inchanged in these conditions.     

实时荧光定量检测中国实验用小型猪肝脏CYP3A29 mRNA表达水平

CYP3A29是猪肝脏最重要的药物代谢关键酶。研究中国实验用小型猪肝脏CYP3A29 mRNA的表达特性对于评估其是否适宜于作为人CYP3A4介导的药理学研究动物模型具有一定意义。以b-actin作校正, 利用TaqMan定量技术对巴马香猪、贵州小型香猪肝脏CYP3A29 mRNA表达水平进行检测, 并以荣昌猪作为对照。结果表明, 巴马香猪、贵州小型香猪、荣昌猪肝脏CYP3A29 mRNA表达水平与报道的人肝脏CYP3A4相近; 三品系(种)猪间肝脏CYP3A29 mRNA表达水平较为接近, 但品系(种)内个体间变异较大。提示巴马香猪、贵州小型香猪作为药物评价的实验动物具有一定可行性。     

Rapid-equilibrium rate equations for the enzymatic catalysis of A+B=P+Q over a range of pH

This article shows how pKs for the enzymatic site and enzyme-substrate complexes can be obtained from kinetic experiments on the reaction A+B=P+Q, with and without the consumption of hydrogen ions. The rapid-equilibrium rate equation makes it possible to obtain the pKs and chemical equilibrium constants involved in the mechanism, the apparent equilibrium constant K' for the catalyzed reaction, and the number of hydrogen ions consumed in the rate-determining reaction. Experimentally-determined Michaelis constants can be adjusted for the pKs of the substrates A, B, P, and Q so that it is easier to obtain the pKs of E, EA, EB, EAB, EQ, and EPQ, and the chemical equilibrium constants. Reaction rates are discussed for the forward reaction ordered A+B=ordered P+Q with zero, one, or two hydrogen ions consumed in the rate-determining reaction and for random A+B=ordered P+Q with zero, one, or two hydrogen ions consumed in the rate-determining reaction. When hydrogen ions are consumed in the rate-determining reaction, there is a new factor 10(n)(pH) in the rate equation, where n is the number of hydrogen ions consumed in the rate-determining reaction for the forward reaction. The integer n can be obtained from rate measurements over a range of pH, but it cannot be determined from thermodynamic measurements.     

NMR experiments for the rapid identification of P=O···H–X type hydrogen bonds in nucleic acids

Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.     

Theoretical insights into the trends in molecular properties of HCY, HSiY and HGeY molecules where Y = N, P, As

To obtain insights into the factors that govern the analogy between HCN and its isostructures, HXY where X = C, Si, Ge and Y = N, P, As, the electronic and structural properties of these species in ground, cationic and anionic states at the QCISD, MP2 and B3LYP levels with 6-311++G** basis set and the first exited state with TD-B3LYP method have been presented. The results suggest that there are some correlations between structural and thermodynamic properties of the smallest member of this group (HCN) and heavier congers. The results of computation at these levels also predict the stability of HCAs in the ground state and HCN, HSiN and HGeN in the cationic state from the energetic point of view. Molecular electrostatic potential map inspection shows that in HXN species nucleophilic region positions on N atom but in HXP and HXAs molecules by increasing the size of central atom nucleophilic region shifts from region near X atom toward terminal atom. Finally, the nature of bonds of HXY moleculs are systematically studied through atoms in molecules (AIM) and natural bond orbital analyses (NBO).     

The three proline residues (P25, P242, and P434) of <Emphasis Type="Italic">Agrobacterium</Emphasis> CP4 5-enolpyruvylshikimate-3-phosphate synthase are crucial for the enzyme activity

Multiple sequence alignments showed that the prolines at the 25th, 129th, 153rd, 242nd, 322nd, and 434th amino acids in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 are strongly conserved in various prokaryotic EPSPS proteins. Single point mutations of the conserved prolines to alanine (P25A, P153A, P242A, P322A, and P434A) were introduced in the CP4 EPSPS in order to investigate the importance of the conserved prolines for the enzyme properties. The point mutations caused decreases in substrate binding affinity and catalytic efficiency as well as the glyphosate resistance, in general. Especially, the 25th and 242nd prolines located in the polypeptide hinges connecting top and bottom domains of CP4 EPSPS as well as the 434th proline at the C-terminus of the enzyme turned out to be crucial for the enzyme activity.