A p.m.r. isotope-exchange method for studying the kinetic properties of dehydrogenases in intact cells.

A method to determine the activity of dehydrogenases in an intact-cell system is described. The method involves the use of n.m.r. to monitor bulk isotope exchange. The approach is illustrated by application to the isotope equilibration of pyruvate and lactate as catalyzed by lactate dehydrogenase in intact erythrocytes. Particular problems peculiar to bulk isotope exchange and its observation by n.m.r. are considered.     

Rat-liver cholesterol 7 alpha-hydroxylase. 1. Development of a new assay based on the enzymic exchange of the tritium located on the 7 alpha position of the substrate.

A new assay is described to measure the activity of cholesterol 7alpha-hydroxylase and compared to the conventional 14C method used by other investigators. This method is based on the mechanism of the enzymic hydroxylation, i.e. a direct and stereospecific substitution of the 7alpha-hydrogen by a hydroxyl group. [7alpha-3H]Cholesterol is incubated at 37 degrees C and in the presence of molecular O2, in a medium buffered by postassium phosphate at pH 7.4 and containing liver microsomes (or 9000 X g supernatant), NADPH, MgCl2 and cysteamine. Tween-80 (1.5 mg/ml) is used to introduce enough substrate (300 muM) in the incubation mixture to saturate the enzyme (Km = 100 muM). Under these conditions the tritiated water released into the incubation medium reflects accurately the enzymic activity. The results obtained with this method are similar to the one obtained with a [4-14C]cholesterol technique (r = 0.96; P less than 0.001). The main advantage of the [7alpha-3H]cholesterol method is a complete independence from further metabolism of the first enzymic product, the 7alpha-hydroxycholesterol, the tritiated water representing the entire cholesterol 7alpha-hydroxylase activity.     

Improvement of the micromethod for the limulus lysate test.

Frauch's micro-slide method was improved to facilitate the endpoint-determination of the Limulus test. Two precise observations, by inverted phase contrast microscopy and with a staining procedure, were newly performed as additions to the slide test. The staining procedure was proposed as an improved method for the Limulus test since it is simple and convenient. In the staining method, bromophenol blue (BPB) solution was used as the staining solution. A negative (-), a strong positive (++) and a weak positive reaction (+) were characterized by a "ring" formation, a "cloud-like" spread of gel and a "spot" in the "cloud" respectively. Since the distinction between (-) and (+) reactions was obvious in the proposed method, determination of the endpoint was easier than in the ordinary tube and Frauch's method. The sensitivity of the present method was equal to or higher than that of other methods. Inverted phase contrast microscopy was utilized to confirm the findings obtained by the staining method. The volume of the lysate used in this method was as little as 1/10 of that used in the tube method.     

Chloroplast Genetics of Chlamydomonas. III. Closing the Circle

A novel mapping procedure is presented for organelle genes or any other genetic system exhibiting a measurable frequency of exchanges occurring at a constant rate over a measurable time interval. For a set of markers in a multiply-marked cross, the exchange rates measure relative map distances from a centromere-like attachment point.With this method, we present mapping data and a linear map of genes in the chlcroplast genome of Chlamydomonas. The data are plotted as log (percent remaining heterozygotes) against time and map distances are taken as proportional to slope.A statistical method which is an adaptation of jackknife methodology to a regression problem was developed to estimate slope values. A single line is fitted to pooled data for each marker from several crosses, and then lines are re-fit to a series of pooled data sets in each of which the observations from a single cross have been omitted. From these data sets a final summary slope is computed as well as a statement of its variability. The relative positions of new markers present in single crosses can then be estimated utilizing data from many crosses. The method does not distinguish between one-armed and two-armed linear or circular maps. However, evaluation of this map in conjunction with cosegregation frequency data (Sager and Ramanis 1976b) provides unambiguous evidence of the genetic circularity of the Chlamydomonas chloroplast genome.     

On the analysis of circular dichroic spectra of proteins.

A new method is presented for analyzing circular dichroism spectra. The method employs integrals over the data and calculates the alpha-helical, beta-sheet, and random coil content of the proteins from such integrals. It is shown that the analyzed alpha-helical content is usually reliable to within 5%, beta-sheet values are somewhat less reliable, and random coil values are least reliable. Curve fitting techniques are shown to be misleading. The method has a number of advantages over existing procedures.     

Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil

The scanning simulation method suggested by Meirovitch is extended to a study of the stability of decaglycine at 100 and 300 K. The model is based on the potential energy function ECEPP (Empirical Conformational Energy Program for Peptides) with rigid geometry and without solvent. The free energy of the statistical coil, which is defined over the whole phase space excluding the region of the right-handed α-helix, is calculated. At 100 K, the molecule is found to be unstable in the statistical coil region, and the method generates (i.e., “folds”) conformations that are left-handed or right-handed α-helices with very high preference. Their free energy is found to be comparable with that obtained by another method developed in our previous paper (paper I) [H. Meirovitch, M. Vásquez, and H. A. Scheraga, (1987) Biopolymers 26 , 651–671]. At 300 K the statistical coil becomes the most stable state; sample conformations of the coil are generated efficiently with the scanning method and the free energy is calculated. It appears that both the scanning method and the method of paper I can be used to carry out a complete analysis of the stability of a polypeptide based on free energy considerations.     

Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models

A two-stage Brownian dynamics simulation method is used to study the diffusion-influenced bimolecular reaction between superoxide and superoxide dismutase (SOD). The crystal structure of the dimeric enzyme is used in constructing detailed topographical and electrostatic models. Several electrostatic models are considered. In the most realistic, the excluded volume of the protein, which is impermeable to penetration by mobile ions, is assigned a dielectric constant of 2 and the surrounding “solvent” is assigned a value of 78. A finite difference method is used to solve the linearized Poisson–Boltzmann equation. For native SOD, the simulations reproduce the pronounced salt dependence of the rate constant observed experimentally. This salt dependence is attributed to electrostatic interactions between enzyme and substrate that are inherently attractive and amplified by the low dielectric constant of the protein interior. The simulation method is also applied to a modified enzyme, acylated SOD.     

The two-wavelength method of microspectrophotometry. II. A set of tables to facilitate the calculations

The calculations required for two-wavelength measurements are time consuming and laborious. In order to circumvent this limitation of the method, a set of tables which combined four operations into one has been designed and is reproduced within. The tables are based on Patau's formulae. The two transmission readings obtained according to the photometric method provide the coordinates which lead directly to a value for the relative absorbance. The product of this absorbance and the area of the photometric field gives the relative amount of chromophore in the field. The range of transmission values covered in the table corresponds to the effective range of the two-wavelength method.     

Computation of the electrophoretic mobility of proteins.

A scheme is presented for computing the electrophoretic mobility of proteins in free solution, accounting for the details of the protein shape and charge distribution. The method of Teubner is implemented using a boundary integral formulation within which the velocity distribution, the equilibrium electrical potential around the molecule, and the potential distribution due to the applied field are solved for numerically using the boundary element method. Good agreement of the numerical result is obtained for spheres with the corresponding semi-analytical specialization of Henry's analysis. For protein systems, the method is applied to lysozyme and ribonuclease A. In both cases, the predicted mobility tensors are fairly isotropic, with the resulting scalar mobilities being significantly smaller than for spheres of equal volume and net charge. Comparisons with previously published experimental results for ribonuclease show agreement to be excellent in the presence of a net charge, but poorer at the point of zero charge. The approach may be useful for evaluating approximate methods for estimating protein electrophoretic mobilities and for using electrophoretic measurements to obtain insight into charge distributions on proteins.     

Synthesis of the human insulin gene. Part III. Chemical synthesis of 5'-phosphomonoester group containing deoxyribooligonucleotides by the modified phosphotriester method. Its application in the synthesis of seventeen fragments constituting human insulin C-chain DNA.

A method for phosphorylating a protected deoxyribooligonucleotide containing phosphotriester linkages is described. The modified phosphotriester method of chemical synthesis is further refined in terms of (i) better final deblocking conditions and (ii) new chromatography solvent systems containing acetone-water-ethyl acetate to yield pure oligomers. The effectiveness of these improvements has been demonstrated in the rapid and efficient synthesis of seventeen fragments constituting the sequence of human insulin C-chain DNA.     

Compartmentalizing the S period.

In order to increase the resolution of interphase analysis we have developed a method which is an alternative to cytofluometric techniques for tissues where cell flow is not applicable. The method combines the estimation of cell frequency in G1, S, G2 and mitosis after a 3H-thymidine pulse with the grouping of interphase cells according to their DNA content, as estimated by cytophotometry in Feulgen stained nuclei. By superimposing both sets of data we get three different artificial compartments within the S period. As a biological test of the resolution reached, the method readily confirmed that hydroxyurea, after one cycle time, accumulates cycling cells of Allium cepa L. root meristems in early S.     

On the standardisation of the twinning rate.

In many studies the twinning rate, being strongly dependent on maternal age (and parity), has been standardised according to the maternal age distribution. The direct method requires very informative twinning data for the target population. The indirect method is used when the data for the target population is not sufficiently informative or when the target population is small. We have earlier introduced an alternative indirect technique for standardising the twinning rate. Our technique requires even less of the twinning data. Besides maternal age, parity is an influential factor, and should, if possible, be taken into account. In this study we present the traditional standardisation methods based on both maternal age and parity, we propose a new direct standardisation method and we develop our standardisation methods so that they take into account both maternal age and parity. We apply these standardisation methods to data from Finland, 1953-1964, from St. Petersburg, Russia, 1882-92, from Canada 1952-1967, and from Denmark, 1896-1967. These methods all give results very similar to those for the Finnish data, but the effect of parity is strongest with the direct methods. This may be due to the fact that, among extramarital maternities, parity has a strongly increasing effect on the twinning rate. This may be attributed to a higher reproduction capacity among unmarried mothers. Standardisations of the Canadian and the Danish data also give reliable results. With the St. Petersburg data, however, the different standardisations show notable discrepancies. These discrepancies are compared with Allen's findings.     

On the computation of the tertiary structure of globular proteins. III. Inter-residue distances and computed structures

An analysis of geometrical models for computing the tertiary structure of globular proteins from the primary structure is presented. The roles of initial configuration, input information on inter-residue distances and the errors in this information are delineated. It is shown that for local information like that on secondary structure, the calculated structure is very sensitive to errors and to the initial configuration. Thus, such information is far from adequate for predicting the tertiary structure. On the other hand, global information on all the inter-residue distances is quite insensitive to errors. A semi-empirical method is presented to estimate these distances and the calculated structures are given for two proteins—pancreatic trypsin inhibitor and parvalbumin. These structures have good resemblances to those determined by X-ray diffraction. A strategy for further refinement of the method is indicated.     

Comparison of lethal mutations of Drosophila melanogaster with D. simulans when detected by the attached-X method.

The purpose of this study was to evaluate the attached-X method compared with the standard Basc method, and, using this method, to find out whether the observed differences in genetic polymorphisms are related to differences in lethal mutation rates in D. melanogaster and D. simulans. When EMS-treated Drosophila melanogaster males are mated to untreated attached-X females, a decrease in the progeny sex ratio (male/female + male) is observed due to the induced lethal mutations on the X chromosome. The decrease in the frequency of male progeny were shown as the attached-X index. The expected male number is calculated from the control sex ratio. The difference between the expected and the observed male numbers, expressed as the ratio to the expected male number, defines the attached-X index. The index values for various EMS concentrations were compared to the lethal frequencies obtained by the standard Basc method for the same EMS treatments, and gave a highly positive correlation (gamma = 0.993, p < 0.01, d.f. = 2), thus providing an alternative method for evaluation of possible mutagens. The attached-X method was applied to D. simulans, of which natural populations are known to have relatively low genetic variation, and frequencies of the EMS-induced X chromosome lethal mutations were estimated and compared with those in D. melanogaster. The results indicate that D. melanogaster is slightly more sensitive in the sperm and spermatogonial stages, but less susceptible in the spermatid stage when compared with D. simulans.(ABSTRACT TRUNCATED AT 250 WORDS)     

条形柄锈菌小麦转化型夏孢子表面微观结构观测方法的建立

小麦条锈菌夏孢子表面微观结构的研究,对于夏孢子的萌发生长以及对条锈菌致病性的研究都具有很重要的意义。本研究以小麦条锈菌32号生理小种（CYR32）为材料,创新的采用硅片为基质,建立了利用原子力显微镜检测夏孢子样品表面的观测方法。结果表明,该方法优于其他基质材料,可以获得较为理想的扫描效果。为进一步研究小麦条锈菌夏孢子以及相近大小的病原体孢子表面特征提供了技术支撑。     

Theoretical studies on the conformation of saccharides. XIV. Structure and conformational properties of the glycosylamines

The 2-methylaminotetrahydropyran was used as a model to study conformational properties of the N-glycosidic linkage in glycosylamines. Relaxed two-dimensional conformational (phi, psi) maps in 20 solvents were calculated by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. Molecular geometry optimization has been carried out for each conformer using the quantum chemical method PCILO. The calculated variations of the geometry are consistent with the results obtained by the statistical analysis of available experimental data retrieved from the Cambridge Structural Database. The calculated abundances of conformers show that the polarity of the solvent has little effect on the anomeric ratio, and the form having the methylamino group equatorial is favored in all considered solvents.     

Non-specificity of a colorimetric method for the estimation of N-acetyl-D-glucosamine.

The colorimetric method of Reissig et al. for the estimation of N-acetylamino sugars, is often used as a specific method for the quantification of the N-acetyl-D-glucosamine. Although this assay is more sensitive to the monomer, it recognizes all soluble N-acetyl-D-glucosamine oligomers. This result is very important because this method is extensively used in biology for the estimation of chitinolytic activity.     

Protamines. III. Synthesis of the tetradecapeptide corresponding to the C-terminal sequence 52--65 of galline.

The synthesis of peptides containing blocks of arginyl residues is proposed through amidination of the corresponding ornithyl analogs. In order to test this strategy the ornithyl analog of the C-terminal sequence 52--65 of galline was synthesized by the conventional method. The amidination reaction, performed on fragments of different length and ornithyl-residue content, quantitatively converts ornithines into arginines. The strategy proposed may represent a powerful tool for the synthesis of protamines and other basic proteins.     

Application of splines to the calculation of bacterial swimming speed distributions.

A new method of extracting information about bacterial speeds from photon correlation spectroscopy is presented. This method has the advantage that an estimation of the translational speed distribution is directly varied so as to achieve a best least-squares fit to the experimental autocorrelation function. The theory of spline approximations to continuous functions is briefly outlined. The importance of the previously disregarded diffusional component of bacterial motion is discussed. Experimental data from Salmonella at a low scattering angle is analyzed by this method of spline approximation and the distribution of translational speeds is obtained.