Microhydrodynamics simulation of protein crystallization. I. Static calculations.

A computer simulation method is proposed to study the effects of hydrodynamic interactions on protein crystallization. It is a combination of Stokesian dynamics and continuum hydrodynamics and is referred to as "microhydrodynamics." The method is checked against analytical expressions for Stokes drag and diffusion coefficients for unit spheres. For a number of protein molecules the diffusion coefficients have been calculated and compared with experimental values. It is shown that the method works well for stationary calculations. Using dynamical calculations interacting protein molecules will be simulated to study the events in the early stages of protein crystallization.     

Estimation of polyhydroxy alcohols in fermentation broths. 2. Quantitative analysis based on t.l.c/f.i.d

A simple and rapid method for the quantitative analysis of polyhydroxy alcohols in fermentation broths has been developed. The method is based on thin layer chromatography (t.l.c.) coupled with a flame ionization detector (f.i.d.) and has been found to be useful in the screening of cultures for fermentative glycerol production.     

Torsional relaxation for biopolymers.

We describe a method for making natural, physical movements in a chained polymer by sequentially adjusting a few neighboring torsion angles in the polymer backbone. In addition to being very fast and easy to implement, the method is also very general. It applies equally well to proteins and nucleic acids. This method is then used to design a local refinement procedure. We test the refinement procedure on the minimization of a simple energy function for proteins. The energy function has a simplified potential for hydrophobic interaction, a hydrogen-bond term, and a term for van der Waals interaction. There is considerable current interest in such simple energy functions for protein folding. When applied to refine structures found by a global search method, the refinement is able to produce large reduction in the hydrogen-bond term and the van der Waal term of the energy. We conclude that the method is particularly effective in finding good "packing" of residues in an initially compact conformation.     

An h.p.l.c. assay for protoporphyrinogen oxidase activity in rat liver.

An h.p.l.c. method is described for the assay of protoporphyrinogen oxidase activity in rat liver. A relatively pure protoporphyrinogen IX substrate was obtained by selectively removing any protoporphyrin IX unreduced by sodium amalgam on a small disposable cartridge packed with a strong anion-exchanger. The protoporphyrin IX formed was extracted with dimethyl sulphoxide/methanol (3:7, v/v) containing mesoporphyrin as the internal standard for separation and quantification by reversed-phase chromatography. The Km for protoporphyrinogen was 9.5 +/- 1.6 microM, and the enzyme activities were 0.59 +/- 0.11 nmol of protoporphyrin IX produced/min per mg of mitochondrial protein and 33.5 +/- 2.7 nmol protoporphyrin IX produced/min per g of liver tissue homogenate. The method is applicable to the determination of enzyme activity in small amounts of human liver biopsy.     

Questions and Answers about C. P. S

Several patients with poliomyelitic paralysis of the muscles used in normal breathing learned a method of breathing consisting of pumping air into the lungs by action of the mouth, cheeks, tongue, pharynx and larynx.The advantages of the method are that the patient can be out of the respirator and on a conventional bed for longer periods, can talk longer and louder, is more easily cared for, and is better able to engage in interesting occupations.     

Purification of cardiac myosin. Application to hypertrophied myocardium.

A method is described for the preparation of high purity myosin from small amounts of cardiac muscle. The method employs homogenization and prolonged extraction of the cardiac tissue. Purification is achieved through three successive precipitation-dissolution cycles and without the use of column chromatographic techniques. Purity of the myosin preparation is assessed at various stages of the purification procedure by sodium dodecylsulfate-acrylamide gel electrophoresis and by measurement of RNA and nucleoprotein content. With 1.5-2.0 g of rabbit right ventricle as the starting tissue, this method yields 4-6 mg myosin per g wet tissue. The method is also shown to give similar results with rabbit right ventricles hypertrophied by pulmonary stenosis.     

Questions and Answers about C. P. S

Several patients with poliomyelitic paralysis of the muscles used in normal breathing learned a method of breathing consisting of pumping air into the lungs by action of the mouth, cheeks, tongue, pharynx and larynx. The advantages of the method are that the patient can be out of the respirator and on a conventional bed for longer periods, can talk longer and louder, is more easily cared for, and is better able to engage in interesting occupations.     

Interactions between arginine-rich histones and deoxyribonucleic acids. I. Thermal denaturation.

Physical properties of histone-DNA complexes very often depend upon the method of complex formation. In an attempt to make the studies of histone-DNA interactions more relevant to biological systems, results from thermal denaturation of native chromatin were used as references for determining how closely a given histone-DNA complex approaches its native state in chromatin. In the case of arginine-rich histones H3 (III or f3) and H4 (IV or f2a1), four methods were used for making complexes with calf thymus DNA: (A) NaCl gradient dialysis with urea; (B) NaCl gradient dialysis without urea; (C) direct mixing in 2.5 x 10(-4) EDTA, pH 8.0; and (D) direct mixing in 0.01 M sodium phosphate, pH 7.0. It was observed that a complex made by direct mixing in phosphate (method D) is closer to the native than is one made by direct mixing in EDTA (method C) than the one made by gradient dialysis with urea (method A) or without urea (method B). Regardless of the method used for complex formation, no substantial differences were observed between complexes with histone H3 dimer with disulfide bond(s) and a reduced H3 without disulfide bond, implying that perhaps a dimer with or without disulfide bond is a natural fundamental subunit in our experimental conditions. When the method of direct mixing in EDTA is used, the melting properties of the complexes vary only slightly with any one of the following H3 histones: from calf thymus, H3 without disulfide bond, H3 dimer, and H3 oligomer with disulfide bonds, also, from duck erythrocyte, H3 monomer and dimer. The complexes formed between DNA and a mixture of H3 and H4 by method D have melting properties similar to those of native chromatin. Since an equimolar mixture of histone H3 and H4 in 0.01 M phosphate, pH 7.0, was shown to form a tetramer (D'Anna, J.A., and Isenberg, I. (1974), Biochem. Biophys. Res. Commun. 61, 343), our results suggest that, a tetramer of H3 and H4, likely to be (H3)2(H4)2, formed from one H3 dimer and one H4 dimer, can bind DNA in a manner similar to that in native chromatin.     

A new spectrophotometric assay for enzymes of purine metabolism. II. Determination of guanase activity.

A new method for the determination of guanase is described. Xanthine, the product of the guanase reaction, is oxidized by xanthine oxidase, forming uric acid and hydrogen peroxide. Hydrogen peroxide is further reduced to water by catalase in the presence of ethanol. The acetaldehyde formed in this reaction step is dehydrogenated NAD or NADP dependent by aldehyde dehydrogenase. The NADH or NADPH production is measured and utilized for the calculation of the guanase activity. The sensitivity of the method can be doubled by the addition of uricase, which oxidizes uric acid to permit the formation of another mole of hydrogen peroxide.     

Disequilibrium Pattern Analysis. I. Theory

We have developed a method, disequilibrium pattern analysis, for examining the disequilibrium distribution of the entire array of two locus multiallelic haplotypes in a population. It is shown that a selected haplotype will produce a distinct pattern of linkage disequilibrium values for all generations while the selection is acting. This pattern will also presumably be maintained for many generations after the selection event, until the disequilibrium pattern is eventually broken down by genetic drift and recombination. Related haplotypes, sharing an allele with a selected haplotype, assume a value of linkage disequilibrium proportional to the frequency of the unshared allele and have a single negative value of the normalized linkage disequilibrium. The analysis assumes zero linkage disequilibrium for all allelic combinations initially. The same basic results continue to apply if the selection involves a new mutant, the occurrence of which creates linkage disequilibrium for some haplotypes. The disequilibrium pattern predicted under selection is robust with respect to the influence of migration and random genetic drift. This method is applicable to population data having linked polymorphic loci including that determined from protein or DNA sequencing.     

Fast approximate motif statistics.

We present in this article a fast approximate method for computing the statistics of a number of non-self-overlapping matches of motifs in a random text in the nonuniform Bernoulli model. This method is well suited for protein motifs where the probability of self-overlap of motifs is small. For 96% of the PROSITE motifs, the expectations of occurrences of the motifs in a 7-million-amino-acids random database are computed by the approximate method with less than 1% error when compared with the exact method. Processing of the whole PROSITE takes about 30 seconds with the approximate method. We apply this new method to a comparison of the C. elegans and S. cerevisiae proteomes.     

The azure dyes: their purification and physicochemical properties. II. Purification of azure B.

A method is described for the purification of the dye azure B in quantities sufficient for biological staining experiments on a larger scale. The method is based on the use of column chromatography. Two columns are employed. In column A with silica gel as adsorbent the azure B fraction is isolated from a suitable substrate ('technical' azure B gained by a modification of Bernthsen's synthesis of methylene blue, or polychrome methylene blue) using an acetate-formate mixture as eluent. In column B, on an Amberlite polymeric adsorbent (XAD-2) the acetate-formate anions are exchanged in chloride. Regeneration of both columns is possible: KMnO4, Na2S2O4 and water are run through column A; 5% NaOH, methanol and water through column B. Purification of azure B on economic terms is thus attained. The opinion is expressed that this method is also applicable to the purification of other cationic dyes.     

Thermodynamic investigations of proteins. I. Standard functions for proteins with lysozyme as an example.

A direct method is proposed for obtaining thermodynamic standard functions for native and denatured proteins using experimental data from scanning calorimetry, isothermal calorimetry and potentiometric titrations. The possibility of this approach is demonstrated on the example of lysozyme in the range of pH 1.5-7.0 and temperature 0-100 degrees C. Tests for the validity of the obtained functions of enthalpy and entropy are presented in the form of cyclic processes using experimental data obtained from thermodynamically different pathways. The Gibbs function is checked by comparison with results of an independent method. The methodic problems in determining and checking standard functions for proteins are discussed in detail.     

Capillary electrophoresis analysis of mangiferin extracted from Mangifera indica L. bark and Mangifera persiciformis C.Y. Wu et T.L. Ming leaves

The flavonoid compound mangiferin is found in the leaves, stem bark, fruit peels and root of Mangifera indica L. and in many other herbal species with many potential pharmacological properties. We have established an analytical method of mangiferin extracted from M. indica L. bark and Mangifera persiciformis C.Y. Wu et T.L. Ming leaves utilizing CZE. An electrolytic buffer containing 0.05 M borate buffer, pH 7.4 with methanol (1:0.3, v/v) was deemed suitable for mangiferin analysis. An ideal mangiferin electropherogram with a migration time at approximately 10.50 min was obtained. Repeatability tests showed that the R.S.D.s for both intra- and inter-day migration time and peak area for all manigferin sources tested were less than 4%. The linearity range of this method was 5-1000 microg/ml. The detection limit of this method was 1.5 microg/ml. Quantitative analysis of mangiferin was also performed with this method. The accuracy of quantitation at 10, 500 and 1000 microg/ml of control mangiferin were 99.00, 99.38 and 99.14%, respectively (n=10). The repeatability of quantitation (R.S.D.) was below 3%. Our results demonstrated that CZE is a simple and reliable method in mangiferin analysis and more studies are needed to detect other mangiferin resources, such as clinical biological samples, in pharmacology and pharmacokinetic studies.     

Solving complex photocycle kinetics. Theory and direct method.

A direct nonlinear least squares method is described that obtains the true kinetic rate constants and the temperature-independent spectra of n intermediates from spectroscopic data taken in the visible at three or more temperatures. A theoretical analysis, which is independent of implementation of the direct method, proves that well determined local solutions are not possible for fewer than three temperatures. This analysis also proves that measurements at more than n wavelengths are redundant, although the direct method indicates that convergence is faster if n + m wavelengths are measured, where m is of order one. This suggests that measurements should concentrate on high precision for a few measuring wavelengths, rather than lower precision for many wavelengths. Globally, false solutions occur, and the ability to reject these depends upon the precision of the data, as shown by explicit example. An optimized way to analyze vibrational spectroscopic data is also presented. Such data yield unique results, which are comparably accurate to those obtained from data taken in the visible with comparable noise. It is discussed how use of both kinds of data is advantageous if the data taken in the visible are significantly less noisy.     

Solid phase synthesis of polynucleotides. VI. Further studies on polystyrene copolymers for the solid support.

A simple solid phase method for the synthesis of oligodeoxyribonucleotides has been developed using the phosphotriester approach. Mononucleotide coupling units are sequentially added to the polystyrene copolymer with 1% divinylbenzene and two kinds of oligonucleotides, d(CACGACCCCTCCACGT) and d(AACTGGTATTACTGGGCG), are synthesized in a relatively high yield. One cycle of the mononucleotide addition is about 70 minutes, and this method is particularly suitable for the automation of the synthesis upon availability of an automatic synthesizer.     

Motif-based fold assignment.

Conventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence-based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the SwissProt annotation of the fold library. When combined with a simple SDP method, the coverage of MBA is comparable to the results obtained with PSI-BLAST. However, the set of the MBA predictions is significantly different from that of PSI-BLAST, leading to a 40% increase of the coverage for the combined MBA/PSI-BLAST method. The MBA approach can be easily adopted to include the results of sequence-independent function prediction methods and alternative motif and annotation databases. The method is available through the web server localized at http://www.doe-mbi.ucla.edu/mba.     

The two-wavelength method of microspectrophotometry. III. An extension based on photographic color transparencies

The two-wavelength method of microspectrophotometry corrects for distributional error and measures the amount of absorbing material by taking advantage of certain spectral characteristics of the specimen. Under certain circumstances, such as the absorption of nucleic acids in the ultraviolet and of black or multiple stains in the visible, the spectral characteristics are not suitable for the application of the method. To circumvent this, a photomicrograph of the object is taken with monochromatic light of a suitable wavelength. A second plate is exposed as a contact print of the photomicrograph and is developed in the presence of a coupling agent. After bleaching and fixation, the positive appears as a monochromatic color transparency. Two-wavelength analysis of such a transparency can be made in terms of the new color. The measurements will be free of distributional error and can be equated to the original object. The necessary formulae are derived, and a method which has proven suitable for color development is given. The photographic and the direct two-wavelength method were found to give equivalent results when both were used on the same series of liver nuclei. The application of the photographic method to ultraviolet absorption has been demonstrated. The new method is potentially applicable to other types of photographic densitometry involving heterogeneous images.     

A new spectrophotometric assay for enzymes of purine metabolism. I. Determination of xanthine oxidase activity.

A new method for the determination of xanthine oxidase activity with xanthine or hypoxanthine is described. The hydrogen peroxide produced by the oxidation of the substrates is reduced by catalase in the presence of high concentrations of ethanol. The acetaldehyde formed is further oxidized by aldehyde dehydrogenase NAD or NADP-dependent. The reduction rate of the coenzymes were measured at 334 nm and utilized as indicators for the xanthine oxidase. The sensitivity of the method with xanthine as substrate can be doubled by the addition of uricase, which oxidizes uric acid to allantoin.     

The affected sib method. III. Selection and recombination.

The affected sib-pair method has been used to investigate the mode of inheritance, and to estimate the "disease" allele frequency, for a number of HLA-associated diseases. One of the assumptions of the original sib-pair method is that the disease confers no selective disadvantage on affected individuals. This is obviously not the situation for most diseases. We have determined the expected HLA haplotype-sharing distribution among affected sib-pairs when selection against individuals with the disease is taken into account. We have shown that if the mode of inheritance of the selectively disadvantageous disease is recessive or additive, the original affected sib-pair analysis, ignoring selection, still estimates the true mode of inheritance, but usually yields an underestimate of the "disease" allele frequency. For intermediate and dominant models of disease predisposition, both the estimates of the degree of penetrance of the "disease" genotypes, and the "disease" allele frequency, are altered if selection is ignored in the analysis. Similarly, allowing for recombination between the "disease" locus and the HLA region does not affect the determination of the mode of inheritance of the disease if it is recessive or additive; in other cases, however, the estimate of the mode of inheritance is affected. The "disease" allele frequency is overestimated when nonzero recombination is ignored for all the modes of inheritance that have been studied.