The molecular surface package

The Molecular Surface Package is a reimplementation, in C, of a set of earlier FORTRAN programs for computing analytical molecular surfaces, areas, volumes, polyhedral molecular surfaces, and surface curvatures. The software does not do interactive molecular graphics, but it will produce pixel maps of smooth molecular surfaces. The polyhedral molecular surfaces are suited to display on graphics systems with real-time rendering of polyhedra.     

Yeast RNA partition accompanying adsorption in salt/PEG two-phase system

Summary Partitioning of yeast total RNA in a salt/PEG two-phase system, i.e., a potassium phosphate/PEG system and a ammonium sulfate/PEG system, was characterized with regard to the dependence on the molecular weights of PEG and RNA. The shift in RNA partitioning was investigated for a PEG molecular weight range from 300 to 20000. RNA was partitioned mainly to the top phase in the system with PEG of a molecular weight up to 1000, mainly at the interface or almost equally to both phases in the system with PEG of a molecular weight 1000–2000, and mainly to the bottom phase in the system with PEG of more than 2000 in a molecular weight . The effect of PEG molecular weight on partitioning of low molecular weight RNA, less than 5.8S molecule, was qualitatively similar to that of high molecular weight RNA, more than 17S molecule. However, partitioning of high molecular weight RNA was more one-sided than that of low molecular weight RNA. In the system with PEG1000–2000, remarkable adsorption of high molecular weight RNA at the interface was investigated; more than 90% of the high molecular weight RNA added was concentrated. Adsorption of RNA at the interface was quantitatively demonstrated as a novel example of adsorption of a soluble macromolecule in an aqueous two-phase system.     

Electron and X-ray microscopic analyses of reaggregated materials obtained after fractionation of dissolved sporopollenin

Summary Exines fromTypha angustifolia L. pollen were dissolved in hot 2-aminoethanol. The solubilisate was successively fractionated and reaggregated via a dialysis cascade with dialysis tubings of different exclusion volumina. Four fractions of reaggregated material with different molecular mass were obtained. Fraction 1 with a molecular mass above 25,000 Da, fraction 2 with a molecular mass between 10,000–25,000 Da, fraction 3 with a molecular mass between 5,000–10,000 Da, and fraction 4 of a molecular mass lower than 5,000 Da. The fractions were comparatively analysed by scanning and transmission electron microscopy and X-ray microscopy. The material of the fractions with a molecular mass above 10,000 Da exhibit high congruence to the initial material. Analysis of the reaggregated material with the lowest molecular mass revealed special distinct substructures which in form and size showed high similarities to substructures of exines described in literature. In detail, spherical substructures consisting of an electron-dense core surrounded by an electron-transparent corona and in addition elongated substructures with a distinctive surface sculpture were detected.Abbreviations SEM scanning electron microscopy - TEM transmission electron microscopy     

Rapid assessment of drug resistance of cancer cells to gefitinib and carboplatin using optical imaging

The overall goal of this study was to evaluate optical molecular imaging approaches to determine the drug response of chemotherapy and molecular targeted agents in drug sensitive and drug resistant cell lines. The optical molecular imaging approaches selected in this study were based on changes in intracellular uptake and retention of choline and glucose molecules. The breast cancer cell lines were treated with a molecular targeted anti-EGFR therapy. The bladder cancer cell lines were treated with a conventional chemotherapy approach. Sensitivity of optical molecular imaging approach was also compared with conventional cell viability and cell growth inhibition assays. Results demonstrate that optical molecular imaging of changes in intracellular uptake of metabolites was effective in detecting drug susceptibility for both molecular targeted therapy in breast cancer cells and chemotherapy in bladder cancer cells. Between the selected metabolites for optical molecular imaging, changes in glucose metabolic activity showed higher sensitivity in discrimination between the drug sensitive and drug resistant cell lines. The results demonstrated that optical molecular imaging approaches more significantly sensitive as compared to the conventional cell viability and growth assays. Overall, the results demonstrate potential of optical molecular imaging of metabolic activity to improve sensitivity of in-vitro drug response assays.     

The molecular weight of Ehrlich tumor cell ribonucleotide reductase and its subunits: Effector-induced changes

The molecular weights of Ehrlich tumor cell ribonucleotide reductase and its individual components were determined by sedimentation equilibrium in the Beckman Airfuge. The distribution of enzyme after sedimentation equilibrium was determined by measurement of the CDP reductase and ADP reductase activities associated with ribonucleotide reductase. The apparent molecular weight of the intact enzyme was 304,000 when assayed for CDP reductase and 254,000 when assayed for ADP reductase. This difference in apparent molecular weights was statistically significant with a P value of 0.0002. The molecular weights of the individual components of ribonucleotide reductase were determined in a similar fashion by assaying in the presence of an excess of the complementary component. The non-heme iron component had a molecular weight of 81,000 when assayed for either CDP or ADP reductase activity. The effector-binding component had an apparent molecular weight of 127,000 when assayed for CDP reductase and 95,000 when assayed for ADP reductase. This difference in apparent molecular weights was statistically significant with a P value of 0.004. The effectors ATP and dGTP altered the apparent molecular weights of the intact enzyme and individual components. In the presence of ATP the molecular weight of intact CDP reductase was 481,000 while the apparent molecular weight of the effector-binding component of CDP reductase alone was 418,000. In the presence of dGTP, the molecular weight of intact ADP reductase was 293,000 while the apparent molecular weight of the effector-binding component of ADP reductase alone was 154,000. These results indicate that the proportion of the non-heme iron component and the effector-binding component is not equimolar and that the composition of the enzyme is not constant but is altered by the presence of effectors. Our data also suggest that CDP reduction and ADP reduction are catalyzed by different molecular species of the enzyme which apparently have different effector-binding components.     

The effect of phenobarbital and amidopyrine on the rate of decomposition of isoforms of cytochrome P-450 in mouse liver microsomes

Separation of microsomal proteins in gradient polyacrylamide gel gives 60 protein bands. The molecular mass range of 48-58 kDa corresponding to cytochrome isozymes contains 7 bands for intact mice and 8 bands for phenobarbital-induced mice. Phenobarbital treatment causes both the appearance of a new cytochrome P-450 isozyme with a molecular mass of 56 kDa and the increase in the content of three isozymes with molecular masses of 54, 52.5 and 50 kDa. The half-life time of cytochrome P-450 isozymes in the livers of intact and phenobarbital-induced mice differs from 15 to 42 hours. Phenobarbital induction results in the breakdown acceleration of the isozyme with a molecular mass of 52.5 kDa and the breakdown retardation of the isozyme with a molecular mass of 54 kDa. Aminopyrine injections to phenobarbital-pretreated mice result in the breakdown acceleration of the cytochrome P-450 isozyme with a molecular mass of 56 kDa.     

Protein sorption with mineral colloids]

A study was made of the effect on sorption of the molecular weight of model proteins (ribonuclease with a molecular weight of 12 10(3), trypsin with a molecular weight of 24-10(3), bovine albumin with a molecular weight of 64-10(3) and gamma-globulin with a molecular weight of 160-10(3)) and dispersity of suspensions of aluminium hydroxide, aluminum phosphate and calcium phosphate used as biopreparation sorbents. The expediency of using phosphate and calcium phosphate used as biopreparation sorbents. The expediency of using for effective sorption of a definite area of sorption surface necessary and adequate for the distribution of protein macromolecules with the best degree of conformational liberty was revealed.     

Junin virus structural proteins.

Polyacrylamide gel electrophoresis of purified Junin virus revealed six distinct structural polypeptides, two major and four minor ones. Four of these polypeptides appeared to be covalently linked with carbohydrate. The molecular weights of the six proteins, estimated by coelectrophoresis with marker proteins, ranged from 25,000 to 91,000. One of the two major components (number 3) was identified as a nucleoprotein and had a molecular weight of 64,000. It was the most prominent protein and was nonglycosylated. The other major protein (number 5), with a molecular weight of 38,000, was a glucoprotein and a component of the viral envelope. The location on the virion of three additional glycopeptides with molecular weights of 91,000, 72,000, and 52,000, together with a protein with a molecular weight of 25,000, was not well defined.     

Molecular properties of a bent-core nematic liquid crystal A131 by multi-level theory simulations

ABSTRACT

Multi-level theory simulations have been performed to model a number of important molecular properties of a bent-core nematic liquid crystal (LC) A131. These important properties include molecular conformations, molecular Raman spectra, differential polarisability ratios, molecular crystals packing, atomic LC structures, order parameters, and Raman depolarisation spectra. The simulations contain four theory levels, involving molecular quantum chemistry, molecular crystal packing, super cell density functional based tight binding optimisation, and super cell molecular dynamics calculations. To heat initial optimised super cell structures, molecular dynamics simulations reveal phase transitions to uniaxial and biaxial nematic phases from molecular crystals. LC atomic structures result in direct calculations on order parameters, which can be further applied to computations on Raman depolarisation spectra with differential polarisability ratios, obtained in the molecular quantum chemistry theory level. The good agreement of simulated Raman depolarisation spectra with the experiment provides a detailed analysis on the unusually low values of experimental uniaxial order parameters.     

Refinement of the NMR structures for acyl carrier protein with scalar coupling data

Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.     

Subcellular localization of high- and low-molecular weight acid phosphatases from chicken liver

The subcellular localization of high and low molecular weight acid phosphatases in chicken liver was studied. The high molecular weight acid phosphatase is mainly associated with the particulate fraction, particularly with the mitochondrial-lysosomal fraction, whereas the low molecular weight form seems to be a soluble cytoplasmic enzyme. Biochemical properties including optimal pH, molecular weight determination and the effect of some modifier substances indicate that mitochondria-lysosomes and microsomes contain the same high molecular weight acid phosphatase form.     

Interaction of N-acylated and N-alkylated chitosans included in liposomes with lipopolysaccharide of gram-negative bacteria

The interactions of lipopolysaccharide (LPS) with the polycation chitosan and its derivatives — high molecular weight chitosans (300 kDa) with different degree of N-alkylation, its quaternized derivatives, N-monoacylated low molecular weight chitosans (5.5 kDa) — entrapped in anionic liposomes were studied. It was found that the addition of chitosans changes the surface potential and size of negatively charged liposomes, the magnitudes of which depend on the chitosan concentration. Acylated low molecular weight chitosan interacts with liposomes most effectively. The binding of alkylated high molecular weight chitosan with liposomes increases with the degree of its alkylation. The analysis of interaction of LPS with chitoliposomes has shown that LPS-binding activity decreased in the following order: liposomes coated with a hydrophobic chitosan derivatives > coated with chitosan > free liposomes. Liposomes with N-acylated low molecular weight chitosan bind LPS more effectively than liposomes coated with N-alkylated high molecular weight chitosans. The increase in positive charge on the molecules of N-alkylated high molecular weight chitosans at the cost of quaternization does not lead to useful increase in efficiency of binding chitosan with LPS. It was found that increase in LPS concentration leads to a change in surface ζ-potential of liposomes, an increase in average hydrodynamic diameter, and polydispersity of liposomes coated with N-acylated low molecular weight chitosan. The affinity of the interaction of LPS with a liposomal form of N-acylated chitosan increases in comparison with free liposomes. Computer simulation showed that the modification of the lipid bilayer of liposomes with N-acylated low molecular weight chitosan increases the binding of lipopolysaccharide without an O-specific polysaccharide with liposomes due to the formation of additional hydrogen and ionic bonds between the molecules of chitosan and LPS.     

DNA分子量标准制备技术：方法与进展

DNA分子量标准是一组分子量大小已知的DNA片段混合物,用于指示核酸电泳中未知样品的分子量大小,从而帮助实验人员判断DNA样品的性质。因而DNA分子量标准成为目前分子生物学和基因工程领域不可或缺的一种电泳耗材。综述了目前各种DNA分子量标准产品的制备方法和技术原理及近年来该领域的一些技术进展情况。     

From oligomers to molecular giants of soybean oil in supercritical carbon dioxide medium: 1. Preparation of polymers with lower molecular weight from soybean oil

Polymers with a low molecular weight derived from soybean oil have been prepared in a supercritical carbon dioxide medium by cationic polymerization. Boron trifluoride diethyl etherate was used as an initiator. Influences of polymerization temperature, amount of initiator, and carbon dioxide pressure on the molecular weight were investigated. It is shown that the higher polymerization temperature favors polymers with relatively higher molecular weights. Larger amounts of initiator also provide polymers with higher molecular weights. Higher pressure favors polymers with relatively higher molecular weights. The applications of these soy-based materials will be in the lubrication and hydraulic fluid areas.     

壳聚糖对植物病原细菌的抑制作用研究

本文通过测定最小抑制浓度和相对抑制率,观察了分子量和脱乙酰度对壳聚糖抑制植物病原细菌(胡萝卜软腐欧文氏菌Erwinia cartovara Var carotovara、油菜黄单孢菌绒毛草致病菌Xanthamonas campestris Pv holcicola、丁香假单孢菌黍致病变种Pseudomonas spyings Pv panici)作用的影响。结果表明：在一定范围内,随分子量和脱乙酰度的增大,壳聚糖的抑菌效果相应降低,而且各种病原细菌对不同,壳聚糖的敏感性也有很大差异。     

Lysozyme oligomers as a molecular mass standard for sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Egg white lysozyme treated with hypochlorous acid links together producing di-, tri-, tetra-, and pentameric derivatives with molecular masses ranging from 14,300 to 90,500. Similar oligomeric products may be obtained by treating lysozyme color derivatives produced by labeling lysozyme with fluorescein, trinitrobenzenesulfonic acid and 2,4-dinitrofluorobenzene, with hypochlorous acid. The oligomeric lysozyme derivatives thus obtained consist of a mixture of proteins with molecular masses equal to multiples of 14,300 (lysozyme molecular mass). This mixture can be applied as a set of molecular mass standards suitable for determination of protein molecular masses on sodium dodecyl sulfate-polyacrylamide gel electrophoresis.     

VESICLE SIZE,SIZE DISTRIBUTION,STABILITY, AND RHEOLOGICAL PROPERTIES OF LIPOSOMES COATED WITH WATER-SOLUBLE CHITOSANS OF DIFFERENT MOLECULAR WEIGHTS AND CONCENTRATIONS

The objectives of this study were to explore the effects of coating with water-soluble chitosans of different molecular weights and concentrations on vesicle size, size distribution, stability, and apparent viscosity of liposomes. The results indicate that the vesicle size of liposomes coated with different concentrations and different molecular weights of water-soluble chitosans decreased with increasing passes of microfluidizing treatment, then reached a constant value. Liposomes subjected to the same microfluidization treatment were larger for those coated with a higher concentration (of the same molecular weight chitosan) or coated with a lower molecular weight (at the same concentration) of water-soluble chitosans. The average particle size of liposomes coated with different molecular weights of water-soluble chitosans decreased with increasing number of passes of microfluidizing treatment. The apparent viscosity of liposomes coated with water-soluble chitosans decreased after the first pass, then reached a constant value after the third pass of microfluidizing treatment. Apparent viscosities of liposomes subjected to different passes of microfluidization treatment were larger for those coated with a higher concentration or a higher molecular weight of water-soluble chitosans. Liposomes coated with 0.5% of different molecular weights of water-soluble chitosans behaved as pseudoplastic fluids. At the same shear rate, the apparent viscosities of liposomes subjected to more passes of microfluidizing treatment were larger than those subjected to fewer passes of microfluidizing treatment. Liposomes coated with water-soluble chitosans are more stable than those without a coating.     

Eukaryotic ribosomal proteins. Molecular weights of proteins from rabbit liver subunits.

The molecular weights of the proteins from rabbit liver ribosomal 40 S and 60 S subunits were determined after preliminary separation of these proteins by two-dimensional electrophoresis: each spot present in the polyacrylamide slab was cut off, eluted and rerun in a SDS one-dimensional polyacrylamide gel. The molecular weights range from 9,000 to 35,000 with a number-average molecular weight of 19,600 for the 40 S proteins, and from 9,400 to 52,000 with a number-average molecular weight of 23,600 for 60 S proteins.     

Interconversion of different molecular weight forms of human erythrocyte orotidylate decarboxylase.

Orotidylate decarboxylase has been purified approximately 300-fold from human erythrocytes. It was shown to exist in three molecular weight forms, a probable monomer of molecular weight 62,000, a dimer, and a tetramer. Conversion of the monomer to higher molecular weight forms was associated with increased stability to thermal inactivation and was promoted by a number of low molecular weight compounds, including orotic acid and competitive inhibitors of the enzyme. Orotic acid phosphoribosyltransferase co-purified with the decarboxylase but was much more susceptible to inactivation. The partially purified orotidylate decarboxylase showed a triphasic Lineweaver-Burk plot when examined over a wide range of substrate concentrations. The separated molecular weight forms gave linear double reciprocal plots with Km values corresponding to the three values obtained with the erythrocyte enzyme preparation. The values obtained were 25, 3, and 0.6 muM for the monomer, dimer, and tetramer forms, respectively.