Average molecular weight and molecular weight distribution of agarose and agarose-type polysaccharides

A procedure to determine the absolute weight-average molecular weight and molecular weight distribution of agarose and agarose-type polysaccharides by aqueous size-exclusion chromatography coupled with low-angle laser light scattering is described. The molecular weights of the majority of the commercial samples investigated were between 80 000 and 140 000 with a polydispersity lower than 1·7. In contrast, most of the laboratory-extracted agarose-type polysaccharides had lower molecular weights.     

Determination of molecular weight and molecular structure of rat-liver pyruvate carboxylase.

The molecular weight of pyruvate carboxylase isolated from pigeon and rat liver mitochondria was examined using analytical ultracentrifugation and electron microscopy. The enzyme molecule appeared as a tetramer with the four subunits arranged at the corners of a square. Sedimentation studies in the analytical ultracentrifuge, extrapolated to infinite dilution, showed the tetramer to have a molecular weight Mc=0r of 280 000 and an So20,w of 12.7 S. The tetramer could be dissociated into trimers and dimers of lower specific enzymic activity by storage at 4 degrees C or incubation at -- 20 degrees C at low protein concentrations. The isolated trimers and dimers had a molecular weight Mc=0r of 210 000 and 140 000, respectively, and an So20,w of 10.85 S and 7.55 S, respectively. Incubation with 2 M urea at 20 degrees C yielded enzymically inactive subunits (Mc=0r = 70 000; So20,w = 4.95 S). The molecular weights (for pyruvate carboxylase and its subunits), as calculated from the subunit diameter observed in the electron microscope, were consistent with the values obtained from sedimentation studies.     

Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations

Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the diisocyanates and diols, in particular changes in the mesogen, were investigated. Introduction of mesogenic segments into the polymers suppresses the ordering. Stiff end substituents (phenyl and alkoxy groups) of the mesogens stabilize the mesophases to such an extent that the negative influence of long polymer chains is compensated and the liquid-crystalline properties are recovered. All-atom molecular dynamics simulations in the Cerius² modeling environment were carried out to characterize the structures of the polymers. Analysis of the dynamic trajectories at 20, 100, 120 and 170 °C revealed changes in conformation of macromolecules, which correlate with DSC measurements.Figure Example of structure relaxation of D4/TDI molecule at indicated simulation times (temperature 20 °C): a complete structure; b backbone structure; c top view of molecule     

The molecular basis of lung cancer: molecular abnormalities and therapeutic implications

Lung cancer is the number one cause of cancer-related death in the western world. Its incidence is highly correlated with cigarette smoking, and about 10% of long-term smokers will eventually be diagnosed with lung cancer, underscoring the need for strengthened anti-tobacco policies. Among the 10% of patients who develop lung cancer without a smoking history, the environmental or inherited causes of lung cancer are usually unclear. There is no validated screening method for lung cancer even in high-risk populations and the overall five-year survival has not changed significantly in the last 20 years. However, major progress has been made in the understanding of the disease and we are beginning to see this knowledge translated into the clinic. In this review, we will summarize the current state of knowledge regarding the cascade of events associated with lung cancer development. From subclinical DNA damage to overt invasive disease, the mechanisms leading to clinically and molecularly heterogeneous tumors are being unraveled. These lesions allow cells to escape the normal regulation of cell division, apoptosis and invasion. While all subtypes of non-small cell lung cancer have historically been treated the same, stage-for-stage, recent technological advances have allowed a better understanding of the molecular classification of the disease and provide hypotheses for molecular early detection and targeted therapeutic strategies.     

Disialogangliosides and their interaction with cholera toxin - investigation by molecular modeling, molecular mechanics and molecular dynamics

Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface disialogangliosides (GD1A, GD1B and GD3) in aqueous environment. The molecular mechanics calculation reveals that water mediated hydrogen bonding network plays a significant role in the structural stabilization of GD1A, GD1B and GD3. These water mediated hydrogen bonds not only exist between neighboring residues but also exist between residues that are separated by 2 to 3 residues in between. The conformational energy difference between different conformational states of gangliosides correlates very well with the number of water mediated and direct hydrogen bonds. The spatial flexibility of NeuNAc of gangliosides at the binding site of cholera toxin is worked out. The NeuNAc has a limited allowed eulerian space at the binding site of Cholera Toxin (2.4%). The molecular modeling, molecular mechanics and molecular dynamics of disialoganglioside-cholera toxin complex reveal that cholera toxin can accommodate the disialoganglioside GD1A in three different modes. A single mode of binding is permissible for GD1B and GD3. Direct and water mediated hydrogen bonding interactions stabilizes these binding modes and play an essential role in defining the order of specificity for different disialogangliosides towards cholera toxin. This study not only provides models for the disialoganglioside-cholera toxin complexes but also identifies the NeuNAc binding site as a site for design of inhibitors that can restrict the pathogenic activity of cholera toxin.     

Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies

Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta-Notch complex have been proposed based on interaction energy parameter and planarity studies.     

Computer assisted simulations and molecular graphics methods in molecular design

A survey is presented of computer-assisted statistical mechanical methods. The general theoretical background is described and special methods are discussed in detail. Practical procedures allowing for the calculation of binding energies are examined. A recent perturbation-relaxation procedure is summarized.     

Construction of a molecular linkage map and development of a molecular breeding technique

Conclusion  Although this research program is in the state of beginning, it seems like that the progress will be made more rapidly than expected. The reason is because new techniques and facilities derived from human genome research and other advanced genome program will overcome the current limitations and difficulties. Genome research cannot be accomplished by one or two research groups. That is why the program should be well organized and planned by scientists in various fields with common interest. Considering the tremendous amounts of time, money, and efforts required for performing genome research, the genome research programs should aim at concrete goals, such as getting new solutions that cannot be obtained by conventional approach, rather than remain as research for research is sake. This paper was presented at the 11th Symposium on Plant Biotechnology entitled “Plant Genes and Genetic Resources” organized by Gynheung An, held July 4–5, 1997, by the Botanical Society of Korea     

Genomic and molecular medicine

Molecular medicine is a new research field underlain by achievements of the Human Genome Project. The review considers the contribution of the Laboratory of Prenatal Diagnostics of the Ott Institute of Obstetrics and Gynecology to the development of molecular medicine in Russia. Special emphasis is placed on molecular diagnostics, predictive medicine, and gene therapy. The lab obtained priority results in devising and promoting methods of molecular diagnostics of the most common severe hereditary disorders such as cystic fibrosis, Duchenne muscular dystrophy, hemophilia A, and fragile X syndrome. Owing to the Russian program Human Genome, St. Petersburg researchers laid the foundations for theoretical and applied predictive medicine, which is aimed at identifying and analyzing the genes associated with predisposition to high-incidence multifactorial disorders. Experiments with mdx mice providing a model of Duchenne muscular dystrophy were carried out to select the optimal way of delivering a transgene (cDNA of the dystrophin gene) contained in various constructs for the purpose of gene therapy.