Role of interstellar molecules in prebiological evolution

Three generations of organic molecules in space are considered: interstellar molecules, molecules synthesised in protosolar cloud and molecules synthesised on the Earth. It is shown that there is no possibilities for amino acid polymers to be synthesised under interstellar cloud conditions. Molecules of the second generation were disintegrated during the Earth accumulation period. The problem of the origin of life is connected with the evolution of molecules of the third generation.     

白细胞与内皮细胞的粘附

白细胞与内皮细胞相互作用由粘附分子介导.整合素、免疫球蛋白及选择素家族的粘附分子在这两种细胞的粘附中起关键作用.粘附的起始阶段由选择素介导,随后由CD11/CD18复合物与ICAM-1形成更为紧密的结合.多种细胞因子及炎症反应可诱导粘附.抗粘附分子单抗、药物等可抑制粘附.     

Molecular simulation of cage occupancy and selectivity of binary THF–H2 sII hydrate

The hydrogen capacity of the binary THF–H₂ sII hydrate is determined by the cage occupancy and by the selectivity of guest molecules. Grand canonical Monte Carlo (GCMC) simulation is used to study the cage occupancy and selectivity of guest molecules from the equilibrium configuration of the binary sII hydrate. The cage framework is regarded as a rigid body and the number of guest molecules is varied to preserve the grand canonical ensemble. The occupancy and selectivity were investigated at a temperature of 270 K for pressures ranging from 0.1 to 200 MPa. It was found that most large cages select THF as guest molecules while small cages include only hydrogen molecules. Multiple occupancy of hydrogen, up to four molecules in large cages and two molecules in small cages, was found as the pressure increases. GCMC results show that the hydrogen capacity is approximately 1.1 wt% at 200 MPa.     

Initial steps in Haemophilus influenzae transformation. Donor DNA binding in the com10 mutant

The com10 mutant of Haemophilus influenzae binds donor DNA reversibly, but is deficient in uptake. The DNA binding has all the characteristics of interaction with a protein receptor; it is saturable, reversible, and specific. However, binding specificity is 6-fold weaker in com10 than is uptake specificity in wild-type. The binding of small (120 base pairs) and large (14,400 base pairs) DNA molecules were compared. For small molecules, binding data fitted a straight line by Scatchard analysis (Bmax = 4.8 DNA molecules/cell, Kd = 0.5 X 10(-9) M). In contrast, for large DNA molecules, the Scatchard plot was not linear. A high affinity binding (Kd = 0.4 X 10(-12) M) and a lower affinity binding (Kd = 1.2 X 10(-11) M) were found with a total number of 3 molecules bound per cell. In wild-type cells, 3.2 large molecules were taken up per cell, whereas up to 40 small 120-base pair DNA fragments were taken up per cell. Uptake of small DNA molecules followed a Michaelis-Menten function with a Km of 0.5 X 10(-9) M and a maximal initial velocity of 1.5 molecules/cell/min at room temperature. For large DNA molecules, maximal initial velocity was approximately 2 molecules/cell/min at room temperature. The analysis of the binding and uptake data suggest to us that a receptor or a receptor complex is responsible for the uptake of either a single large DNA molecule or, successively, a number of small DNA molecules.     

The refinement and the structure of the dimer of alpha-chymotrypsin at 1.67-A resolution

The two molecules of the asymmetric unit of the pH 3.5 conformer of alpha-chymotrypsin have been refined at 1.67-A resolution using restrained least squares methods with Hendrickson's program (PROLSQ). The final R factor is 0.179 (including 247 water molecules). The folding of the main chain of the independent molecules is the same within experimental error but the same does not generally apply to the side chain stereochemistry. From this we conclude that the folding of a protein structure is basically independent of most of the detailed stereochemistry of its side chains. The side chains of the interface region between the independent molecules display pronounced asymmetry. This asymmetry suggests that dynamic and asymmetrical structural changes take place at the time of oligomerization leading to more energetically favorable interactions for the dimer. Comparison of the structures of the independent molecules of alpha-chymotrypsin with the structure of monomeric gamma-chymotrypsin revealed that although the folding of the three molecules is essentially the same, numerous and significant differences pervade the side chain stereochemistry attributable to general flexibility. The specificity site of alpha-chymotrypsin is occupied by ordered water molecules in a similar way to gamma-chymotrypsin and other proteins. Some of these water molecules are displaced when substrate binds to the enzyme, while the others appear to help identify and position the aromatic side chain in catalysis.     

Tropomyosin as a regulator of the sliding movement of actin filaments

We examined the capacity of tropomyosin molecules regulating the sliding movement of actin filaments on myosin molecules in the presence of ATP molecules to be hydrolyzed. For this objective, we prepared tropomyosin molecules modified to be a little bit stiffer compared to the intact ones by applying a fixed cross-linker between a pair of twisted tropomyosin monomers. The cross-linked tropomyosin molecules, when complexed with actin filaments, were found to inhibit the sliding movement of the filaments on myosin molecules even in the absence of calcium-regulated troponin molecules. It is then suggested that the mechanical flexibility of tropomyosin molecules may be instrumental to actualizing the proper functional regulation of the sliding movement of actin filaments.     

Ionic strength and transition metals control PrPSc protease resistance and conversion-inducing activity

The essential component of infectious prions is a misfolded protein termed PrPSc, which is produced by conformational change of a normal host protein, PrPC. It is currently unknown whether PrPSc molecules exist in a unique conformation or whether they are able to undergo additional conformational changes. Under commonly used experimental conditions, PrPSc molecules are characteristically protease-resistant and capable of inducing the conversion of PrPC molecules into new PrPSc molecules. We describe the effects of ionic strength, copper, and zinc on the conformation-dependent protease resistance and conversion-inducing activity of PrPSc molecules in scrapie-infected hamster brains. In the absence of divalent cations, PrPSc molecules were > 20-fold more sensitive to proteinase K digestion in low ionic strength buffers than in high ionic strength buffers. Addition of micromolar concentrations of copper or zinc ions restored the protease resistance of PrPSc molecules under conditions of low ionic strength. These transition metals also controlled the conformation of purified truncated PrP-(27-30) molecules at low ionic strength, confirming that the N-terminal octapeptide repeat region of PrPSc is not required for binding to copper or zinc ions. The protease-sensitive and protease-resistant conformations of PrPSc were reversibly interchangeable, and only the protease-resistant conformation of PrPSc induced by high ionic strength was able to induce the formation of new protease-resistant PrP (PrPres) molecules in vitro. These findings show that PrPSc molecules are structurally interconvertible and that only a subset of PrPSc conformations are able to induce the conversion of other PrP molecules.     

Muscle-derived agrin in cultured myotubes: expression in the basal lamina and at induced acetylcholine receptor clusters.

The synaptic basal lamina (SBL) directs key aspects of the differentiation of regenerating neuromuscular junctions. A range of experiments indicate that agrin or a closely related molecule is stably associated with the SBL and participates in inducing the formation of the postsynaptic apparatus after damage to adult muscle. The selective concentration of agrin-related molecules in the SBL suggests that agrin is secreted locally by cellular components of the nerve-muscle synapse. In vivo studies on aneural embryonic muscle indicate that the muscle cell is one source of the agrin-like molecules in the SBL. Here we have used cultured chick muscle cells to study the expression of agrin-related molecules in the absence of innervation. Immunofluorescence and immunoelectron microscopy show that myogenic cells in culture express agrin-related molecules on their surfaces, and that at least a subset of these molecules are associated with the basal lamina. Moreover, in short term cultures agrin-like molecules accumulate on the surfaces of myogenic cells grown in unsupplemented basal media. We quantified the expression of agrin-like molecules on the cell surface using a solid-phase radioimmune assay. The expression of these molecules is relatively low during the first 6 days of culture and increases fourfold during the second week. The stimulation of the expression of agrin-related molecules in these long-term cultures requires the presence of chick embryo extract or fetal calf serum. We also characterized the expression of muscle-derived agrin-like molecules at clusters of AChR. These agrin-related molecules are not consistently colocalized at spontaneous AChR aggregates; however, they are selectively concentrated at greater than or equal to 90% of the AChR clusters that are induced by Torpedo agrin. These data, together with previous results from in vivo developmental experiments indicate that the agrin-like molecules in the synaptic basal lamina are derived at least in part from the muscle cell. In addition, the expression of agrin-like molecules can be regulated by soluble factors present in CEE and FBS. Finally, the selective localization of these molecules at induced AChR clusters, taken together with their localization in the basal lamina, suggests that agrin-like molecules secreted by the muscle cell play an important role in the formation and/or the stabilization of the postsynaptic apparatus.     

The creation of a database of odorous compounds focused on molecular rigidity and analysis of the molecular features of the compounds in the database

It is important to select odorous molecules for experiments on olfaction and for the development of an electronic nose. Odorous molecules having a small number of conformers, namely structurally rigid molecules, are assumed to interact with a small number of types of olfactory receptor proteins or to interact with the proteins in a simpler manner than that of fairly flexible molecules. Focusing on the rigidity of molecular structures, we collected 287 odorous molecules from data sources, which included 1205 chemicals in total and a database of the 287 odorous molecules (DB_odMOL) was created using CS ChemFinder Pro (version 5.0). The logarithmic value of the octanol/water partition coefficient (log P) and melting point, boiling point and vapour pressure of the molecules were estimated using CS Chem3D Pro. The database DB_odMOL accumulates these estimated data in addition to literature values for odour quality, odour detection thresholds and the safety of molecules. The rigidity of the 287 molecules was further analysed by conformational analysis performed by molecular mechanics using Conformer in CS Chem3D Pro (version 5) and 72 rigid odorous molecules were selected. The 287 molecules were also analysed based on atomic composition, substructure and molecular size. Sixty-two odorous molecules among the 72 rigid odorous molecules were further selected based on their atomic composition. The 62 rigid molecules with simple atomic composition that were finally selected should be useful for researchers in choosing odorous molecules for the study of olfaction, including the fields of molecular biology, physiology, structure-odour relationships and other fields of the study concerning odour.     

Molecular dynamics simulation of diffusion behaviour of gas molecules within oil–paper insulation system

The diffusion behaviour of hydrogen, carbon monoxide, carbon dioxide, methane, acetylene, ethylene and ethane in oil and paper medium was examined using molecular dynamics to reveal the diffusion mechanism of gas molecules in transformer oil–paper insulation system at the microscopic level. These compounds are commonly used in the dissolved gas analysis of power transformers and produced during the ageing process of oil–paper composite insulating material. Two groups of models were constructed using molecular dynamics simulation software to simulate the diffusion behaviour of the aforementioned seven types of small gas molecules in oil and paper. The diffusion coefficients, displacement features, free volume characteristics and interaction energies of the gas molecules were investigated. In particular, the diffusion micro-mechanism of the gas molecules was observed. The differences in diffusion features among the gas molecules were discussed, and the factors influencing the diffusion of the gas molecules were compared. Simulation results indicate that the diffusion coefficients of gas molecules in cellulose is an order of magnitude lower than that in oil, and the diffusion coefficients of these gas molecules in the two types of insulation media have different orders. Free volume of gas molecules is the main factor that influences the diffusion behaviour in oil, whereas intermolecular interaction is the main influencing factor of diffusion behaviour in cellulose.     

On the influence of pigment-protein interactions on the energy transfer processes in photosynthetic membrane structures. 2. LH2 complex of Rhodobacter sphaeroides

Low-temperature heterogeneous absorption and circular dichroism spectra of the Rb. sphaeroides LH2 complexes are calculated within the framework of the mini-exciton theory and diagonal static random disorder for the pure electronic transitions of the monomeric Bchl molecules. The coupling of Bchl molecules with the surrounding amino acid residues has been shown to change both the exciton distribution between the pigment molecules in each of the exciton states. The value of the delocalization index depends on the excitation wavelength and varies between 2-6 Bchl molecules. The optical transitions occurring at 780-790 and 820 nm have been found to be strongly mixed so that all Bchl molecules of the LH2 complex predetermine absorption in these spectral regions. On the other hand, absorption at 800 and 850 nm is mainly determined by the cycles of 9 and 18 Bchl molecules, respectively. Thus, the light energy absorbed by the B800 molecules at 800 nm is transferred to the B850 molecules by the interlevel exciton relaxation processes due to the population of the heavily mixed 820-nm exciton levels. The width of the heterogeneous absorption band for the cyclic monomeric aggregate has been shown to decrease as compared with the monomeric absorption band by square root(Ndel) time, where Ndel is the mean number of pigments over which the exciton is delocalized within the excited absorption band.     

Electron microscopical localization of the alpha 2-macroglobulin thiol ester sites

The active thiol ester groups of alpha 2-macroglobulin (alpha 2M) were reacted with a biotin derivative and the sites labelled with avidin-ferritin complexes. Electron micrographs show a strong preference of attachment of the ferritins to the ends of the rods of the H-shaped molecules. A mutual "cross-labelling" was observed in an alpha 2M preparation which yielded dimers of the molecules which must have been formed during purification. The molecules were mostly attached to each other at the ends of the rods of the H-shaped molecules. It is concluded that the thiol esters responsible for the covalent attachment of the proteinases (and other molecules) may be located more in the distal parts of the alpha 2M molecules, while the proteinase molecules are finally trapped near to the centre of the alpha 2M molecules.     

X-ray studies of water structure in 2 Zn insulin crystal

The water structure of rhombohedral 2 Zn insulin crystal which contains about 280 water molecules and 0.55-0.60 mol citrate molecules per dimer has been studied by X-ray crystallographic refinement with 1.1 A resolution data. Atomic parameters of 83 fully occupied and 258 partially occupied water molecules and 0.3 mol of citrate were obtained. Full matrix least-squares method with isotropic temperature factor was used for the refinement of partially occupied water molecules. The water molecules in this crystal exist in one of the three states: fully occupied water, partially occupied water and water continuum, and a schematic model of water structure in protein crystal was proposed. The flexibility of water molecules is described.     

Thermodynamic model of the formation of bridges between nucleic acid molecules in a liquid crystal]

A thermodynamic model of the formation of bridges consisting of alternating daunomycin molecules and copper ions and connecting neighboring nucleic acid molecules in a particle of a liquid crystalline dispersion was constructed. The model is based on the conception that ligands are adsorbed on lattices of reaction centers which are formed in a liquid crystal at a particular spatial arrangement of adjacent nucleic acid molecules (phasing). Equations were derived that describe typical experimentally obtained S-shaped dependences of bridge concentration on the concentration of copper ions and daunomycin molecules in an initial solution. It was shown that dependences of this kind take place in two variants of the adsorption model: when the binding of daunomycin with adjacent nucleic acid molecules is considered to be independent on the formation of bridges and when bridges compete with single daunomycin molecules for the sites on adjacent nucleic acid molecules.     

Multilayer adsorption of lysozyme on a hydrophobic substrate.

Macromolecular adsorption is known to occur as a complex process, often in a series of steps. Several models are discussed in the literature which describe the microscopic structure of the adsorbate. In the present study we investigated the adsorption of hen egg white lysozyme on alkylated silicon oxide surfaces. A combination of fluorescence excitation in the evanescent field and fluorescence recovery after photobleaching allowed us to measure the amount of adsorbed fluorescent lysozyme and the equilibrium exchange kinetics with molecules in solution. We found that a model with at least three classes of adsorbed molecules is necessary to describe the experimental results. A first layer is formed by the molecules which adsorb within a short time after the beginning of the incubation. These molecules make up approximately 65% of the final coverage. They are quasi-irreversibly adsorbed and do not measurably exchange with bulk molecules within one day even at temperatures up to 55 degrees C. A second layer, which reaches equilibrium only after several hours of incubation, shows a pronounced exchange with bulk molecules. The on-off kinetics show a distinct temperature dependence from which an activation barrier of delta E approximately 22 kcal/mol is derived. A third layer of molecules that exchange rapidly with the bulk can be seen to comprise approximately 10% of the total coverage. The exchange rate is on the order of fractions of a second. The binding of the latter two classes of adsorbed molecules is exothermic. From the temperature dependence of the coverage, the binding enthalpy of the slowly exchanging layer was estimated to be delta Hads approximately 3.8 kcal/mol. The second and third class of molecules remain enzymatically active as a muramidase, which was tested by the lysis of the cell walls of Micrococcus lysodeiktikus. The molecules in the first layer, on the other hand, showed no enzymatic activity.     

Enzymatic cleavage of superhelical DNA in a liquid crystal state]

Superhelical pBR322 DNA molecules form liquid-crystalline dispersions in water-salt solutions containing poly(ethyleneglycol). The formation of the liquid-crystalline dispersions from superhelical DNA molecules results in the appearance of two sites inside the DNA molecules that are split by Micrococcal nuclease. The first site of digestion does not differ from the standard site split by this enzyme in water-salt solutions, whereas the second one represents a new site specific only for the DNA molecules forming liquid-crystalline dispersions. Splitting of the DNA molecule through the first site is accompanied by formation of its linear form; splitting of a new site results in the formation of two linear DNA fragments with molecular masses equal to half of the initial DNA molecules. Enzyme digestion of superhelical DNA molecules forming liquid-crystalline dispersions induces a reformation of the "nonspecific" space organization of dispersions to the cholesteric one. A hypothetic model for packing of the superhelical DNA molecules inside liquid-crystalline dispersions and its transformation under enzyme action is suggested.     

Regulation of intracellular trafficking of human CD1d by association with MHC class II molecules

CD1 family members are antigen-presenting molecules capable of presenting bacterial or synthetic glycolipids to T cells. Here we show that a subset of human CD1d molecules are associated with major histocompatibility complex (MHC) class II molecules, both on the cell surface and in the late endosomal/lysosomal compartments where class II molecules transiently accumulate during transport. The interaction is initiated in the endoplasmic reticulum with class II-invariant chain complexes and appears to be maintained throughout the class II trafficking pathway. A truncated form of CD1d which lacks its cytoplasmic YXXZ internalization motif is transported to late endosomal/lysosomal compartments in the presence of class II molecules. Furthermore, the same CD1d deletion mutant is targeted to lysosomal compartments in HeLa cells expressing class II molecules and invariant chain by transfection. The deletion mutant was also found in lysosomal compartments in HeLa cells expressing only the p33 form of the invariant chain. These data suggest that the intracellular trafficking pathway of CD1d may be altered by class II molecules and invariant chain induced during inflammation.