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PubMed2006

The cytomatrix as a cooperative system of macromolecular and water networks.

Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.

Animals↗
PubMed1971

Antibacterial nitroacridine, Nitroakridin 3582: binding to nucleic acids in vitro and effects on selected cell-free model systems of macromolecular biosynthesis.

Nitroakridin 3582 (NA) formed complexes with native deoxyribonucleic acid (DNA) and with transfer ribonucleic acid (tRNA) species from Escherichia coli. Spectrophotometric titrations of NA with these nucleic acids produced numerical results from which nonlinear adsorption isotherms were derived. These curves indicated the existence of more than one class of binding sites on the polymers to which NA was bound by more than one process. The stoichiometry of strong binding of NA to double helical DNA was in agreement with a conventional value (1 ligand molecule per 4.2 component nucleotides) for complete intercalation binding. NA inhibited the DNA-dependent DNA polymerase I and RNA polymerase reactions, the first strongly and the second appreciably. These inhibitions corresponded to the extents to which NA inhibits DNA and RNA biosyntheses in vivo. Evidently, NA interferes with the template function of DNA. The drug also inhibited the polymerization of phenylalanine in a cell-free E. coli ribosome-polyuridylic acid [poly (U)] system. The effect paralleled an inhibition of the poly (U)-directed binding of phenylalanyl tRNA to ribosomes. Ethidium bromide acted similarly. The antimalarial drug, chloroquine, stimulated polyphenylalanine synthesis, apparently as a result of stimulating the poly (U)-directed binding of phenylalanyl tRNA to ribosomes.

Acridines↗
PubMed1994

Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens.

The DNA sequence of a cluster of pKM101 conjugal transfer genes was determined and aligned with the genetic map of the plasmid. Eighteen genes were identified, at least eight and probably 11 of which are required for efficient conjugation. These tra genes are homologous to and colinear with genes found in the virB operon of Agrobacterium tumefaciens Ti plasmids. Seven pKM101 tra genes are also homologous to ptl genes of Bordetella pertussis, which direct the export of pertussis toxin. We used TnphoA to construct translational fusions between pKM101 genes and the Escherichia coli phoA gene, which encodes alkaline phosphatase, and provide evidence that at least 11 of the 18 genes are either fully or partially exported from the cytoplasm.

Agrobacterium tumefaciens↗
PubMed1988

The determination of equilibrium constants for heterogeneous macromolecular interactions. Systems forming 2:1 complexes.

In developing a method for analyzing the heterogeneous association nA + mB in equilibrium AnBm, we have specifically investigated the case of n = 2, m = 1 for both the specific case of no appreciable intermediates and the more general case allowing intermediates. Computer-simulated three-dimensional surfaces of the 2:1 model generated from total concentrations of species A and B and the resulting weight-average molecular weights were analyzed with a Gauss-Newton nonlinear least-squares minimization routine. The surfaces generated included normalized random error of varying standard deviations imposed upon both the concentrations and weight-average molecular weights. For comparison purposes, these surfaces were analyzed not only by using the correct 2:1 model, but also by an incorrect (1:1) model and by the other (incorrect) 2:1 model. Except for those situations where the 'experimental' noise was consistently higher than the concentration of one of the species, correct K values were obtained and the correct model was easily distinguished from the incorrect model. The computer routine similarly distinguished between data correctly described as 1:1 and the same data incorrectly analyzed as either 2:1 model. For those cases in which a microscopic Ki value predicts an association such that all species involved for that particular Ki are in appreciable amounts, the Ki value is returned correctly. Correct overall equilibrium constants are also converged upon as long as adequate amounts of A2B, B and A are present.

Kinetics↗
PubMed1980

On the effect of inhibitors of mitochondrial macromolecular-synthesizing systems and respiration on the growth of cultured chick embryo cells.

We have found that chick embryo fibroblasts (DEF) cultivated in the presence of tryptose phosphate broth (TPB) are inherently resistant to the growth inhibitory effect of ethidium bromide (EB). As demonstrated by cytochrome oxidase activity and oxygen consumption measurements, analyses of reduced-minus-oxidized cytochrome spectra and electron microscopic observations, TPB did not seem to prevent the inhibitory effect of EB on mitochondrial DNA transcription. EB-treated chick cell populations cultivated in the presence of TPB behave essentially the same as populations treated with chloramphenicol (CAM) and grow with mitochondria devoid of a functional respiratory chain. In contrast to CAM-treated CEF populations, however, the respiratory activity of EB-treated cell populations did not reappear when the cells were shifted back to EB-free medium. Attempts to demonstrate that TPB confers resistance to the growth inhibitory effect of carbomycin and mikamycin, inhibitors of the mitochondrial protein-synthesizing system, have failed, the drugs being cytotoxic at doses where protein synthesis on mitoribosomes is not suppressed. On the other hand, the present results demonstrated that chick cell populations proliferate in the presence of the respiratory inhibitors rotenone, antimycin A, amytal and oligomycin whether or not TPB is present in the growth medium.

Amobarbital↗
PubMed2004

Block copolymer libraries: modular versatility of the macromolecular Lego system.

The synthesis and characterization of a new 4 x 4 library of block copolymers based on polystyrene and poly(ethylene oxide) connected by an asymmetrical octahedral bis(terpyridine) ruthenium complex at the block junction are described, while initial studies on the thin film morphology of the components of the library are presented by the use of Atomic Force Microscopy, demonstrating the impact of a library approach to derive structure-property relationships.

Journal Article↗
PubMed2001

Automatic epitope recognition in proteins oriented to the system for macromolecular interaction assessment MIAX.

In the present work we evaluate the performance of an algorithm for the automatic recognition of binding sites in proteins as well as in other macromolecules whose interactions are involved in many cellular and physiological processes. The algorithm is a combination of an unsupervised learning algorithm - based on Kohonen self organizing maps - to characterize the properties of patches of protein solvent accessible surfaces and a filtering algorithm to establish both the physical boundaries of the patches as well as the level of contribution of different and distant atoms involved in the interaction. We have found that the algorithm performs extremely well in a set of randomly selected protein complexes for which the interaction interfaces are extracted and compared with the results of the algorithm. A statistical evaluation of the algorithm is additionally performed by analysis of the degree of hydrophobicity and hydrophilicity of the output patches and comparison with that of the observed interface constituent amino acids.

Algorithms↗
PubMed1973

Lung surface-active fraction as a model system for macromolecular ultrastructural studies with Crotalus atrox venom.

The dog lung surface-active fraction and phosphatidylcholine constituents were subjected to hydrolysis by Crotalus atrox phospholipase A(2). Relative rates of hydrolysis were: dipalmitoyl glycerophosphorylcholine > phosphatidylcholine isolated from the surface-active fraction > phosphatidylcholine as an integral component of the intact surface-active macromolecular structure. Cholesterol markedly inhibited, whereas tripalmitin increased, the rate of hydrolysis with both pure phosphatidylcholine substrates. The effect of temperature on the velocity indicated the enzyme was most active when the substrates were in the gel state. These kinetic results, in conjunction with surface chemistry studies, can be interpreted to indicate that the phosphatidylcholine in the intact surface-active macromolecular particle is liquid crystalline due to molecular interactions with other constituents. Gas-liquid chromatographic analysis of the 2-lysophosphatidylcholines and fatty acids produced from the enzymatic hydrolysis of the intact surface-active fraction indicated that palmitoyl residues were more accessible to the enzyme, perhaps because they occupied positions near the surface of the particle.

Animals↗
PubMed1980

A hypothesis of the code of nerve impulses.

There is probably only one information system in living nature - the macromolecular system including DNA, RNA and protein. Its unity for the genetic and nervous activity can be followed in the storage of information (heredity, memory) and in its processing (recombination and selection of both genetic and mental information). According to the hypothesis of the code of nerve impulses, nucleotide triplets of the nucleus, or more likely amino acids of the surface protein of the impulse generating area of a neuron, generate a limitd variety of interspike intervals so that each amino acid corresponds to a certain interspike interval and this particular interval initiates by means of a specific neurotransmitter, the synthesis of the same amno acid (or nucleotide triplet) in the postsynaptic neuron. Thus, a series of impulses produces in the postsynaptic neuron a sequence of amino acids in a form of a polypeptide identical to the polypeptide of the presynaptic neuron.

Amino Acids↗
PubMed1982

A new test system for screening macromolecular antitumor antibiotics and its application to culture fluids of actinomycetes.

In searching for macromolecular antitumor antibiotics, a new screening method was developed that consisted of 1) a macromolecular antibiotic detecting system employing macro-molecule permeable mutants of Escherichia coli, 2) a system to detect DNA-affecting antibiotics using DNA repair mutants, and 3) a mutagenicity detecting system, employing a valine resistance test. This new test system was applied to about 2,900 kinds of culture fluids of Actinomycetes and consequently 15 samples were found which contained macromolecular antibiotics with DNA affecting properties.

Actinomycetales↗
PubMed2003

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level.

Algorithms↗
PubMed2000

The importance of glassy biopolymer components in food.

The glassy state is not just important in low moisture and frozen foods, where it influences the physical and chemical stability and the crispness of some foodstuffs: glassy biopolymer components affect the physical properties of most food systems and low moisture biological systems. Glassy foods are not always fragile and crispy in texture. Therefore, the relationship between mechanical behaviour and molecular dynamics in low-moisture biopolymer systems will be considered. Vitrification of a macromolecular system only requires a mutual fixation of a certain proportion of the chain segments. The higher the rigidity of the chains, the lower the number of the chain segments which must be mutually fixed to vitrify the system. Mechanical stress can help the thermal movement to re-activate the motion of mutually fixed segments and involves a long deformation of glassy material. The stress required to effect long deformation presumably increases up to the strength of the material as the temperature decreases from the glass transition to the temperatures of brittleness (crispness). Vitrification of a loaded viscoelastic system results in an accumulation of mechanical energy (memory effect), which can be released (elastic recovery) above the glass transition temperature due to heating and or addition of a plasticizer. The effects of memory and elastic recovery could be of particular importance for producing foodstuffs which change their form, e.g. self-stirring dry foods and drinks on re-hydration in hot water. The importance of glassy biopolymer ingredients from the viewpoint of food formulation and processing is discussed.

Biopolymers↗
PubMed1998

Time-resolved crystallography.

Time-resolved crystallography has been successfully applied on the time scale from seconds via milliseconds and nanoseconds to picoseconds on a variety of systems. This brief review largely deals with macromolecular systems, on which there has been substantial recent progress. The strategies for design of a successful experiment that eliminates or minimizes potential artefacts have been identified, and the specifically crystallographic components of these strategies have been implemented. The remaining computational challenge is to identify and extract time-independent structures, each corresponding to a distinct reaction intermediate, whose populations vary with time and give rise to the time-dependent X-ray diffraction data. The fourth dimension, time, has been added to the three spatial dimensions of crystallography; it can no longer be regarded as purely a static technique.

Animals↗
PubMed2006

Orientation-independent spectra for biaxial systems in polarized Raman microspectrometry.

From an extension of the scattering intensity expressions in polarized Raman macrospectrometry to the case of micro-Raman backscattering experiments, we have established theoretical expressions to calculate orientation-independent intensity sums. This approach makes use of the K2 Raman invariant and of correction coefficients due to integration of the Raman scattering over the cone of collection of the objective lens, and it may be applied to uniaxial as well as to biaxial symmetry systems. The intensity sums thus obtained are expected to be orientation insensitive and allow one to compare conformational changes in various biaxially oriented polymer samples, either amorphous and/or semicrystalline thin films. As application examples we have compared the polarized Raman results obtained for various biaxially oriented amorphous and semicrystalline polystyrene (PS), poly(ethylene terenaphthalate) (PEN), and poly(ethylene terephthalate) (PET) thin film samples with their respective "isotropic spectrum" and have considered the different main conformational changes in related polymer systems. The method is thus tested on these macromolecular systems and appears quite successful in providing evidence for the molecular conformational changes without interferences from spectral contributions due to orientation.

Journal Article↗
PubMedDate not supplied

On the hydrodynamic analysis of macromolecular conformation.

Hydrodynamics provides a powerful complementary role to the traditional "high resolution" techniques for the investigation of macromolecular conformation, especially in dilute solution, conditions which are generally inaccessible to other structural techniques. This paper describes the state of art of hydrodynamic representations for macromolecular conformation, in terms of (1) simple but straightforward ellipsoid of revolution modelling; (2) general triaxial ellipsoid modelling; (3) hydrodynamic bead modelling; (4) the ability, especially for polydisperse macromolecular systems, to distinguish between various conformation types; (5) analysis of macromolecular flexibility.

Journal Article↗
PubMed2000

Self-assembly of nanoparticles into structured spherical and network aggregates

Multi-scale ordering of materials is central for the application of molecular systems in macroscopic devices. Self-assembly based on selective control of non-covalent interactions provides a powerful tool for the creation of structured systems at a molecular level, and application of this methodology to macromolecular systems provides a means for extending such structures to macroscopic length scale. Monolayer-functionalized nanoparticles can be made with a wide variety of metallic and non-metallic cores, providing a versatile building block for such approaches. Here we present a polymer-mediated 'bricks and mortar' strategy for the ordering of nanoparticles into structured assemblies. This methodology allows monolayer-protected gold particles to self-assemble into structured aggregates while thermally controlling their size and morphology. Using 2-nm gold particles as building blocks, we show that spherical aggregates of size 97 +/- 17 nm can be produced at 23 degrees C, and that 0.5-1 microm spherical assemblies with (5-40) x 10(5) individual subunits form at -20 degrees C. Intriguingly, extended networks of approximately 50-nm subunits are formed at 10 degrees C, illustrating the potential of our approach for the formation of diverse structural motifs such as wires and rods. These findings demonstrate that the assembly process provides control over the resulting aggregates, while the modularity of the 'bricks and mortar' approach allows combinatorial control over the constituents, providing a versatile route to new materials systems.

Journal Article↗