Investigation of early stages of fibrin association

Interactions between fibrinogen molecules proteolytically cleaved with thrombin were investigated using atomic force microscopy (AFM) and dynamic light scattering (DLS). Gradually decreased fibrinogen concentrations were used to study the fibrin network, large separated fibrils, small fibrils in the initial association stages, and protofibrils. In addition, a new type of structure was found in AFM experiments at a low fibrinogen concentration (20 nM): the molecules in these single-stranded associates are arranged in a row, one after the other. The height, diameter, and distance between domains in these single-stranded associates were the same as those in the original fibrinogen molecules. DLS data assumed formation of extended associates in bulk solution at fibrinogen concentration as low as 20 nM.     

The early stages of taxol biosynthesis: an interim report on the synthesis and identification of early pathway metabolites

The biosynthesis of the anti-cancer drug taxol (paclitaxel) has required the collaborative efforts of several research groups to tackle the synthesis and labeling of putative biosynthetic intermediates, in concert with the identification, cloning and functional expression of the biosynthetic genes responsible for the construction of this complex natural product. Based on a combination of precursor labeling and incorporation experiments, and metabolite isolation from Taxus spp., a picture of the complex matrix of pathway oxygenation reactions following formation of the first committed intermediate, taxa-4(5),11(12)-diene, is beginning to emerge. An overview of the current state of knowledge on the early-stages of taxol biosynthesis is presented.     

Studies toward soraphen A: an aldol-metathesis avenue to the macrocyclic framework

[reaction: see text] We describe a convergent approach to soraphen A, 1, that involves coupling of two fragments by an aldol condensation-olefin metathesis sequence. This route permits rapid access to congeners of 1.     

Late stages in the biosynthesis of abnormal erythrina alkaloids

The incorporation of (±)-, N-norprotosinomenine, N-nor-orientaline, N-nor-reticuline, norlaudanosoline, protosinomenine, and N-[2-(3-hydroxy-4-methoxyphenyl)ethyl]-2-(4-hydroxyphenyl) ethylamine into coccuvine has been studied, and the specific utilisation of the (±)-norprotosinomenine demonstrated. A double labelling experiment with (±)-[1-³H,4'-methoxy-¹⁴C]-N-norprotosinomenine showed that the 4'-O-Me group of the precursor is retained in the bioconversion and the erythrinan ring system is not formed by addition of secondary amino function onto an ortho-quinone system. Feeding of (±)-[1-³H, 7-methoxy-¹⁴C]norprotosinomenine established that O-demethylation is the terminal step in the biosynthesis of coccuvine. Feeding of labelled abnormal Erythrina alkaloids revealed that isococculidine is converted into coccoline via coccuvinine and isococculine into coccolinine via coccuvine.     

Enzymatic study of the late stages of protoberberine alkaloid biosynthesis

A specific methyltransferase which converts tetrahydrocolumbamine to tetrahydropalmatine, and oxidase activity which converts tetrahydroberberine, tetrahydrocolumbamine and tetrahydropalmatine, but not tetrahydrojatrorrhizine, to their quaternary counterparts are demonstrated.     

Modeling the early stages of self-assembly in nanophase materials

The early stages of self-assembly of the elementary building blocks of nanophase materials are studied. The relative roles of entropic and energetic factors in determining the relative abundance of the final products present is analyzed using both a kinetic mean field model and a mesoscopic approach in which self-assembly is viewed as an encounter-controlled process on a discrete lattice. The relevance of the results in zeolite synthesis in connection with the ordered liquid phases recently discovered in these materials is discussed.     

Mass spectrometric interrogation of thioester-bound intermediates in the initial stages of epothilone biosynthesis

Direct detection of thioester intermediate mixtures bound to EpoC, a 195 kDa polyketide synthase, has been achieved using limited proteolysis and Fourier-transform mass spectrometry (FTMS). Incubation with various N-acetylcysteamine thioester (S-NAC) substrate mimics produced mass shifts on the EpoC ACP domain consistent with their condensation with an enzyme-bound carbanion produced by the decarboxylation of methylmalonyl-S-EpoC. Reconstitution of EpoA-ACP, EpoB, and EpoC gave a +165.0 Da mass shift consistent with the formation of the methylthiazolyl-methacrylyl product by incorporation of acetyl-CoA, cysteine, and methylmalonyl-CoA. Thioester-templated reaction intermediates and products are typically characterized by quantifying radioactive substrates, either enzyme bound or chemically hydrolyzed. In contrast, the MS-based methodology described here provides semiquantifiable ratios of free enzyme, intermediate, and product occupancy and reveals that certain substrates result in a >50% formation of nonproductive intermediates.     

Heterogeneous directional mobility in the early stages of polymer crystallization

Recently, we demonstrated via large-scale molecular dynamics simulations a "coexistence period" in polymer melt ordering before crystallization, where nucleation and growth mechanisms coexist with a phase-separation mechanism [Gee et al., Nat. Mater. 5, 39 (2006)]. Here, we present an extension of this work, where we analyze the directional displacements as a measure of the mobility of monomers as they order during crystallization over more than 100 ns of simulation time. It is found that the polymer melt, after quenching, rapidly separates into many ordered hexagonal domains separated by amorphous regions, where surprisingly, the magnitude of the monomer's displacement in the ordered state, parallel to the domain axial direction, is similar to its magnitude in the melt. The monomer displacements in the domain's lateral direction are found to decrease during the time of the simulation. The ordered hexagonal domains do not align into uniform lamellar structures during the timescales of our simulations.     

The early stages of the sol-gel processing of TEOS

The reactivity of tetraethoxysilane (TEOS) used in many sol-gel syntheses can be increased by prehydrolysis. In contrast to one-step prehydrolysis acidic two-step prehydrolysis causes an increase of the reactivity of the low molecular species provided the total water/TEOS ratios are the same in both cases. By choice of the processing conditions of the hydrolysis—shown on variation of water content, hydrolysis steps and heat treatment—the degree of condensation, the ratio of hydrolyzable (-OC₂H₅) and hydrolyzed groups (-OH) and the structure of the low molecular species (short chains, 3-membered and 4-membered rings) can be influenced systematically. The development of the building units formed in the early reaction stages is ascertained by molybdate method and ²⁹Si NMR measurements.     

Techniques for analyzing the early stages of crystallization reactions

This paper will — in a semi-review-like form — describe the problems in analyzing nucleation reactions, and approaches towards a solution of these problems. Attempts to pinpoint the nucleation event can start from the solution state, and the development of precursors for the solid state can be traced with mass spectrometry. Alternatively, one can try to obtain information on ever earlier stages of the solids formation itself, thus approaching the nucleation event from the side of the solid already formed. A highly suitable tool for this purpose is a tubular reactor, where crystallization reactions can be carried out continuously.     

Data visualization during the early stages of drug discovery

Multidimensional compound optimization is a new paradigm in the drug discovery process, yielding efficiencies during early stages and reducing attrition in the later stages of drug development. The success of this strategy relies heavily on understanding this multidimensional data and extracting useful information from it. This paper demonstrates how principled visualization algorithms can be used to understand and explore a large data set created in the early stages of drug discovery. The experiments presented are performed on a real-world data set comprising biological activity data and some whole-molecular physicochemical properties. Data visualization is a popular way of presenting complex data in a simpler form. We have applied powerful principled visualization methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), to help the domain experts (screening scientists, chemists, biologists, etc.) understand and draw meaningful decisions. We also benchmark these principled methods against relatively better known visualization approaches, principal component analysis (PCA), Sammon's mapping, and self-organizing maps (SOMs), to demonstrate their enhanced power to help the user visualize the large multidimensional data sets one has to deal with during the early stages of the drug discovery process. The results reported clearly show that the GTM and HGTM algorithms allow the user to cluster active compounds for different targets and understand them better than the benchmarks. An interactive software tool supporting these visualization algorithms was provided to the domain experts. The tool facilitates the domain experts by exploration of the projection obtained from the visualization algorithms providing facilities such as parallel coordinate plots, magnification factors, directional curvatures, and integration with industry standard software.     

Growth versus cyclization in the early stages of the polycondensation of metal alkoxides

The early steps of the polycondensation of transition metal alkoxide have been studied from the chemical and structural points of view. Polyoxoalkoxides are described like macromolecules by the composition of the repeating unit, the degree of polymerization (N), and the radius of gyration (R). The fraction p of binding sites of the coordination sphere of the metal centers occupied by terminal ligands determines N as follows: N proportional, variant pdf (dA-df), where df is the fractal dimension and dA is defined by Np proportional, variant RdA. This approach addresses difficulties raised by both coordinative unsaturation and cyclization in the modelization of the polycondensation of metal alkoxides. The coordinative unsaturation is accounted for by a particularly small value of dA= 1 in the very early steps, while the cyclization frequency is measured by the difference dA-df. This difference is not constant along the polycondensation process, and its dependence on the extent of reaction provides clues for understanding the high apparent kinetics order of gelation often reported in the literature.     

Biochemical and structural insights of the early glycosylation steps in calicheamicin biosynthesis

The enediyne antibiotic calicheamicin (CLM) gamma(1)(I) is a prominent antitumor agent that is targeted to DNA by a novel aryltetrasaccharide comprised of an aromatic unit and four unusual carbohydrates. Herein we report the heterologous expression and the biochemical characterization of the two "internal" glycosyltransferases CalG3 and CalG2 and the structural elucidation of an enediyne glycosyltransferase (CalG3). In conjunction with the previous characterization of the "external" CLM GTs CalG1 and CalG4, this study completes the functional assignment of all four CLM GTs, extends the utility of enediyne GT-catalyzed reaction reversibility, and presents conclusive evidence of a sequential glycosylation pathway in CLM biosynthesis. This work also reveals the common GT-B structural fold can now be extended to include enediyne GTs.     

Investigation of the origin of C2 units in biosynthesis of streptolydigin

[reaction: see text] Isotope labeling studies show that malonate, not acetate, furnishes all four C(2) units in the acyltetramic acid streptolydigin. The results are compared with those for pramanicin, and implications for the biosynthetic pathway are discussed.     

Particle morphology in the early stages of radiation-induced heterophase polymerization of vinyl chloride

Investigations of the particle morphology of poly(vinyl chloride) produced under quiescent conditions during radiation-induced bulk polymerization over the temperature range ?30 to 70°C were carried out. The observations were mainly confined to the early stages of polymerization. For polymerization temperatures below about 20°C, the systems remain predominantly homogeneous during the entire polymerization and the polymer particles increase in size linearly with conversion. At higher temperatures the polymer particles rapidly settle and become cemented together. The findings are discussed in the light of the kinetic data on vinyl chloride polymerization, and a process of particle formation and growth, resembling that recently proposed by Fitch for emulsion systems, was formulated. Primary particles are initially formed by the coiling up of single macromolecules or single macroradicals and, subsequently, they increase in size by sweeping up growing free radicals from the liquid monomer phase. The free radicals which escape capture give rise to new primary particles, but their number progressively decreases as the number of the dispersed particles increases. Simultaneously, the polymer particles undergo flocculation which in a short time results in the formation of large agglomerates. As the volume of the resulting agglomerates increases, the flocculation rate decreases and, eventually, becomes so low that the flocculation does not proceed further. At low temperatures the flocculation almost ceases when the agglomerates are still small enough for sedimentation to occur only very slowly. However, this is not the case at higher temperatures. The addition of substances such as alcohols, brings about a reduction in the flocculation rate and, hence, in the size of the agglomerates formed at the end of the flocculation process. In this way, one can also obtain at high temperatures agglomerates of small sizes which remain dispersed for a long time.     

Thermokinetic features of the early stages of hydration of slag alkaline binders

This paper presents results of thermokinetic studies on the early stages of hydration of some slag minerals, slag alkaline binders of traditional and new-generation compounds. A possibility of adjustment and control of hardening processes through thermokinetic indices of hydration (intensity and completeness of heat evolution) for various compounds, types and quantities of the alkaline components and temperatures is proved.     

In-situ and ex-situ examination of the early stages of chemical vapor deposition

A cold working steel was coated both with high temperature CVD (TiN) and moderate temperature CVD (Ti[C,N]). AES depth profiles show a significant difference at the interface, where a thin oxide layer remains detectable at deposition temperatures of 750 °C. It could be shown that an impedance signal at a frequency of 13 MHz is well suited to detect the early stages of the growth of a CVD coating. Received: 15 July 1997 / Revised: 5 February 1998 / Accepted: 9 February 1998     

Effect of three-body interactions on the early stages of atomic cluster growth

The sequence of conformations a cluster assumes as it grows from a trimer into a thirteen-atom aggregrate under a given model potential has been studied. The model potential proposed is a construction composed of a van der Waals pairwise term and a three-body term composed of the triple dipole contribution and the exchange overlap contribution. A parametric study of the thermodynamically preferred structures is given. After reaching a boundary between regions in the parameter space, equilibrium mixtures of isomers with different packings are obtained. The normal frequency spectrum is given for clusters up to thirteen atoms.     

Towards the understanding of molecular mechanisms in the early stages of heat-induced aggregation of beta-lactoglobulin AB

Heat-induced aggregation of bovine β-lactoglobulin AB (10 mg/ml) was studied at 68.5 °C at two different pH values (6.7, 4.9) using gel electrophoresis techniques and matrix-assisted laser desorption ionization mass spectrometry (MALDI–TOF MS). Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS–PAGE) analysis under non-reducing and reducing conditions showed that in the early stages of the aggregation of β-lactoglobulin disulfide linked aggregates were formed on heating at pH 6.7, but not at pH 4.9. We related this result to the pH-dependent activity of the free thiol group at C121. Mass spectrometric analyses were conducted in two steps. The first involved the analysis of intact non-native monomers and dimers following their ultrasonic passive elution into a suitable solvent mixture in order to confirm the identity of the different gel bands. The second step comprises the analysis of in-gel digests for the determination of disulfide patterns in non-native monomers, covalent dimers and trimers. The results of in-gel digestions analyzed by mass spectrometry suggest that non-native dimers could result from the formation of inter-molecular disulfide bonds C121–C66, C160–C160, or C121–C160. Moreover, two inter-molecular bonds C121–C66 and C160–C160 between two and the same monomer units have been detected, which may play an important role in limiting the process of covalent β-lactoglobulin network formation. The combination of SDS–PAGE and MALDI–TOF MS enables us to understand the mechanism of β-lactoglobulin aggregation at the macromolecular level.     

Kinetics of the formation of silver dimers: early stages in the formation of silver nanoparticles

Silver clusters too small to support a plasmon band possess interesting fluorescence properties as well as being a convenient route to studying the early stages of nanoparticle formation. Fluorescent silver clusters are synthesized in toluene solution, and the formation is monitored herein by laser flash photolysis (LFP). Kinetic analysis of the formation of the Ag clusters is consistent with the formation of the smallest possible clusters, silver dimers (Ag(2)), whereby a mechanism for the formation of these clusters is provided as well as the first reported extinction coefficient and association constant for Ag(0) to form Ag(2). The formation of Ag(2) clusters is contrasted with the formation of Ag nanoparticles in aqueous media, and the particular stability and selectivity toward Ag(2) in this system is also studied using LFP.