Intramolecular Heterogeneity Research Articles

Intramolecular structural heterogeneity altered by long-range contacts in an intrinsically disordered protein

Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function.

Изотопия углерода индивидуальных ароматических соединений нефти для понимания их геохимии

The article analyzes published and original data related to the carbon isotopic composition of individual aromatic compounds of fossil organic matter and oil. It has been shown that there is reliable evidence of the intramolecular isotopic heterogeneity of a number of molecules. For example the isotopically depleted carbon of the methyl group of alkylnaphthalenes and the terminal methyl of n-alkanes. The 13C inheritance from the biochemical precursor during the aromatization is also well documented in the example of diterpenes in the series abietic acid — dehydroabietane — simonellite — retene, as well as in the other terpene and steroid series. At the same time, there is evidence of carbon isotopic fractionation during the formation of several aromatic compounds from a single precursor. The increasing aromatization of the prebuild polycyclic structure does not change the 13C value of the molecule, and the formation of aromatic compounds with different numbers of aromatic rings in competing reactions leads to isotope differentiation in accordance with the thermodynamically determined distribution of carbon isotopes. If the suggestion is correct, it is the key to the understanding of specific petroleum aromatic hydrocarbons formation mechanism. It is possible that a comparison of 13C values for pairs of compounds formed during the transformation of one precursor will also provide information on the temperature conditions for the occurrence of the corresponding reactions.

Supercooled melt structure and dynamics of single-chain nanoparticles: A computer simulation study.

By using coarse-grained molecular dynamics simulations, we have investigated the structure and dynamics of supercooled single-chain cross-linked nanoparticle (SCNP) melts having a range of cross-linking degrees ϕ. We find a nearly linear increase in glass-transition temperature (Tg) with increasing ϕ. Correspondingly, we have also experimentally synthesized a series of polystyrene-based SCNPs and have found that the measured Tg estimated from differential scanning calorimetry is qualitatively consistent with the trend predicted by our simulation estimates. Experimentally, an increase in Tg as large as ΔTg = 61K for ϕ = 0.36 is found compared with their linear chain counterparts, indicating that the changes in dynamics with cross-links are quite appreciable. We attribute the increase in Tg to the enlarged effective hard-core volume and the corresponding reduction in the free volume of the polymer segments. Topological constraints evidently frustrate the local packing. In addition, the introduction of intra-molecular cross-linking bonds slows down the structural relaxation and simultaneously enhances the local coupling motion on the length scales within SCNPs. Consequently, a more pronounced dynamical heterogeneity (DH) is observed for larger ϕ, as quantified by measuring the dynamical correlation length through the four-point susceptibility parameter, χ4. The increase in DH is directly related to the enhanced local cooperative motion derived from intra-molecular cross-linking bonds and structural heterogeneity derived from the cross-linking process. These results shed new light on the influence of intra-molecular topological constraints on the segmental dynamics of polymer melts.

Silsesquioxane-Polythiophene Hybrid Copolymer as an Efficient Modifier for Single-Walled Carbon Nanotubes

One silsesquioxane-polythiophene hybrid copolymer, with combined star-like structure and intramolecular heterogeneity, was synthesized and sufficiently characterized via various methods, including FTIR, NMR, and SEC measurements. According to the exploration and characterization results, it was much more efficient at modifying SWNTs than its linear analogs in aqueous solution. The hydrophobic silsesquioxane core and PEDOT chains could locally anchor to the surface of the nanotubes, while the soluble flexible copolymer chains extended into the solution and rigid conjugated chains provided some π-π stacking effect to enhance adhesive force with the conjugated structure of the carbon nanotube, imparting steric stabilization to nanotube dispersion. The noncovalent interaction with SWNTs and solubility in aqueous solution improved the electrochemical characteristics of the modified-SWNT composite and availed for the preparation of a flexible and transparent electroactive film. Accordingly, this kind of silsesquioxane-polythiophene hybrid copolymer will be forwarded to apply to the assembling of flexible optoelectronic devices.

Recent Advances of Using Ionic Liquids for Biopolymer Extraction and Processing.

The evolution of petroleum-derived polymers is one of the crowning accomplishments of the past century. Although the significant economic gains from this industrial model of resource utilization are achieved, the environmental impacts are fatal. One of the principles of sustainable development is to replace such polymers with potential alternatives derived from renewable materials. Biopolymers derived from natural resources afford a new, versatile, environmentally benign feedstock that could exhibit closed-loop life cycles as part of a future material's industrial ecology. However, the solubility and processability of biopolymer materials provoke a serious bottleneck owing to their dense networks of inter - and intramolecular bondings and structural heterogeneity. Recently, ionic liquids (ILs) have emerged as promising green solvents and acquired augmented appreciation for their peerless power of biopolymer processing. Among the fourteen principle of green chemistry, the two key elements encourage the exploitation of renewable raw materials by using environmentally benign solvents that cover in dissolution of biopolymers using ILs. This mini review represents a brief overview of the comprehensive ILs assisted extraction and processing of various biopolymeric materials for value-added applications.

Nanostructuring Single-Molecule Polymeric Nanoparticles via Macromolecular Architecture

Heterogeneous polymer-based nanoparticles comprise a very promising family of materials for a broad range of applications. Here, we present a detailed study of structural heterogeneities in nanostructured single-molecule nanoparticles in various environments by means of atomistic molecular dynamics simulations. The nanoparticles consist of mikto-arm star copolymers with two types of chemically incompatible arms, namely poly(ethylene oxide) (PEO) and polystyrene (PS), (PS) n,(PEO) n, where n is the number of arms. The immiscibility between the two components gives rise to intramolecularly nanostructured particles. The nanostructured objects resemble either "Janus-like" or "patchy-like" particles, depending on the number or the length of the arms (or both) as well as the interaction with the surrounding medium. The degree of intramolecular heterogeneity increases with increasing number of arms and with decreasing affinity of star components to the polymer host. We provide a detailed analysis of the internal structure of the star-shaped particles, focusing on the intramolecular packing and the spatial arrangement of the arms. The results of our study can be used to design heterogeneous, internally nanostructured particles with two phases of distinct static properties for challenging specific applications of next-generation materials.

Modeling 3D-CSIA data: Carbon, chlorine, and hydrogen isotope fractionation during reductive dechlorination of TCE to ethene

Reactive transport modeling of multi-element, compound-specific isotope analysis (CSIA) data has great potential to quantify sequential microbial reductive dechlorination (SRD) and alternative pathways such as oxidation, in support of remediation of chlorinated solvents in groundwater. As a key step towards this goal, a model was developed that simulates simultaneous carbon, chlorine, and hydrogen isotope fractionation during SRD of trichloroethene, via cis-1,2-dichloroethene (and trans-DCE as minor pathway), and vinyl chloride to ethene, following Monod kinetics. A simple correction term for individual isotope/isotopologue rates avoided multi-element isotopologue modeling. The model was successfully validated with data from a mixed culture Dehalococcoides microcosm. Simulation of Cl-CSIA required incorporation of secondary kinetic isotope effects (SKIEs). Assuming a limited degree of intramolecular heterogeneity of δ37Cl in TCE decreased the magnitudes of SKIEs required at the non-reacting Cl positions, without compromising the goodness of model fit, whereas a good fit of a model involving intramolecular CCl bond competition required an unlikely degree of intramolecular heterogeneity. Simulation of H-CSIA required SKIEs in H atoms originally present in the reacting compounds, especially for TCE, together with imprints of strongly depleted δ2H during protonation in the products. Scenario modeling illustrates the potential of H-CSIA for source apportionment.

Molecular chain heterogeneity of a branched polyethylene resin using cross-fractionation techniques

The typical standard long chain branching (LCB) polyethylene (PE) SRM1476 is issued by the American National Bureau of Standards, which is widely used as a standard reference material in chromatographic experiments. Although some works have been reported in literatures, they are not consistent, such as the data about its molecular weight and molecular weight distribution. Therefore, it is necessary to further investigate the microstructure features of SRM1476 in order to better serve as a reference object in comparison with other unknown resins. In this study, the molecular chain heterogeneity of SRM1476 is investigated extensively and compared with the linear PE SRM1475. Based on the characterization of the original sample, SRM1476 actually has both LCB and short chain branching (SCB) structures, as well as the SCB content is more than LCB content in 13C-NMR results. After successive self-nucleation and annealing (SSA) thermal fractionation, SRM1476 shows a broad-range endotherm with multiple melting peaks (more than eight peaks), which proves the molecular chain heterogeneity in SRM1476. SRM1476 is fractionated into nine fractions by preparative temperature rising elution fractionation (TREF). At the high elution temperature region, the amounts of fractions are more than 90 %, and their molecular weights are higher. At the low elution temperature region below 50 °C, molecular weights of fractions are lower and their amounts are less than 5 %. Differential scanning calorimetry (DSC) melting curves of TREF fractions with higher elution temperatures shift toward higher temperature with sharper melting peaks. In the results of TREF-SSA cross-fractionation, each fraction shows a broad-range endotherm with multiple melting peaks that shift toward the high elution temperature region with the elution temperature. The arithmetic mean methylene sequence lengths of TREF fractions gradually increase from 33 to 105 as elution temperature increases. Results from TREF-DSC and TREF-SSA cross-fractionations indicate that SRM1476 and its TREF fractions have both intramolecular and intermolecular heterogeneity.

13C isotopic fractionation during biodegradation of agricultural wastes

Significant differences in δ13C signatures occur within and between plant tissues and their constituent biochemical entities, and also within and between heterotrophic bacteria and fungi and their metabolic products. Furthermore, 13C isotopic fractionation occurs during the biodegradation of organic molecules as seen in the substrate, respired CO2 and the microbial biomass, which could be related to substrate composition and/or microbial metabolism. The 13C isotopic fractionation observed during the decomposition of a single defined C substrate appears to be due to the intra-molecular heterogeneity in 13C in the substrate and to 13C isotopic fractionation during microbial metabolism. Very limited data suggest that the latter may be quantitatively more important than the former. Studies with defined fungi in culture media have highlighted the complexities associated with the interpretation of the observed patterns of 13C isotopic fractionation when a single defined C source is added to the culture medium which itself contains one or more C sources. Techniques involving 13C enrichment or paired treatments involving an equivalent C3- and C4-derived substrate have been devised to overcome the problem of background C in the culture medium and 13C isotopic fractionation during metabolism. Studies with complex substrates have shown an initial 13C depletion phase in respired CO2 followed by a 13C enrichment phase which may or may not be followed by another 13C depletion phase. Basic studies involving an integrated approach are required to gain a new insight into 13C isotopic fractionation during organic residue decomposition, by simultaneous measurements of δ13C in all C moieties. New analytical tools to measure real-time changes in δ13CO2 and the intra-molecular δ13C distribution within plant biochemical entities offer new opportunities for unravelling the complex interactions between substrate and microbial metabolism with respect to 13C isotopic fractionation during biodegradation.

Study of intramolecular isotope heterogeneity of organic oxy acids in order to detect sophisticated wines and juice drinks

According to International Code of Oenological Practices it is allowed to use acide L(+)tartrique for wine acidification, while use of synthetic dihydroxysuccinic acid is forbidden. Today it is impossible to differentiate natural dihydroxysuccinic acid from synthetic one by standard techniques. Even by using very sensitive method of isotope mass spectrometry certain difficulties emerge because total isotope characteristics of carbon of dihydroxysuccinic acid of different nature have the same values. However, isotope characteristics of carbon of intramolecular structural groups of dihydroxysuccinic acid made of different raw materials differ significantly. This allows specifying the nature of dihydroxysuccinic acid that is used for making of wines and juice drinks. In Russia, scientific and research institute of beer brewing and wine-making industry carried out a work for studying isotope characteristics of intramolecular isotope heterogeneity of dihydroxysuccinic acid from different origins in order to identify wines and juice drinks. Isotope characteristics of organic oxy acids from different origins were studied including them obtained by synthetic way and numeric range of value δ13 C,‰ were specified. The obtained results allow performing identification tests of wines and juice drinks to find out the products that contain not specified additives as that allowed for its use in production process.

Influence of copolymer fraction composition in ultrahigh molecular weight polyethylene blends with ethylene/1‐hexene copolymers on material physical and tensile properties

AbstractThe reactor blends (RBs) with bimodal molecular weight distribution on the base of ultrahigh molecular weight polyethylene (UHMWPE) and low molecular weight random ethylene/1‐hexene copolymers (CEH) were synthesized by two‐step processes including ethylene polymerization followed by ethylene/1‐hexene copolymerization over rac‐(CH3)2Si(Ind)2ZrCl2/methylaluminoxane catalyst. The four series of blends differed in a composition of copolymer fraction that was varied in a wide range (from 3.0 to 37.0 mol % of 1‐hexene). The differential scanning calorimetric study shows the double melting behavior of the net semicrystalline CEHs, which can be attributed to intramolecular heterogeneity in chain branch distribution. The introduction of CEHs leads to the modification of nascent RB crystalline and amorphous phases. Physical and tensile properties as well as melting indexes of the materials depend not only on the percentage of copolymer fraction that varied from 6.9 to 35.8 wt % but also on its composition. The increase of copolymer fraction with high content of 1‐hexene (≥11.0 mol %) in the blends leads to the change of the character of stress–strain curves; the materials behave as elastomers. Controlled regulation of copolymer fraction characteristics in the synthesis yields RBs combining the enough high strength, good plastic properties with enhanced melting indexes as compared with the net UHMWPE. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40151.

Fluctuating exciton localization in giant π-conjugated spoked-wheel macrocycles

Conjugated polymers offer potential for many diverse applications, but we still lack a fundamental microscopic understanding of their electronic structure. Elementary photoexcitations (excitons) span only a few nanometres of a molecule, which itself can extend over microns, and how their behaviour is affected by molecular dimensions is not immediately obvious. For example, where is the exciton formed within a conjugated segment and is it always situated on the same repeat units? Here, we introduce structurally rigid molecular spoked wheels, 6 nm in diameter, as a model of extended π conjugation. Single-molecule fluorescence reveals random exciton localization, which leads to temporally varying emission polarization. Initially, this random localization arises after every photon absorption event because of temperature-independent spontaneous symmetry breaking. These fast fluctuations are slowed to millisecond timescales after prolonged illumination. Intramolecular heterogeneity is revealed in cryogenic spectroscopy by jumps in transition energy, but emission polarization can also switch without a spectral jump occurring, which implies long-range homogeneity in the local dielectric environment.

Isotopologs and isotopomers: New analytical aspects of isotopic mass spectrometry in biology

Metabolic products of biological systems in most cases are polyatomic molecular structures containing polyisotopic elements (hydrogen, carbon, nitrogen, oxygen, sulfur, chorine, etc.) that are different in genesis and biosynthetic pathways. In the molecules carrying two and more atoms of polyisotopic element in different positions (sites), the probability of detection of isotopes by sites in the pool (array) of analyzed molecules may be different, i.e., there is intramolecular isotopic heterogeneity by the specified element. Detection and quantitative estimation of isotopic heterogeneity of polyisotopic elements in molecules by the methods of isotopic mass spectrometry is a novel source of information about the processes involving the respective polyisotopic element. An isotopic equation has been proposed, the coefficients of which are normalized peak intensities of isotopically different molecular ions in the mass spectrum of the analyte. Solutions of this equation reflect the abundance ratios of isotopic atoms of polyisotopic element by its positions in molecules comprising the analyzed pool. During homogenous (equally probable) distribution of isotopic atoms of the element by all of its sites in molecules of the analyzed pool, solutions of the isotopic equation are equal to each other. In the case of non-homogenous isotope distribution of the polyisotopic element in the pool of molecules, solutions of the isotopic equation take on different values and may be presented by both real and complex numbers. Solutions of the isotopic equation reflect the peculiarities of distribution of element isotopes in a molecule and possible pathways of formation of a pool of analyzed molecules under laboratory and natural conditions.

Effect of the Sequence Length Distribution on the Lamellar Crystal Thickness and Thickness Distribution of Polyethylene: Perfectly Equisequential ADMET Polyethylene vs Ethylene/α-Olefin Copolymer.

The morphology of ADMET-synthesized polyethylene with n-butyl branches precisely spaced on every 39th carbon (EH39) was studied in comparison with an ethylene/1-hexene addition copolymer possessing the same branching probability, the goal being to elucidate the effect of the intramolecular sequence length heterogeneity on the lamella crystal thickness and its distribution. EH39 was found to have an orthorhombic crystalline polymorphism, which is normal for commercialized polyethylenes and different from that of the other ADMET polyethylenes with shorter CH2 spacing (C15, C21). EH39 exhibits a narrow lamella thickness distribution; the average thickness (lc,av.) corresponds exactly to the space length between two consecutive branches, suggesting the complete exclusion of n-butyl branches from the crystal stem. The average thickness, lc,av. mentioned above is also coincident with that obtained from WAXS and SAXS. On the other hand, the 1-hexene copolymer forms much thicker lamellae and a broader thickness d...

Phase Structure and Crystallization Behavior of Polypropylene in-Reactor Alloys: Insights from Both Inter- and Intramolecular Compositional Heterogeneity

Systematic investigation on the compositional heterogeneity, phase structure, the crystallization and subsequent melting behavior of two commercial in-reactor alloys EB−P and EP−P (ethylene-co-butylene polypropylene and ethylene-co-propylene polypropylene) from Basell were conducted. The composition of the alloys and the chain structure of each component were characterized by combinatorial using of preparative TREF and 13C NMR technique. The compositional heterogeneities of both samples were further studied by SSA technique, and possible thermal fractionation mechanisms were then inferred. Correlations between the mechanical properties and the molecular architectures and phase structures were discussed. The results show that the excellent balance between toughness and rigidity of sample EB−P primarily benefits from the crystalline polyethylene homopolymer (HPE) phase and the amorphous ethylene-α-olefin copolymer (EC) component, which is proved to be enriched at the interface between the dispersed polyprop...

Evidence for substantial intramolecular heterogeneity in the stable carbon isotopic composition of phytol in photoautotrophic organisms

The ubiquitous isoprenoid, phytol, was isolated from a range of algae, terrestrial plants and a bacterium, and its two terminal carbon atoms were quantitatively removed by chemical oxidation. The product, 6,10,14-trimethylpentadecan-2-one, was depleted in 13C by 1–4‰ relative to the parent phytol. This difference is significant, and indicates that the pathway for biosynthesis of phytol induces substantial intramolecular stable carbon isotopic fractionation. The nature and magnitude of the fractionation suggest strongly that it is associated both with the biosynthesis of isopentenyl pyrophosphate via the 2-C-methylerythritol-4-phosphate pathway and with the formation of carotenoids and phytol from geranyl-geraniolphosphate. As a result of these large, intramolecular isotopic differences, diagenetic products formed by loss of C, such as pristane, may be naturally depleted in 13C by several permil relative to phytane.

The isolated MUC5AC gene product from human ocular mucin displays intramolecular conformational heterogeneity

Atomic force microscopy (AFM) has been used to show that human ocular mucins contain at least three distinct polymer conformations, separable by isopycnic density gradient centrifugation. In this work we have used affinity purification against the anti(mucin peptide core) monoclonal antibody 45M1 to isolate MUC5AC gene products, a major component of human ocular mucins. AFM images confirm that the affinity-purified polymers adopt distinct conformations that coidentify with two of those observed in the parent population, and further reveal that these two different conformations can be present within the same polymer. AFM images of the complexes formed after incubation of 45M1 with the parent sample reveal different rates of binding to the two MUC5AC polymer types. The variability of gene products within a mucin population was revealed by analyzing the height distributions along the polymer contour and periodicities in distances between occupied antibody binding sites. AFM analysis of mucin polymers at the single molecule level provides new information about the genetic origins of individual polymers and the contributions of glycosylation to the physicochemical properties of mucins, which can be correlated with information obtained from biochemistry, antibody binding assays, and molecular biology techniques.

Formation of New Original Material Based on the Genetic Heterogeneity of the Disomic Offspring of Aneuploid Wheat Plants

A series of disomic lines of spring wheat Opal developed on the basis of monosomic lines of this cultivar has been studied. The lines have been tested for combining ability, and the heterosis effect has been studied in disomic lines of F1 hybrids obtained by topcrossing. The line have been demonstrated to differ both from one another and from cultivar Opal in the expression of quantitative traits, combining ability, and the degree of heterosis in F1. These data suggest that recombinations accompanying the formation of the monosomic series have changed their genetic program. To test this suggestion, intramolecular heterogeneity of 42-chromosome plants has been analyzed using polymerase chain reaction (PCR) and isoenzyme analysis. The results confirmed the differences at the DNA and protein levels. According to the results of molecular analyses, A-genome lines are the most polymorphic. Strong heterosis effects have been detected in hybrid combinations contributed by D- and B-genome lines, which are characterized by medium and low degrees of molecular genetic polymorphism. Lines that are promising in terms of breeding programs have been identified.

Physical and mechanical properties of polyethylene for pipes in relation to molecular architecture. I. Microstructure and crystallisation kinetics

Ethylene/α-olefin copolymers having bimodal molar weight distribution are investigated in comparison with unimodal copolymers in order to understand the incidence of the molecular architecture on the stress cracking resistance. The preferred introduction of the co-units in the longest chains of bimodal copolymers is suggested to favour the occurrence of intercrystalline tie molecules during crystallisation. The more complex is the molecular architecture, the greater is the difficulty for crystallisation by regular chain folding. Intermolecular chemical heterogeneity resulting from preferred incorporation of the co-units in the long chains enhances the co-unit disturbing effect on crystallisation without reducing crystallinity. Intra-molecular heterogeneity of the co-unit distribution is also suggested to be an efficient means to generate tie molecules and random chain folding at the expense of regular chain folding. Isothermal crystallisation is used to probe the effect of molecular architecture on the crystallisation kinetics. It appeared that the correlations between kinetics, molecular architecture and molecular topology of unimodal copolymers no longer hold when considering bimodal copolymers. In contrast, the crystal surface free energy proved to be sensitive to topological changes resulting from molecular architecture modifications.

Characterization of Intramolecular Composition Heterogeneity of Metallocene‐Based and Conventional Ethylene‐Butene Copolymers using TREF/DSC

A new and convenient method for the qualitative characterization of intramolecular composition heterogeneity was established. The metallocene-based and conventional ethylene-butene copolymers were fractionated with preparative temperature rising elution fractionation (TREF) technique, and some selected fractions were directly characterized with differential scanning calorimetry (DSC) after stepwise crystallization. The observed multiple endotherms in the melting traces of some fractions were attributed to intramolecular composition heterogeneity after other possibilities were excluded. It is found that intramolecular composition heterogeneity is present in both metallocene-based and conventional ethylene-butene copolymers, but the metallocene-based copolymers may have a relatively narrower intramolecular composition distribution. Moreover, the mechanism of this method and its applicable range are also discussed.