Formation Of Ordered Structures Research Articles

Monitoring of duplex and triplex formation by 19F NMR using oligodeoxynucleotides possessing 5-fluorodeoxyuridine unit as 19F signal transmitter

We prepared oligodeoxynucleotides (ODNs) possessing a 5-fluorodeoxyuridine (5-FU) unit as a 19F-signal transmitter, and characterized their structures including single strand, duplex, and triplex using 19F NMR. The change in chemical shift induced by incorporation of 5-FU into the ODNs and the formation of higher order structures allowed monitoring of structural changes. Data from UV melting experiments and CD spectra were consistent with the spectral changes in the NMR studies. These 19F-labeled ODNs may be promising molecular probes for the identification of DNA structures in complicated biological conditions.

Higher order structure of short collagen model peptides attached to dendrimers and linear polymers

Collagen, which is used as a biomaterial, is the most abundant protein in mammals. We have previously reported that a dendrimer modified with collagen model peptides, (Gly-Pro-Pro)(5), formed a collagen-like triple-helical structure, showing thermal reversibility. In this study, various collagen-mimic dendrimers of different generations and at different binding ratios were synthesized, to investigate the relationship between the peptide clustering effect and the higher order structure formation. The formation of the higher order structure was influenced by the binding ratios of the peptide to the dendrimer, but was not influenced by the dendrimer generation. A spacer, placed between the dendrimer terminal group and the peptide, negatively contributed to the formation of the higher order structure. The collagen model peptides were also attached to poly(allylamine) (PAA) and poly-L-lysine (poly(Lys)) to compare them with the collagen-mimic dendrimers. The PAA-based collagen-mimic compound, bearing more collagen model peptides than the dendrimer, exhibited a thermally stable higher order structure. In contrast, this was not observed for the collagen-mimic polymers based on poly(Lys). Therefore, dendrimers and vinyl polymers act as a scaffold for collagen model peptides and subsequently induce higher order structures.

Molecular Properties of Telomeric TRF1/TRF2 - DNA Systems

Telomeres are nucleoprotein complexes that protect the ends of linear eukaryotic chromosomes from degradation and fusion. Human telomeric DNA contains tandem arrays of double stranded TTAGGG repeats. Telomeric DNA forms specific complexes with many different proteins (shelterins), among which TRF1 and TRF2 are the most essential for the maintenance of telomere structure and function. TRF1 is a negative regulator of telomere length whereas TRF2 is involved in formation of telomeric higher order structures (t-loops), and functions more related to capping the DNA end. Both proteins bind to DNA as pre-formed homodimers. Although cellular functions of both these proteins are different, their structures are very similar. Both TRF1 and TRF2 contain two conserved sequence motives which form specific domains, namely homodimerisation and Myb-DNA binding domains.In order to reveal the molecular properties of both proteins and also differences between binding modes of TRF1 and TRF2 to telomeric DNA, detailed studies of both binding domains have been performed. We carried out molecular dynamic simulations of TRF1 and TRF2 binding domains and their complexes with DNA. Starting models of studied systems were based on X-ray structures of TRF1 and TRF2 Myb-DNA binding domains [1]. The results have revealed structural differences between bound proteins and structural differences of their binding patterns with DNA. Additionally, we provide experimental evidence that interaction of both shelterins and DNA can be specifically perturbed by small molecular weight ligands. These results support the idea that TRF1/TRF2 - DNA systems are potential new targets for anticancer therapy.1. R. Court, L. Chapman, L. Fairall, D. Rhodes, EMBO Reports 6 (2005) 39-45.

Spontaneous molecular orientation of polyimides induced by thermal imidization (5). Effect of ordered structure formation in polyimide precursors on CTE

Abstract Six poly(amic acid) (PAA) systems based on pyromellitic dianhydride (PMDA) formed some ordered structures with optical anisotropies clearly detectable on an optical polarizing microscope (POM) in N -methyl-2-pyrrolidone (NMP) at room temperature at high solute concentrations (15–25 wt.%) with complete sol–gel transition reversibility, whereas PAA systems based on 3,3′,4,4′-biphenyltetracarboxylic dianhydride (s-BPDA) with a variety of diamine components showed no optical anisotropy in solution. However, a fluorescence probe technique combined with solution viscosity measurements suggested that a PAA derived s-BPDA with 1,4-phenylenediamine (PDA), i.e., PAA(s-BPDA/PDA) forms some ordered structure with a POM-undetectable very local scale during prolonged storage in NMP at room temperature. The introduction of the biphenyldiimide (BPDI) units at 33% into the PAA(s-BPDA/PDA) main chains by copolymerization allowed the formation of optically anisotropic gels with a smectic liquid crystal-like ordered structure by cooling the NMP solution at −20 °C. PI films derived from s-BPDA with PDA, i.e., PI(s-BPDA/PDA) were prepared upon thermal imidization of the BPDI-containing PAA films dried at 40 °C for 2.5 h. An increase in the BPDI content caused a gradual decrease in the linear coefficient of thermal expansion (CTE) of the PI films. This can be interpreted as a result of an intensified pre-orientation at the stage of the PAA cast films by incorporation of the BPDI units. When the BPDI-containing PAA solutions were heated at 70 °C for 4 min prior to the drying process at 40 °C, the ordered structures can be cancelled without imidization, and the CTE values of the resulting PI films appreciably increased compared to the case without heating at 70 °C. A similar effect was observed even in the BPDI-free original s-BPDA/PDA system. The results suggest the presence of a POM-undetectable very locally ordered structure in the PAA cast films, which promotes the pre-orientation of the PAA chains in the cast films and consequently can contribute to a further decrease in the CTE of the PI(s-BPDA/PDA) films.

Modified Debye screening potential in a magnetized quantum plasma

The effects of quantum mechanical influence and uniform static magnetic field on the Shukla–Nambu–Salimullah potential in an ultracold homogeneous electron–ion Fermi plasma have been examined in detail. It is noticed that the strong quantum effect arising through the Bohm potential and the ion polarization effect can give rise to a new oscillatory behavior of the screening potential beyond the shielding cloud which could explain a new type of possible robust ordered structure formation in the quantum magnetoplasma. However, the magnetic field enhances the Debye length perpendicular to the magnetic field in the weak quantum limit of the quantum plasma.

Polyimides Containing Trans-1,4-cyclohexane unit (III). Ordered Structure and Intermolecular Interaction in s-BPDA/CHDA Polyimide

Polyimide (PI) derived from 3,3',4,4'-biphenyltetracarboxylic dianhydride (s-BPDA) with trans-1,4-cyclohexanediamine (CHDA), i.e., s-BPDA/CHDA was investigated from the viewpoint of ordered structure and intermolecular interaction. Thermodynamic parameters of the model compounds for melting behavior suggested significantly restricted conformational changes in the trans-1,4-cyclohexylene unit and the presence of strong BPDI—BPDI interaction in s-BPDA/CHDA. The effect of diamine structure on the fluorescence yield also supported the presence of the BPDI—BPDI interaction or the BPDI dimer in s-BPDA-based semi-cycloaliphatic PIs. The results of the fluorescence depolarization measurements can be rationalized by a proposed mechanism assuming the presence of the BPDI dimer sites, where the fluorescence of s-BPDA/CHDA occurs by excitation of the lower energy trap sites consisting of the BPDI dimer via excitation energy migration or direct excitation of the dimer. The structure-sensitive infrared band around 550 cm-1 gradually shifted toward higher frequency with simultaneous narrowing with increasing cure temperature, suggesting gradual ordered structure formation in s-BPDA/CHDA. Thermal imidization at 400 °C caused splitting of the C—H stretching band around 2940 cm-1, corresponding to the disappearance of distinct glass transition for the s-BPDA/CHDA system.

Enzyme Susceptibility of High‐Amylose Starch Precipitated from Sodium Hydroxide Dispersions

ABSTRACTType III resistant starch (RS) is understood to be due to the ordered structure formation in the process of retrogradation. Most treatments of granular high‐amylose maize starch (HAMS) do not completely eliminate the original ordered structure. We hypothesized that residual ordered structure would constrain subsequent physical reassociation of chains and the formation of RS. The objective was to generate differences in enzyme susceptibility using two means of precipitation of fully dispersed starch and to relate differences in enzyme susceptibility to the structure of the precipitates. Dispersions in sodium hydroxide were precipitated either with ethanol or ammonium sulfate. RS and the timecourse of digestion were determined. Crystallinity and helicity were estimated using wide‐angle X‐ray diffraction and solid‐state 13C CP/MAS NMR, respectively. Precipitation of whole starch with ethanol led to lower RS values (≈24%) than precipitation with ammonium sulfate (≈39%) and also to higher reaction rate constants for an early component of digestion. Ethanol precipitation of a branched starch fraction gave essentially no RS, whereas ammonium sulfate precipitation of the same branched material had >20% RS. Ethanol precipitates contained single helices, in most but not all cases, contributing to V‐type crystallinity. Ammonium sulfate precipitates had double helices contributing to B‐type crystallinity.

수성 알루미나/탄화규소 슬러리의 동결주조와 층상복합체의 제조: (I) 슬러리의 분산과 유동성

Zeta potential, sedimentation bulk density and rheology in the dispersion system have been studied in terms of solid loading (40-55 vol%), and types of additives. Ammonium polymethacrylate, glycerol, ethoxylated acetylenic diol, and polyvinyl alcohol have been used as the dispersant, cryo-protectant, surfactant, and binder, respectively. Sedimentation density greatly increased upon adding dispersant; the effect was more pronounced with ionic alumina suspension compared with covalent silicon carbide. With further addition of cryo-protectant and surfactant to dispersant, the sedimentation density increased somewhat. The suspension viscosity generally behaviored in an opposite manner to the sedimentation density, i.e., high sedimentation gave low high-shear viscosity, indicative of low order structure formation in the suspended particles. Shear rate rheology in shear rate of 2-300 sec?¹ showed a shear thinning and its onset began at similar shear rate (~100 sec?¹), regardless of solid loading.

Nanometer-scale higher order structure formation in molecular assembly

Nanometer-scale higher order structure formation in molecular assembly

Interface peptide of Alzheimer’s amyloid beta: Application in purification

Protein precipitation is a process commonly observed during bacterial expression of heterologous proteins. The high concentration of currently used solubilizing agents limits the scope of purification procedures. Protein solubilizers acting at very low concentrations will allow function-based purification protocols. Such applications are possible where sequence dependent protein–protein interactions occur. Oligomerization and higher order structure formation by proteins are examples where the interface peptide sequences are inhibitors of such interactions. In this study, we show that a partial sequence of Alzheimer’s amyloid beta (Aβ) peptide can inhibit the aggregation. This enables the purification of protein containing Aβ sequence.

Suspension Characteristics and Rheological Properties of Aqueous Alumina/Zirconia Freeze Casting Slurries

The dispersion and rheological behavior of aqueous alumina, zirconia, and mixed alumina/ zirconia slurries have been studied in terms of solid loading and the incorporated multiple processing additives. Darvan-C, Dynol 604, Glycerol, and PVA were used as the dispersant, surfactant, cryoprotectant, and binder, respectively. Sedimentation density increased significantly on adding the dispersant; its effectiveness was similar for both the alumina and zirconia suspensions. With further addition of binder, the sedimentation density decreased. The suspension viscosity generally behaved in an opposite manner to the sedimentation density, i.e., low sedimentation density gave high low-shear viscosity, indicative of high order structure formation in the suspended particles. Shear rate rheology of suspensions with high dispersant content showed a shear thinning but with low dispersant content (≤2 wt.%), however, it showed a shear thickening at high shear rate (>600 s-1).

Influence of Film Casting Condition and Thermal Treatment on Order Structure of Polyurethane Block Copolymer

An attempt has been made to investigate the influence of film casting temperature and thermal ageing on order structure formation of segmented polyurethane (SPU) block copolymer. For this purpose films were casted at three different temperature of 60, 80, or 100°C and thermal aged at 100, 120, 130, or 150°C. The structure of films were investigated by Fourier-transform infrared (FT-IR), wide angle X-ray diffraction (WAXD) and differential scanning calorimetry (DSC). Film casted at slow solvent evaporation has more regular structure than the film casted at rapid solvent evaporation. Crystaline structure decreases with increase in casting temperature due to chain entanglement, which makes crystallization process tougher. The effect of ageing temperature on crystalline structure formation remains unclear. Decrease of ordered structure was observed when the samples were heat treated at 100 or 120°C, however, slight increase of ordered structures were observed for the samples heat treated at 130 or 150°C. Therefore, the influence of thermal ageing has been explained in terms of order-disorder temperature of block copolymer.

Effect of ordered structure and domain boundary on low-loss Ba[Mg1/3(Nbx/4Ta(4−x)/4)2/3]O3microwave dielectric ceramics

The microstructure of Ba[Mg1/3(NbxTa(4−x)/4)2/3]O3ceramics (x= 1, 2, 3, and 4) was investigated. Ordered structure and domain boundary were observed by high-resolution transmission electron microscopy. The disordered structure of 0.41 nm lattice modulation and the 1:2 ordering structure of 0.71 nm lattice modulation in the [111] direction are both formed in Ba[Mg1/3(NbxTa(4−x)/4)2/3]O3ceramics. Except for the incoherent interface between disordered and 1:2 ordering domain, the coherent interface between two 1:2 ordering domains can also be observed in the Ba[Mg1/3(NbxTa(4−x)/4)2/3]O3ceramics. In the Ba[Mg1/3(Nb1/4Ta3/4)2/3]O3ceramic, the formation of an extra ordering structure (lattice modulation of 1.24 nm in the [111] direction) on the antiphase domain boundary with proper Nb substitution contributes to lower dielectric loss due to the stabilization of the domain boundary.

Solution and gas phase hydrogen/deuterium exchange of oligoamide complexes by nanoelectrospray mass spectrometry

Hydrogen bonding is crucial to biological systems and is intrinsic to non-covalent interactions. They are important in the formation of higher order structures of proteins as well as in the interactions of proteins with other biological molecules. Electrospray ionization (ESI) is an important tool in the study and characterization of molecular complexes and has proven to be extremely powerful and invaluable in the studying of biomolecular structures and non-covalent interactions. We have utilized solution and gas phase hydrogen/deuterium exchange (HDX) as a method to determine the specificity of supramolecular complex formation using monomers possessing sites containing hydrogen-bond donor and acceptor groups. By comparing the average number of exchanges for the monomer subunits to the average number of exchanges for the complex, we can distinguish if a specific complex is formed in solution, or whether it is the artifact of a gas phase process during ESI. In this paper we have investigated several non-covalent supramolecular complexes by nanoelectrospray (nanoESI) mass spectrometry (MS). By using the solution and gas phase HDX, we were able to identify several specific supramolecular complexes. Thus, solution and gas phase HDX combined with nanoESI-MS provides for a convenient method in ascertaining the origin and stability of non-covalent complexes.

P3-289: Protein sequence

Histones are basic nuclear proteins that are responsible for the nucleosome structure within the chromosomal fiber in eukaryotes. See 142711. Albig et al. (1996) identified a gene, which they called H3.4, encoding a member of the H3 class of histones. Albig and Doenecke (1997) designated this gene H3t. By sequence analysis, Albig et al. (1996) found that H3t differs by 4 amino acid residues from the consensus mammalian H3 structure, and shows the consensus promoter and 3–prime flanking portions typical of replication–dependent histones. Preliminary data indicated that H3t is expressed in testicular cells. By analysis of a somatic cell hybrid panel and by fluorescence in situ hybridization, Albig et al. (1996) mapped the H3t gene to 1q42, outside the gene clusters that contain the other replication–dependent H3 genes. Histones are the basic nuclear proteins responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two each of the core histones (H2A, H2B, H3, and H4) form an octamer, as the protein moiety of the core structure of the nucleosome. The linker histone H1 is involved in sealing 2 rounds of nucleosome DNA at the surface of the nucleosome core and is also involved in the formation of higher order structures of chromatin. Because of their function in organizing chromosomal structure, histones contribute to virtually all chromosomal processes, such as gene regulation, chromosome condensation, recombination, and replication.

On the origin of telomeres: a glimpse at the pre-telomerase world

Chromosomes may be either circular or linear, the latter being prone to erosion caused by incomplete replication, degradation and inappropriate repair. Despite these problems, the linear form of DNA is frequently found in viruses, bacteria, eukaryotic nuclei and organelles. The high incidence of linear chromosomes and/or genomes evokes why and how they emerged in evolution. Here we suggest that the primordial terminal structures (telomeres) of linear chromosomes in eukaryotic nuclei were derived from selfish element(s), which caused the linearization of ancestral circular genome. The telomeres were then essential in solving the emerged problems. Molecular fossils of such elements were recently identified in phylogenetically distant genomes and were shown to generate terminal arrays of tandem repeats. These arrays might mediate the formation of higher order structures at chromosomal termini that stabilize the linear chromosomal form by fulfilling essential telomeric functions.

Interrelation Between H‐Bond and Pi‐Electron Delocalization

AbstractFor Abstract see ChemInform Abstract in Full Text.

Interrelation between H-Bond and Pi-Electron Delocalization

Among many various kinds of molecular interactions, the H-bond has a special position. The term is ubiquitous in the world that surrounds us, but also it is often applied in different ways. The H-bond is of great importance in natural sciences. This relates particularly to biological aspects, such as molecular recognition that could be a basis for the creation of life,1-4 formation of higher order structures of peptides and nucleic acids,5 and biochemical processes, particularly the enzymes catalyzed.6,7 One can say that the H-bond plays a double role in biological systems: on one hand, as a relatively strong directional interaction, it leads to relatively stable supramolecular structures, and on the other hand, because of dynamic features of the proton, it is an active site for initiation of chemical reactions. H-bonds are the source of specific properties of associated liquids, with water being the most popular among them.8 Water as a medium in which life was most probably created is saturated by H-bonds with highly mobile protons in between, even in the solid state.9 In many crystal lattices of organic compounds, the H-bonds are a decisive factor governing packing.10 In designing new interesting crystal structures, which is the subject of fast developing crystal engineer* To whom correspondence should be addressed. E-mail: slagra@ uni.lodz.pl or slagra@ccmsi.us. Fax: +48-42-6790447. 3513 Chem. Rev. 2005, 105, 3513−3560

Polypeptide Substrate Recognition by Calnexin Requires Specific Conformations of the Calnexin Protein

Calnexin is an endoplasmic reticulum chaperone that binds to substrates containing monoglucosylated oligosaccharides. Whether calnexin can also directly recognize polypeptide components of substrates is controversial. We found that calnexin displayed significant conformational lability for a chaperone and that heat treatment and calcium depletion induced the formation of calnexin dimers and higher order oligomers. These conditions enhanced the chaperone activity of calnexin toward glycosylated and non-glycosylated major histocompatibility complex (MHC) class I heavy chains, and enhanced calnexin binding to MHC class I heavy chains. In contrast to these observations, calnexin binding to oligosaccharide substrates has been reported to be impaired under calcium-depleting conditions. Calnexin dimers were induced in HeLa cells upon heat shock and under calcium-depleting conditions, and heat shock enhanced calnexin binding to MHC class I heavy chains in HeLa cells. Virus-induced endoplasmic reticulum stress also resulted in the appearance of calnexin dimers. Tunicamycin treatment of HeLa cells induced a slow accumulation of calnexin dimers, the appearance of which correlated with enhanced calnexin binding to deglycosylated MHC class I heavy chains. In vitro, the presence of calnexin-specific oligosaccharides inhibited the formation of calnexin dimers and higher order structures. Together, these data indicate that polypeptide binding is favored by conditions that induce partial unfolding of calnexin monomers, whereas oligosaccharide binding is favored by conditions that enhance the structural stability (folding) of calnexin monomers. Conditions that induce the calnexin "polypeptide-binding" conformation also induce self-association of calnexin if the concentration is sufficiently high; however, calnexin dimerization/oligomerization per se is not essential for polypeptide substrate binding.

Influence of superlattice and antiphase domain boundaries on dielectric loss in Ba[Mg1∕3(Nbx∕4Ta(4−x)∕4)2∕3]O3 ceramics

The Ba[Mg1∕3(Nbx∕4Ta(4−x)∕4)2∕3]O3 ceramics (x=0, 1, 2, 3, and 4) synthesized by a solid reaction method were sintered at 1650 °C for 9 h. The quality factor (Q,∼1∕tanδ,tanδ: dielectric loss) and superlattice structure were investigated by the cavity method and high-resolution electron microscopy. The excellent Q value of 17 600 obtained at appropriate Nb content (x=1). The disorder structure (superlattice modulation∼0.41nm), 1:2 ordering structure (superlattice modulation∼0.71nm) and antiphase domain boundary (APB) were revealed in Ba[Mg1∕3(Nbx∕4Ta(4−x)∕4)2∕3]O3 ceramics. The formation of extra ordering structure (superlattice modulation∼1.24nm) on the APBs contributed to the improved Q value with the stabilization of ordering-induced domain boundaries.