Higher-order Architecture Research Articles

Morphological and Dimensional Control via Hierarchical Assembly of Doped Oligoaniline Single Crystals

Single crystals of doped aniline oligomers are produced via a simple solution-based self-assembly method. Detailed mechanistic studies reveal that crystals of different morphologies and dimensions can be produced by a "bottom-up" hierarchical assembly where structures such as one-dimensional (1-D) nanofibers can be aggregated into higher order architectures. A large variety of crystalline nanostructures including 1-D nanofibers and nanowires, 2-D nanoribbons and nanosheets, 3-D nanoplates, stacked sheets, nanoflowers, porous networks, hollow spheres, and twisted coils can be obtained by controlling the nucleation of the crystals and the non-covalent interactions between the doped oligomers. These nanoscale crystals exhibit enhanced conductivity compared to their bulk counterparts as well as interesting structure-property relationships such as shape-dependent crystallinity. Furthermore, the morphology and dimension of these structures can be largely rationalized and predicted by monitoring molecule-solvent interactions via absorption studies. Using doped tetraaniline as a model system, the results and strategies presented here provide insight into the general scheme of shape and size control for organic materials.

Hybridization of inorganic nanoparticles and polymers to create regular and reversible self-assembly architectures

Inorganic nanoparticles (NPs) with diversified functionalities are promising candidates in future optoelectronic and biomedical applications, which greatly depend on the capability to arrange NPs into higher-order architectures in a controllable way. This issue is considered to be solved by means of self-assembly. NPs can participate in self-assembly in different manners, such as smart self-organization with blended molecules, as the carriers of host molecules for assembly and disassembly with guest molecules, as netpoints to endow the architectures specific functionalities, and so forth. To enhance the structural stability of the as-prepared assembly architectures, polymers have been utilized to create NP-polymer composites. Meanwhile, such a strategy also demonstrates the possibility of integrating the functionalities of NPs and/or polymers by forming regular architectures. The emerging interest in the current optoelectronic and biological areas strongly demands intelligent nanocomposites, which are produced by combination of the excellent functionalities of NPs and the responsiveness of polymers. On the basis of the recent progress in fabricating NP-polymer composites, this critical review summarizes the development of new methods for fabricating regular self-assembly architectures, highlights the reversible assembly and disassembly behavior, and indicates the potential applications.

Intermolecular Alignment in Y145Stop Human Prion Protein Amyloid Fibrils Probed by Solid-State NMR Spectroscopy

The Y145Stop mutant of human prion protein, huPrP23-144, has been linked to PrP cerebral amyloid angiopathy, an inherited amyloid disease, and also serves as a valuable in vitro model for investigating the molecular basis of amyloid strains. Prior studies of huPrP23-144 amyloid by magic-angle-spinning (MAS) solid-state NMR spectroscopy revealed a compact β-rich amyloid core region near the C-terminus and an unstructured N-terminal domain. Here, with the focus on understanding the higher-order architecture of huPrP23-144 fibrils, we probed the intermolecular alignment of β-strands within the amyloid core using MAS NMR techniques and fibrils formed from equimolar mixtures of (15)N-labeled protein and (13)C-huPrP23-144 prepared with [1,3-(13)C(2)] or [2-(13)C]glycerol. Numerous intermolecular correlations involving backbone atoms observed in 2D (15)N-(13)C spectra unequivocally suggest an overall parallel in-register alignment of the β-sheet core. Additional experiments that report on intermolecular (15)N-(13)CO and (15)N-(13)Cα dipolar couplings yielded an estimated strand spacing that is within ∼10% of the distances of 4.7-4.8 Å typical for parallel β-sheets.

Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus

Establishment and segregation of distinct chromatin domains are essential for proper genome function. The insulator protein CCCTC-binding factor (CTCF) is involved in creating boundaries that segregate chromatin and functional domains and in organizing higher-order chromatin structures by promoting chromosomal loops across the vertebrate genome. Here, we investigate the insulation properties of CTCF at the human and mouse homeobox gene A (HOXA) loci. Although cohesin loading at the CTCF binding site is required for looping, we found that cohesin is dispensable for chromatin barrier activity at that site. Using mouse embryonic stem cells in both a pluripotent and differentiated neuronal progenitor state, we determined that embryonic stem cell pluripotency factor OCT4 antagonizes cohesin loading at the CTCF binding site. Loss of OCT4 in the committed and differentiated neuronal progenitor cells results in loading of cohesin and chromosome looping, which contributes to heterochromatin partitioning and selective gene activation across the HOXA locus. Our analysis reveals that chromatin barrier activity of CTCF is evolutionarily conserved and is responsible for the coordinated establishment of chromatin structure, higher-order architecture, and developmental expression of the HOXA locus.

Structural insights into chondroitin sulfate binding in pregnancy-associated malaria

Malaria during pregnancy is caused when parasite-infected erythrocytes accumulate within the placenta through interactions between the VAR2CSA protein on the infected erythrocyte surface and placental CSPGs (chondroitin sulfate proteoglycans). This interaction is the major target for therapeutics to treat or prevent pregnancy-associated malaria. Here we review the structural characterization of CSPG-binding DBL (Duffy-binding like) domains from VAR2CSA and summarize the growing evidence that the exquisite ligand specificity of VAR2CSA results from the adoption of higher-order architecture in which these domains fold together to form a ligand-binding pocket.

Calibrating Mid-Permian to Early Triassic Khuff sequences with orbital clocks

ABSTRACTThe Middle East Geologic Time Scale (ME GTS) seeks to document and age-calibrate Arabian Plate transgressive-regressive (T-R) depositional sequences using: (1) Geological Time Scale of the International Commission on Stratigraphy (GTS), and (2) Arabian Orbital Stratigraphy time scale (AROS). AROS is based on an orbital-forcing glacio-eustatic model that offers three orbital clocks to date T-R sequences: (1) Stratons @ ca. 405 Ky; (2) Dozons @ ca. 4.86 My (12 stratons); and Orbitons @ ca. 14.58 My (36 stratons, three dozons). The Earth today is in Orbiton 0, which started ca. 1.5 Ma (SB 0); the ages of lower boundaries of orbitons can be estimated with the formula SB n = n × 14.58 + 1.5 Ma. This scheme was used to calibrate the Arabian Plate’s Mid-Permian to Early Triassic Khuff sequences, which contain one of the largest gas-bearing carbonate reservoirs in the World.The Khuff and equivalent formations have been interpreted by several authors in terms of six long-period sequences in outcrop belts and subsurface sections (Khuff sequences KS6 to KS1 in ascending order). Their type sections are briefly reviewed with emphasis on their boundaries, higher-order architecture and stage assignments. The age calibration starts at the basal Khuff Sequence Boundary (Khuff SB, Sub-Khuff Unconformity) defined in a type section in Al Huqf outcrop in Oman. Above the Khuff SB (ca. 268.9 Ma) the type sections of the oldest Khuff sequences KS6 (ca. 268.9–264.0 Ma) and KS5 (ca. 264.0–259.1 Ma) are defined in Oman and interpreted to each consist of twelve subsequences (stratons) with the predicted architecture of two consecutive dozons. By biostratigraphy they span the Mid-Permian (Guadalupian Epoch), Wordian and Capitanian stages.Type-Sequence KS4 (ca. 259.1–254.2 Ma) is defined in Iran and corresponds to the Wuchiapingian Stage. The Iranian type-Khuff Sequence KS3 (ca. 254.2–249.4 Ma) contains nine subsequences (stratons) grouped between two major exposure surfaces. By correlation to the Changhsingian Stage and Permian/Triassic Boundary (PTrB) type section in South China, it is interpreted as a dozon with three missing stratons. Khuff Sequence KS2 (ca. 249.4–247.8 Ma) contains the PTrB with an orbital age of ca. 249.0 Ma, compared to 251.0 ± 0.4 in GTS and 249.0–253.0 Ma by radiometric dating in its type section. Khuff sequences KS2 and KS1 contain 13 subsequences (stratons) between ca. 249.4–244.1 Ma spanning latest Permian and Early Triassic. The boundary of the Khuff with the overlying Sudair Formation, Sudair Sequence Boundary, is defined in Borehole SHD-1 (Central Saudi Arabia) and calibrated at ca. 244.1 Ma falling near the age of the Early/Mid-Triassic Boundary in GTS. The enclosed Chart shows a work-in-progress correlation of the six Khuff sequences across the Arabian Plate.

Self-Healing Self-Assembly of Aspect-Ratio-Tunable Chloroplast-Shaped Architectures

Challenges are emerging that demand facile approaches to control the self-assembly of nanocrystal morphology-specific higher-order architectures. Herein, we show a novel reversible wet-chemical approach to control the self-assembly of ZnS nanocrystals into well-defined, uniform, three-dimensional, aspect-ratio-tuned, micrometer-scale, self-healing architectures, which resemble chloroplast in shape. We can control the aspect ratio and the chemical potential of the 3D chloroplast-shaped architectures by adjusting the concentration of ammonia and the ratio of S2−ions to Zn2+ ions. Possible mechanism of the controllable self-assembly is proposed. This self-assembly concept can also be applicable to a wide range of other transition-metal sulfide chloroplast-shaped architectures, such as CdS, CuS, and Ag2S.The present study could open a new avenue to understand the important nanocrystal self-assembly phenomenon.

RAFT Polymer End-Group Modification and Chain Coupling/Conjugation Via Disulfide Bonds

End-group modification of polymers prepared by reversible addition–fragmentation chain transfer (RAFT) polymerization was accomplished by the conversion of trithiocarbonate or dithioester end-groups into a pyridyl disulfide (PDS) functionality. Several different polymers, such as poly(methyl methacrylate), polystyrene, poly(oligoethylene glycol-acrylate), poly(hydroxypropylacrylamide), and poly(N-isopropylacrylamide) were prepared by RAFT polymerization, and subjected to aminolysis in the presence of 2,2′-dithiodipyridine to yield thiol-terminated polymers with yields in the range 65–90% dependent on the polymer structure. Furthermore, this PDS end-group was utilized to generate higher-order architectures, such as diblock copolymers with high yields and selectively. In addition, the PDS end-groups were used for the bioconjugation of different biomolecules, such as oligonucleotides, carbohydrates, and peptides. The successful modification of well-defined polymers was confirmed by a combination of UV-vis, NMR spectroscopy, and gel permeation chromatography.

Life as a Nanoscale Phenomenon

The nanoscale is not just the middle ground between molecular and macroscopic but a dimension that is specifically geared to the gathering, processing, and transmission of chemical-based information. Herein we consider the living cell as an integrated self-regulating complex chemical system run principally by nanoscale miniaturization, and propose that this specific level of dimensional constraint is critical for the emergence and sustainability of cellular life in its minimal form. We address key aspects of the structure and function of the cell interface and internal metabolic processing that are coextensive with the up-scaling of molecular components to globular nanoobjects (integral membrane proteins, enzymes, and receptors, etc) and higher-order architectures such as microtubules, ribosomes, and molecular motors. Future developments in nanoscience could provide the basis for artificial life.

Visualization of Transient Ultra-Weak Protein Self-Association in Solution Using Paramagnetic Relaxation Enhancement

Ultra-weak macromolecular self-association is exceptionally difficult to both detect and visualize using conventional biophysical techniques owing to the very low population of the associated species, yet such weak intermolecular interactions coupled with nucleation events play an important role in driving spontaneous self-assembly to form higher-order architectures (such as crystals, viral capsids, and amyloid fibrils). In this article, we detect and characterize transient, ultra-weak self-association (KD >or= 15 mM) involving the histidine-containing protein HPr by means of paramagnetic relaxation enhancement (PRE), using EDTA-Mn2+ conjugated at three separate sites (E5C, E25C, and E32C, one at a time). Large intermolecular PRE effects, above the background observed with hydroxylamine-EDTA-Mn2+ as a control, are observed for two of the three paramagnetically labeled sites, E5C and E32C. The extent of self-association can be modulated (significantly reduced) by increasing the ionic strength or by the introduction of a negative charge (S46D mutation) within a positively charged surface patch, and abolished upon the addition of the N-terminal domain of enzyme I (EIN) to form a specific EIN-HPr complex. The PRE profiles observed for E5C and E32C can be fitted simultaneously and accounted for quantitatively using conjoined rigid body/torsion angle dynamics-simulated annealing with an ensemble of states to represent the distribution of one molecule of HPr relative to its partner.

Synthetic Strategies and Structural Aspects of Metal‐Mediated Multiporphyrin Assemblies

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions

The regulation of gene expression is mediated by interactions between chromatin and protein complexes. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation. Increasing evidence indicates that gene activation or silencing is often associated with repositioning of the locus relative to nuclear compartments and other genomic loci. At the same time, however, structural constraints impose limits on chromatin mobility. Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation.

Linker Histone H1 per se Can Induce Three-Dimensional Folding of Chromatin Fiber

Higher-order architectures of chromosomes play important roles in the regulation of genome functions. To understand the molecular mechanism of genome packing, an in vitro chromatin reconstitution method and a single-molecule imaging technique (atomic force microscopy) were combined. In 50 mM NaCl, well-stretched beads-on-a-string chromatin fiber was observed. However, in 100 mM NaCl, salt-induced interaction between nucleosomes caused partial aggregation. Addition of histone H1 promoted a further folding of the fiber into thicker fibers 20-30 nm in width. Micrococcal nuclease digestion of these thicker fibers produced an approximately 170 bp fragment of nucleosomal DNA, which was approximately 20 bp longer than in the absence of histone H1 ( approximately 150 bp), indicating that H1 is correctly placed at the linker region. The width of the fiber depended on the ionic strength. Widths of 20 nm in 50 mM NaCl became 30 nm as the ionic strength was changed to 100 mM. On the basis of these results, a flexible model of chromatin fiber formation was proposed, where the mode of the fiber compaction changes depending both on salt environment and linker histone H1. The biological significance of this property of the chromatin architecture will be apparent in the closed segments ( approximately 100 kb) between SAR/MAR regions.

Segmental Duplications and Copy-Number Variation in the Human Genome

The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement associated with genomic disease. However, an assessment of the role of segmental duplications in normal variation has not yet been made. On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. We observed an equal frequency of duplications and deletions, as well as a 4-fold enrichment of CNPs within hotspot regions, compared with control BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-scale variation in the human genome. Importantly, segmental duplications themselves were also significantly enriched >4-fold within regions of CNP. Almost without exception, CNPs were not confined to a single population, suggesting that these either are recurrent events, having occurred independently in multiple founders, or were present in early human populations. Our study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and it suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements. Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders.

Repression of PML nuclear body-associated transcription by oxidative stress-activated Bach2.

Several lines of evidence suggest that gene expression is regulated not only by the interaction between transcription factors and DNA but also by the higher-order architecture of the cell nucleus. PML bodies are one of the most prominent nuclear substructures which have been implicated in transcription regulation during apoptosis and stress responses. Bach2 is a member of the BTB-basic region leucine zipper factor family and represses transcription activity directed by the 12-O-tetradecanoylphorbol-13-acetate response element, the Maf recognition element, and the antioxidant-responsive element. Bach2 forms nuclear foci associated with PML bodies upon oxidative stress. Here, we demonstrate that transcription activity associated with PML bodies is selectively repressed by the recruitment of Bach2 around PML bodies. Fluorescence recovery after photobleaching experiments revealed that Bach2 showed rapid turnover in the nuclear foci. The Bach2 N-terminal region including the BTB domain is essential for the focus formation. Sumoylation of Bach2 is required for the recruitment of the protein around PML bodies. These observations represent the first example of modulation of transcription activity associated with PML bodies by a sequence-specific transcription factor upon oxidative stress.

On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes.

The proper function of the genome largely depends on the higher-order architecture of the chromosome. To understand the detailed chromosome structure in a native state, we developed an on-substrate procedure of subcellular fractionation suitable for the observation by atomic force microscopy (AFM). HeLa cells on a coverslip were successively treated with a detergent and a high-salt solution to remove the cytoplasmic and nucleoplasmic materials. A closer observation of the nucleus by AFM revealed that the interphase chromosome is composed of a granular unit of approximately 80 nm in diameter. Subsequent mild treatment with deoxyribonuclease I (10 U ml(-1)) exposed these units more clearly, which enabled us to uncover the 80-nm granules forming a fibre of approximately 80 nm width. In the cytoplasmic regions, cytoskeletal fibres with varying widths (10-70 nm) were observed. These observations suggest that the 80 nm granular fibre is a fundamental structural unit of the interphase chromosome. This on-substrate procedure was also applied to Escherichia coli. Cells attached on a coverslip were successively treated with lysozyme and detergent to partially release the nucleoid onto the substrate. The AFM observation revealed that the approximately 80 nm fundamental structural unit forms a granular fibre similar to that of HeLa cells. These results suggest that the fundamental mechanism of chromosome packing is common in both prokaryotes and eukaryotes.

Growth, development, and gene expression in a persistent Streptococcus gordonii biofilm.

A model for the protracted (30-day) colonization of smooth surfaces by Streptococcus gordonii that incorporates the nutrient flux that occurs in the oral cavity was developed. This model was used to characterize the biphasic expansion of the adherent bacterial population, which corresponded with the emergence of higher-order architectures characteristic of biofilms. Biofilm formation by S. gordonii was observed to be influenced by the presence of simple sugars including sucrose, glucose, and fructose. Real-time PCR was used to quantify changes in expression of S. gordonii genes known or thought to be involved in biofilm formation. Morphological changes were accompanied by a significant shift in gene expression patterns. The majority of S. gordonii genes examined were observed to be downregulated in the biofilm phase. Genes found to be upregulated in the biofilm state were observed to encode products related to environmental sensing and signaling.

Higher-order organization by mesoscale self-assembly and transformation of hybrid nanostructures.

The organization of nanostructures across extended length scales is a key challenge in the design of integrated materials with advanced functions. Current approaches tend to be based on physical methods, such as patterning, rather than the spontaneous chemical assembly and transformation of building blocks across multiple length scales. It should be possible to develop a chemistry of organized matter based on emergent processes in which time- and scale-dependent coupling of interactive components generate higher-order architectures with embedded structure. Herein we highlight how the interplay between aggregation and crystallization can give rise to mesoscale self-assembly and cooperative transformation and reorganization of hybrid inorganic-organic building blocks to produce single-crystal mosaics, nanoparticle arrays, and emergent nanostructures with complex form and hierarchy. We propose that similar mesoscale processes are also relevant to models of matrix-mediated nucleation in biomineralization.

Recombinant angiopoietin-1 restores higher-order architecture of growing blood vessels in mice in the absence of mural cells

Interactions between endothelial cells (ECs) and perivascular mural cells (MCs) via signaling molecules or physical contacts are implicated both in vascular remodeling and maintenance of vascular integrity. However, it remains unclear how MCs regulate the morphogenic activity of ECs to form an organized vascular architecture, comprising distinct artery, vein, and capillary, from a simple mesh-like network. A clear elucidation of this question requires an experimental model system in which ECs are separated from MCs and yet form vascular structures. Here we report that injection of an antagonistic mAb against PDGFR-β into murine neonates provides such an experimental system in the retina by completely blocking MC recruitment to developing vessels. While a vascular network was formed even in the absence of MCs, it was poorly remodeled and leaky. Using this vascular system ideal for direct assessment of the activities of MC-derived molecules, we show that addition of recombinant modified angiopoietin-1 restored a hierarchical vasculature, and also rescued retinal edema and hemorrhage in the complete absence of MCs. These observations demonstrate the potential of Ang1 as a new therapeutic modality for MC dropout in diseases such as diabetic retinopathies.

Recombinant angiopoietin-1 restores higher-order architecture of growing blood vessels in mice in the absence of mural cells

Interactions between endothelial cells (ECs) and perivascular mural cells (MCs) via signaling molecules or physical contacts are implicated both in vascular remodeling and maintenance of vascular integrity. However, it remains unclear how MCs regulate the morphogenic activity of ECs to form an organized vascular architecture, comprising distinct artery, vein, and capillary, from a simple mesh-like network. A clear elucidation of this question requires an experimental model system in which ECs are separated from MCs and yet form vascular structures. Here we report that injection of an antagonistic mAb against PDGFR-β into murine neonates provides such an experimental system in the retina by completely blocking MC recruitment to developing vessels. While a vascular network was formed even in the absence of MCs, it was poorly remodeled and leaky. Using this vascular system ideal for direct assessment of the activities of MC-derived molecules, we show that addition of recombinant modified angiopoietin-1 restored a hierarchical vasculature, and also rescued retinal edema and hemorrhage in the complete absence of MCs. These observations demonstrate the potential of Ang1 as a new therapeutic modality for MC dropout in diseases such as diabetic retinopathies.