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PubMed2025

Discovery of bimodal hepatitis B virus ribonuclease H and capsid assembly inhibitors.

Hepatitis B virus (HBV) ribonuclease H (RNaseH) inhibitors are a potent class of antivirals that prevent degradation of the viral pregenomic RNA during reverse transcription and block formation of mature HBV DNAs. Development of HBV RNaseH inhibitors is entering advanced preclinical analyses. To ensure the mechanism of action was fully understood, we defined the effects of RNaseH inhibitors on other steps of HBV replication. Some N-hydroxypyridinedione (HPD) HBV RNaseH inhibitors significantly reduced accumulation of capsids in HBV-replicating cells. A representative HPD 1466, with a 50% effective concentration against HBV replication of 0.25 µM, decreased capsid and core protein accumulation by 50-90% in HepDES19 and HepG2.2.15 cells. Surprisingly, 1466 did not affect pregenomic RNA encapsidation, demonstrating a specific effect on empty capsids. HBV genomic replication was not necessary for 1466's inhibitory effect as it decreased capsid accumulation in cells transfected with replication-deficient mutants blocking pgRNA encapsidation (Δ-bulge), DNA synthesis (YMHA), and RNaseH (D702A) activities. 1466 also decreased capsid and core protein accumulation in cells transfected with a core protein expression plasmid, indicating that other HBV products are unneeded. 1466 reduced initial capsid assembly rates in biochemical assembly reactions employing purified core protein (Cp149), demonstrating a specific effect on HBV core protein. We conclude that the bimodal HPD HBV RNaseH inhibitor 1466 is the prototypic member of a new class of capsid assembly modulators (CAM) that inhibits capsid assembly rather than accelerating it, as all other CAM classes do. We propose that this class be called CAM-I, for CAM-inhibitor. These results lay the foundation for identifying bimodal HBV antivirals targeting the RNaseH and capsid assembly.

Hepatitis B virus↗
PubMed2004

Competing hydrophobic and screened-coulomb interactions in hepatitis B virus capsid assembly.

Recent experiments show that, in the range from approximately 15 to 45 degrees C, an increase in the temperature promotes the spontaneous assembly into capsids of the Escherichia coli-expressed coat proteins of hepatitis B virus. Within that temperature interval, an increase in ionic strength up to five times that of standard physiological conditions also acts to promote capsid assembly. To explain both observations we propose an interaction of mean force between the protein subunits that is the sum of an attractive hydrophobic interaction, driving the self-assembly, and a repulsive electrostatic interaction, opposing the self-assembly. We find that the binding strength of the capsid subunits increases with temperature virtually independently of the ionic strength, and that, at fixed temperature, the binding strength increases with the square root of ionic strength. Both predictions are in quantitative agreement with experiment. We point out the similarities of capsid assembly in general and the micellization of surfactants. Finally we make plausible that electrostatic repulsion between the native core subunits of a large class of virus suppresses the formation in vivo of empty virus capsids, that is, without the presence of the charge-neutralizing nucleic acid.

Algorithms↗
PubMed2003

HIV capsid assembly.

HIV Gag assembly is the first and most essential step in the formation of virus particles. Following protein synthesis, Gag relocates from ribosomes and forms a virus particle at the plasma membrane, using host factors and machinery. Early studies focused on mapping the regions within Gag required for assembly and identified three distinct domains (M, I, and L), although their precise locations within the three-dimensional structure of Gag awaited later study. In this review, I summarize the mapping results in the light of recent progress on Gag structures made by nuclear magnetic resonance and X-ray crystallography as well as further functional analysis. These data are largely consistent and provide sufficient information for an understanding of the interactions and functions of the assembly domains at a macromolecular level. Current studies have moved on to the identification of the host factors and machinery used in the process of Gag assembly. Cumulative data suggest that the dynamics of Gag assembly and transport are achieved not by simply using, but rather by taking control of, cellular machinery. Key area in the process include interactions with TSG101, L domain receptor which normally functions in the endosomal sorting pathway and with lipid rafts, a type of M domain receptor, which has been suggested to be the sites for effective concentration of Gag. The review provides a summary of these data and discusses the likely direction of future studies.

Capsid Proteins↗
PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗
PubMed2003

Expression of human papillomavirus type 6 L1 and L2 isolated in China and self assembly of virus-like particles by the products.

To study variations of genome late region of human papillomavirus type 6 (HPV-6) isolated in China and assembling capabilities of the encoded capsid proteins, HPV-6 L1 and L2 sequences were cloned and used for expression in Bac-to-Bac baculovirus expression systems (Gibco BRL). Based upon L1 and L2 overlapping sequence two sequences (GenBank accession number AY015006, AY015008) of HPV-6 late region (2869 bp long) were assembled and classified into HPV-6b by phylogenetic analysis. Compared with prototype sequence, nine point mutations were found, including four missense mutations. L1, instead of L2, could self-assemble into virus-like particles (VLPs) in Sf9 nucleus. VLPs self-assembled by L1 alone (L1-VLPs) and by L1 plus L2 (L1+L2-VLPs) were purified and further characterized. Both types of VLPs were spherical particles with a diameter of approximately 50 nm. L1+L2 VLPs comprising L1 and L2 in the molar ratio of about 4:1 possessed the HPV-6 L1 VLP surface and conformational epitopes. In co-expression assay with a series of MOI combination of L1 and L2 recombinant baculoviruses (total MOI=10), existence of L2 of certain level enhanced L1 production by 0.8 fold and VLP production by 3 - 4 folds under experimental conditions. In conclusion, variation rate of HPV-6 genome late region is less than 0.28% and the substitutions A to G at position 7081 and G to A at 7099 may represent region characteristics. The cloned HPV-6 L1 and L2 sequences can be expressed efficiently in Sf9 cells, and the expressed products (L1 or L1+L2) can self-assemble into VLPs that resemble naturally occurring virions.

Animals↗
PubMed1996

In vivo microtubule dynamics during experimentally induced conversions between tubulin assembly states in Allogromia laticollaris.

A distinctive property of foraminiferan tubulin is that, in addition to microtubules (MTs), it exists in an alternate assembly state, helical filaments. Here, we have examined in vivo MT dynamics during experimentally induced conversions between these two assembly states in the reticulopods of the marine foraminiferan Allogromia laticollaris. Exposure to high extracellular concentrations of Mg2+ (165 mM) resulted in a complete conversion of MTs into helical filaments. However, Mg2+ treatment also induced a retrograde movement of organelles and cytoplasm, and it was necessary to inhibit this response in order to assess the effects of assembly state changes on individual MTs. This was accomplished by simultaneous treatment with high extracellular Mg2+ and 2,4-dinitrophenol (DNP). The resulting loss in MTs was detected by video enhanced DIC (VEC-DIC) microscopy as either an endwise MT shortening (at an average rate of 474 microns/min) or transformation into one or more irregularly shaped fibrils, which we termed residual fibrils. Correlative immunofluorescence and video microscopy showed residual fibrils to be composed of helical filaments. Removal of extracellular Mg2+/DNP initiated a reversal in assembly state, from helical filaments into MTs, which was completed within 5 min. VEC-DIC microscopy showed that MTs reformed by an endwise lengthening at an average rate of 216 microns/min. These results suggest that conversion between alternate tubulin assembly states provides a more rapid means to build and dismantle MTs than conventional subunit-driven pathways.

2,4-Dinitrophenol↗
PubMed1997

The role of central apparatus components in flagellar motility and microtubule assembly.

In order to generate the complex waveforms typical of beating cilia and flagella, the action of the dynein arms must be regulated. This regulation not only depends on the presence of multiple dynein isoforms, but also clearly involves other structures in the axoneme such as the radial spokes and central apparatus; mutants lacking these structures have paralyzed flagella. In this article, we review recent progress in identifying protein components of the central apparatus and discuss the role of these components in regulation of flagellar motility and central apparatus assembly. The central apparatus is composed of two single microtubules and their associated structures which include the central pair projections, the central pair bridges linking the two tubules, and the central pair caps which are attached to the distal or plus ends of the microtubules. To date, the genes encoding four components of the central apparatus have been cloned, PF15, PF16, PF20 and KLP1. PF16, PF20 and KLP1 have been sequenced and their gene products localized. Two additional components have been identified immunologically, a 110 kD polypeptide recognized by an antibody generated against highly conserved kinesin peptide sequence, and a 97 kD polypeptide recognized by CREST antisera. Based on a variety of data, one model that has emerged to explain the role of the central apparatus in flagellar motility is that the central apparatus ultimately regulates dynein through interactions with the radial spokes. The challenge now is to determine the precise mechanism by which the polypeptides comprising the central apparatus and the radial spokes interact to transduce a regulatory signal to the dynein arms. In terms of assembly, the central apparatus microtubules assemble with their plus ends distal to the cell body but, unlike the nine doublet microtubules, they are not nucleated from the basal bodies. Since some central apparatus defective mutants fail to assemble the entire central apparatus, their gene products may eventually prove to have microtubule nucleating or stabilizing properties. By continuing to identify the genes that encode central apparatus components, we will begin to understand the contribution of these microtubules to flagellar motility and gain insight into their nucleation, assembly, and stability.

Animals↗
PubMed1997

Viscosity and elasticity during collagen assembly in vitro: relevance to matrix-driven translocation.

In order to better understand the gelation process associated with collagen assembly, and the mechanism of the in vitro morphogenetic phenomenon of "matrix-driven translocation" [S.A. Newman et al. (1985) Science, 228, 885-889], the viscosity and elastic modulus of assembling collagen matrices in the presence and absence of polystyrene latex beads was investigated. Viscosity measurements at very low shear rates (0.016-0.0549 s(-1)) were performed over a range of temperatures (6.9-11.5 degrees C) in a Couette viscometer. A magnetic levitation sphere rheometer was used to measure the shear elastic modulus of the assembling matrices during the late phase of the gelation process. Gelation was detected by the rapid increase in viscosity that occurred after a lag time tL that varied between O and approximately 500 s. After a rise in viscosity that occurred over an additional approximately 500 s, the collagen matrix was characterized by an elastic modulus of the order of several Pa. The lag time of the assembly process was relatively insensitive to differences in shear rate within the variability of the sample preparation, but was inversely proportional to the time the sample spent on ice before being raised to the test temperature, for test temperatures > 9 degrees C. This suggests that structures important for fibrillogenesis are capable of forming at 0 degrees C. The time dependence of the gelation process is well-described by an exponential law with a rate constant K approximately 0.1 s(-1). Significantly, K was consistently larger in collagen preparations that contained cell-sized polystyrene beads. From these results, along with prior information on effective surface tension differences of bead-containing and bead-lacking collagen matrices, we conclude that changes in matrix organization contributing to matrix-driven translocation are initiated during the lag phase of fibrillogenesis when the viscosity is < or = 0.1 Poise. The phenomenon may make use of small differentials in viscosity and/or elasticity, resulting from the interaction of the beads with the assembling matrix. These properties are well described by standard models of concentrated solutions.

Animals↗
PubMed1998

Role of M-line proteins in sarcomeric titin assembly during cardiac myofibrillogenesis.

A rat polyclonal anti-M-line protein antiserum and three mouse monoclonal anti-titin antibodies (E2, F3, and A12) were used to study the spatiotemporal relationship between M-line proteins and titin during myofibril assembly in cultured chicken cardiomyocytes by immunofluorescence microscopy. In day 2 cultures, M-line proteins and titin were detected as punctate staining in most cardiomyocytes, which possessed many nonstriated fibrils. At a late stage (day 3 cultures), M-line proteins were incorporated into dot-like structures along nonstriated fibrils, while titin staining was continuous on these structures. As development progressed, M-line proteins were registered in periodic pattern in the mid-A band. In cardiomyocytes from day 5 cultures, the titin bands were separated by an unstained region, and achieved their adult doublet pattern. Thus, the organization of titin in the sarcomere appears to occur later than that of M-line proteins in the M-line. Our morphological data indicate that the early registration of M-line proteins in primitive myofibrils may guide titin filament alignment via interaction between M-line proteins and titin. In order to investigate the role of M-line proteins in the assembly of titin filaments, anti-M-line protein or anti-titin antibodies were introduced into cultured cardiomyocytes by electroporation to functionally bind the respective proteins, and the profile of myofibril assembly was examined. Cardiomyocytes from day 2-3 cultures with incorporated anti-M-line protein antibodies became shrunk, and exhibited defective myofibrillar assembly, as shown by the failure of titin to assemble into a typical sarcomeric pattern. Incorporation of anti-titin antibody E2, which recognizes the M-line end domain of titin, resulted in the failure of M-line proteins organized into the M-line structure, as shown by random, sporadic staining with anti-M-line protein antibody. These studies confirm the essential role of M-line proteins in the organization of titin filaments in the sarcomere and that the interaction between titin and M-line proteins is crucial to the formation of the M-line structure.

Animals↗
PubMed1997

Capsid assembly and DNA packaging in herpes simplex virus.

The genome of HSV-1 contains 80-85 open reading frames. Genetic and biochemical evidence suggests that at least 39 of these genes encode proteins that are components of the HSV-1 virion. The architecture of the HSV-1 virion consists of a trilaminar lipid envelope, an amorphous layer known as the tegument, a capsid shell, and a DNA-containing core. The capsid is an icosahedral shell whose major morphological features are 162 capsomers. It is composed of a major capsid protein called VP5 and three less abundant proteins, VP19C, VP23 and VP26. VP5 is the structural subunit of all 162 capsomers while VP19C and VP23 are located in the space between the capsomers. In addition to the structural proteins, capsid assembly involves participation of the HSV-1-encoded protease and the scaffolding protein, preVP22a. DNA packaging involves participation of DNA, empty capsids, and at least seven additional HSV-1-encoded proteins. Considerable advances have been made in understanding the structure of the capsid shell, largely as the result of applying cryoelectron microscopy techniques. Use of recombinant baculoviruses has allowed for a detailed analysis of the proteins required for capsid assembly. More recently, an in vitro system has been developed which has aided in defining the assembly pathway by identifying intermediates in the assembly of intact capsids. The in vitro system has identified a fragile roundish procapsid which matures into the polyhedral capsid in a transition similar to that undergone by bacteriophage proheads. This review is a summary of our present knowledge with respect to the structure and assembly of the HSV-1 capsid and what is known about the seven genes involved in DNA packaging. Copyright 1997 John Wiley & Sons Ltd.

Journal Article↗
PubMed1998

Assembly of the TCR/CD3 complex: CD3 epsilon/delta and CD3 epsilon/gamma dimers associate indistinctly with both TCR alpha and TCR beta chains. Evidence for a double TCR heterodimer model.

The TCR/CD3 complex is composed of six subunits which are expressed on the cell surface in a coordinate fashion after assembly in the endoplasmic reticulum (ER). The TCR/CD3 complex is assembled after a series of pairwise interactions involving the formation of dimers of CD3 epsilon with either CD3 gamma or CD3 delta. These dimers assemble with TCR alpha and TCR beta chains, and finally, the CD3 zeta homodimer is added to allow export of the full complex from the ER. A model has been proposed suggesting that during assembly the CD3 epsilon/CD3 gamma dimer interacts exclusively with TCR beta and the CD3 epsilon/CD3 delta dimer with TCR alpha to form a complex with a single TCR alpha/beta heterodimer. We show in this study, by immunoprecipitation and two-dimensional gel electrophoresis, that in the human T cell line Jurkat as well as in total human thymocytes, this preferential interaction does not occur and instead, the CD3 epsilon/CD3 gamma and CD3 epsilon/CD3 delta dimers associate with both TCR chains simultaneously and indistinctly. These data are confirmed by the analysis of the TCR alpha-negative T cell line MOLT-4 in which TCR beta is found separately associated with CD3 epsilon/CD3 gamma and with CD3 epsilon/CD3 delta dimers. Indirectly, our results support a model of stoichiometry in which two TCR alpha/beta heterodimers are present in a TCR/CD3 complex. Furthermore, immunoprecipitation with anti-CD3 gamma and anti-CD3 delta antibodies from 1% NP40 and 1% Brij96 cell lysates showed that these subunits form independent partial complexes which are cross-linked through the CD3 zeta homodimer. This suggests that CD3 zeta mediates the interaction between both TCR alpha/beta heterodimers contained in the double TCR complex. Further proof for this hypothesis is obtained after analysis of a Jurkat cell transfectant containing a point mutation in the transmembrane domain of TCR beta that impairs the association of CD3 zeta. In this mutant cell line, unlike a control line with wild-type TCR beta, the CD3 gamma- and CD3 delta-containing complexes were found completely independent. Altogether, these results support a model of TCR/CD3 assembly and stoichiometry in which two TCR-alpha/beta heterodimers form two hemicomplexes containing either CD3 epsilon/gamma or CD3 epsilon/delta dimers which become associated via the CD3 zeta homodimer.

Dimerization↗
PubMed2001

The role of actin filaments and microtubules in hepatocyte spheroid self-assembly.

Cultured rat hepatocytes self-assemble into three-dimensional structures or spheroids that exhibit ultrastructural characteristics of native hepatic tissue and enhanced liver-specific functions. The spheroid formation process involves cell translocation and changes in cell shape, indicative of the reorganization of the cytoskeletal elements. To elucidate the function of the cytoskeleton, hepatocytes undergoing spheroid formation were treated with drugs that disrupt the different cytoskeletal components. Cytochalasin D, which targets the actin filaments, caused inhibition of spheroid formation. The role of microtubules in this process was assessed by incubating the cells with taxol or nocodazole. Perturbation of microtubules had minimal effects on spheroid assembly. Scanning electron micrographs showed no morphological differences between spheroids formed in control cultures and those formed in the presence of taxol or nocodazole. In addition, the effects of those agents on hepatocyte functions were investigated. Albumin secretion and cytochrome P450 2B1/2 activities of hepatocytes were comparable in spheroids formed in the presence of taxol or nocodazole to those formed in control cultures. The levels of these liver-specific activities were lower in cytochalasin D--treated cultures where only dispersed cells or cell clumps were found but spheroids had not found. Thus, hepatocytes require an intact actin network to self-assemble efficiently into functional tissue-like structures. Perturbation of the microtubule lattice does not impair the formation process. Events that transpire during hepatocyte spheroid self-assembly exhibit striking similarities to processes commonly observed in tissue morphogenesis. The results provide insight into the mechanisms that cells employ to organize into tissues and can contribute to our understanding of how to control the cellular assembly in tissue engineering and clinical applications.

Actins↗
PubMed2001

Fluorescent and electroactive cyclic assemblies from perylene tetracarboxylic acid bisimide ligands and metal phosphane triflates.

Tetraaryloxy-substituted perylene tetracarboxylic acid bisimides with one or two 4-pyridyl receptor substituents at the imide functionality were synthesized and employed in transition metal directed self-assembly with Pd(II) and Pt(II) phosphane triflates. Upon mixing of the components, quantitative formation of functional molecular square-type complexes containing four dye molecules and model complexes of a 2:1 (perylene bisimide ligand:transition metal ion) stoichiometry was observed. The isolated metallosupramolecular squares were characterized by 1H and 31P [1H] NMR spectroscopy as well as conventional electrospray ionization (ESI) and ESI-FTICR mass spectrometry, which gave evidence for the structure and the high stability of these giant cyclic dye assemblies (molecular weight (3a) 8172, Pt-Pt corner diagonal ca. 3.4 nm). Studies of the optical absorption and fluorescence properties and the electrochemistry and spectroelectrochemistry of both the perylene bisimide ligands and the perylene bisimide metal complexes show that Pt(II) coordination does not interfere with the optical and electrochemical properties of the perylene bisimide ligands; this gives squares with high fluorescence quantum yields (phiF (3a)=0.88) and three fully reversible redox couples. The latter could be unambiguously related to quantitative formation of perylene bisimide radical cations (E1/2 = +0.93 V vs. Fc/Fc+), radical anions (E1/2= - 1.01 V vs. Fc/Fc+), and dianions (E1/2 = -1.14 V vs. Fc/Fc+); these redox reactions change the charge state of the cyclic assembly from +12 to zero. In contrast, Pd(II) coordination influenced the electrochemical properties of the assembly because of an irreversible palladium reduction at E1/2= -1.15 V versus Fc/Fc+. Finally, dynamic ligand exchange processes between different metallosupramolecular assemblies were investigated by multinuclear NMR and electrospray mass spectrometry. These studies confirmed the reversible nature of the pyridine-Pt(II)/Pd(II) coordination process.

Journal Article↗
PubMedDate not supplied

Electrogenerated chemiluminescence of luminol in neutral and alkaline aqueous solutions on a silver nanoparticle self-assembled gold electrode.

The electrochemiluminescence (ECL) behaviour of luminol on a silver nanoparticle self-assembled gold electrode in neutral and alkaline solutions was investigated using conventional cyclic voltammetry (CV). The silver nanoparticle self-assembled gold electrode exhibited excellent ECL properties for the luminol ECL system. In neutral solutions, four ECL peaks (ECL-1-ECL-4) were observed at 0.73, 1.15, -0.46 and -1.35 V (vs. SCE), respectively. The intensities of these peaks were enhanced significantly compared with those on a bulk gold electrode and a gold nanoparticle self-assembled gold electrode. It was found that ECL-1 and ECL-2 on a silver nanoparticle-modified electrode were about 1000 and 1770 times stronger than those on a bare Au electrode and were about 17 and 15 times stronger than those on a gold nanoparticle-modified electrode, respectively. In alkaline solutions, four ECL peaks were also observed that were much stronger than those in neutral solutions, and ECL-1 and ECL-2 were enhanced by about three orders and one order of magnitude compared with those on a bare Au electrode and on a gold nanoparticle self-assembled electrode, respectively. Moreover, the silver nanoparticle-modified electrode exhibited good stability and reproducibility for luminol ECL. These peaks were found to depend on a number of factors, including silver nanoparticles on the surface of the modified electrode, potential scan direction, scan rate, scan range, the presence of O2 or N2, pH values, the concentrations of NaBr and luminol, and buffer solutions. The emitter of the ECL was confirmed as 3-aminophthalate by analysing the CL spectra. The surface state of the silver nanoparticle self-assembled electrode was characterized by scanning electron microscopy (SEM) and the interface property of the electrode was studied by electrochemical impedance spectroscopy (EIS). A mechanism for the formation of these ECL peaks is proposed. The results demonstrate that luminol has excellent ECL properties, such as strong ECL intensity and good reproducibility on a silver nanoparticle-modified gold electrode, in both neutral and alkaline solutions, which is of great potential in analytical applications.

Air↗
PubMed2006

Controlled hierarchical assembly of switchable DNA-multiprotein complexes.

Directed, biologically-driven self-assembly has the potential to yield hybrid multicomponent architectures with applications ranging from sensors and diagnostics to catalysts and responsive materials. To enable these applications, it is critical to gain control over the precise orientation and geometry of biomolecules interacting with one-another and with surfaces. Such control has thus far been difficult to achieve in even the simplest biomolecular designs. We report a novel methodology for the design and synthesis of functional, oriented, and reversibly switchable hierarchical assemblies at the nanoscale using DNA-protein and protein-protein interactions. The biomolecular assembly relies on the highly selective recognition between transcription factors (TFs) and their cognate DNA motifs that serve as transcription factor binding sites (TFBSs) along with the calmodulin (CaM)-calmodulin binding peptide (CBP) interaction that is regulated by Ca2+. Through these two types of controllable interactions, we achieved the sequential and hierarchical self-assembly of multiprotein complexes complete with embedded fluorescence and catalytic capabilities, which may serve as a paradigm for multifunctional assemblies.

Biotin↗
PubMed1990

Intracellular assembly of newly synthesized canine cardiac myosins.

To investigate how newly synthesized cardiac myosins are assembled into myofilaments, we analysed the distribution of newly produced alpha-myosin heavy chain isozyme in sarcomeres by immunoelectron microscopy using a monoclonal antibody (CMA19), which is specific for alpha-myosin heavy chain. Isozymic changes in myosin heavy chains from beta to alpha type were induced in canine ventricular muscles and cultured ventricular myocytes by administration of 1-thyroxine. We incubated the glycerinated ventricular muscles or cultured ventricular myocytes with the enzyme (horseradish peroxidase) labelled Fab fragment of CMA19. After the reaction with 3, 3'-diaminobenzidine and osmification, we prepared ultrathin sections of the ventricular muscles or cultured ventricular myocytes and analysed their staining patterns by electron microscopy. There was apparent heterogeneity in the staining intensity of the myofilaments among different cells, among different myofibrils and even intramyofibrillarly. Higher magnification revealed that there were scattered foci of strong reaction which appeared to be foci of assembly of the newly synthesized alpha-myosin heavy chain. Immunocytochemical study also showed heterogeneous reactions within myofilaments and that there were scattered foci of myofilament assembly, which were closely associated with polyribosomes producing newly induced alpha-myosin heavy chain. These data suggest that newly synthesized cardiac myosins are assembled into myofilaments from the sites of synthesis, that is polyribosomes. This may explain the heterogeneity of the assembly pattern of newly synthesized cardiac myosins at the subcellular level.

Actin Cytoskeleton↗
PubMed2004

Sterically and guest-controlled self-assembly of calix[4]arene derivatives.

In solvents such as chloroform or benzene, tetraurea calix[4]arenes 1 form dimeric capsules in which one solvent molecule is usually included as guest. To explore the structural requirements for the formation of such hydrogen-bonded dimers we replaced one p-tolylurea residue by a simple acetamide function. The resulting calix[4]arene 2 a, substituted at its wide rim with one acetamide and three p-tolylurea functions, assumes a C(1)-symmetrical conformation in apolar solvents as shown by (1)H NMR, which is not compatible with the usual capsule. In the crystalline state, four molecules of 2 a, adopting a pinched cone conformation, assemble into a quasi S(4)-symmetrical tetramer stabilized by a cyclic array of 24 NH.O==C hydrogen bonds and four NH.pi interactions. Four acetamide groups are hydrogen-bonded to each other and pack tightly in the center of the assembly. All polar residues are buried inside the tetramer, the surface of which is lipophilic. Extensive NMR studies revealed similar structures in apolar solvents such as [D]chloroform or [D(6)]benzene for calixacetamides 2 a-c. The formation of these tetramers in solution is critically dependent on the size of the amide fragment, so that propionamide 2 d, butyramide 2 e, and p-tolylamide 2 f form only ill-defined aggregates. This is caused by steric crowding inside the tetrameric assembly. The tetramers persist during molecular dynamics simulations, and the optimized average structure of the MD run is similar to that found in the crystalline state. Theoretical studies revealed that cooperation of hydrogen bonds with multiple NH.pi, C--H.pi, and pi.pi attractions make the tetramer more stable than the capsular dimer with the solvent as guest. In the presence of tetraethylammonium salts, however, compounds 2 a-e form dimeric capsular assemblies, each incorporating a single ammonium cation. Only one of two possible regioisomeric dimers is formed, in which both acetamide groups are surrounded by two urea residues. These examples give striking evidence of how self-assembly in solution can be strongly dependent on subtle structural factors and of how the formation of dimeric capsules can be induced by the presence of an appropriate guest.

Journal Article↗
PubMed2005

Two-component gel-phase materials--highly tunable self-assembling systems.

In the past 10 years, the molecular self-assembly and network formation of small molecule gelators has become one of the most active frontiers of the emergent area of nanochemistry. Increasingly, research efforts have begun to focus on multicomponent gelators, which rely on the initial interaction of distinct individual components to form a complex that subsequently self-assembles into a fibrous supramolecular polymer. In true two-component systems, an individual component can be present in isotropic solution, and only on addition of the second component will a gel actually form. In some cases, however, two-component gels are reported in which the second component significantly modifies the behaviour of a known gelator. Both systems are discussed in this article. The additional level of supramolecular control in the hierarchical self-assembly of two-component gels confers exquisite tunability and controllability. Functionality can be readily built into the material by simple variation of one of the individual components. This article discusses the key approaches used to control self-assembly by manipulating single molecular-recognition events and illustrates how controlling the transcription of information from the molecular to the macroscopic level by the simple addition of a second component allows complex functional materials to be selectively assembled from simple building blocks.

Journal Article↗