Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Assembly process”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources

Membrane biogenesis in anoxygenic photosynthetic prokaryotes.

Following the discovery of photosynthetic bacteria in the nineteenth century, technical developments of the 1950s led to their use in membrane biogenesis studies. These investigations had their origins in the isolation of subcellular particles designated as 'chromatophores' by Roger Stanier and colleagues, which were shown to be photosynthetically competent by Albert Frenkel, and to originate from the intracytoplasmic membrane (ICM) continuum observed in electron micrographs. These ultrastrucutral studies by the G. Drews group, Germaine Cohen-Bazire and others also suggested that the ICM originates by invagination of the cytoplasmic membrane, as later established in the biochemical and biophysical work of the R. Niederman and Drews groups. Through a combination of genetic approaches, first introduced in the early 1980s by Barry Marrs, and the atomic resolution structures determined for light-harvesting antennae and reaction centers, a detailed understanding is emerging of mechanisms regulating their levels in the membrane and the roles played by specific protein domains and additional factors in their assembly and supramolecular organization. Prospects for additional progress during the twenty-first century include further elucidation of molecular aspects of the assembly process and the application of newer spectroscopic probes to photosynthetic unit formation.

Journal Article↗

Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli.

Gram-negative bacteria are known to produce two types of surface organelles: flagella, which are required for motility and chemotaxis, and pili (fimbriae), which play a part in the interaction of bacteria with other bacteria and with eukaryotic host cells. Here we report a third class of E. coli surface organelles for which we propose the name curli. Curli are coiled surface structures composed of a single type of subunit, the curlin, which differs from all known pilin proteins and is synthesized in the absence of a cleavable signal peptide. Although the gene encoding this structural subunit, crl, is present and transcribed in most natural isolates of E. coli, only certain strains are able to assemble the subunit protein into curli. This assembly process occurs preferentially at growth temperatures below 37 degrees C. The ability of curli to mediate binding to fibronectin may be a virulence-associated property for wound colonization and for the colonization of fibronectin-coated surfaces.

Amino Acid Sequence↗

Self-assembly of nanoparticles into structured spherical and network aggregates

Multi-scale ordering of materials is central for the application of molecular systems in macroscopic devices. Self-assembly based on selective control of non-covalent interactions provides a powerful tool for the creation of structured systems at a molecular level, and application of this methodology to macromolecular systems provides a means for extending such structures to macroscopic length scale. Monolayer-functionalized nanoparticles can be made with a wide variety of metallic and non-metallic cores, providing a versatile building block for such approaches. Here we present a polymer-mediated 'bricks and mortar' strategy for the ordering of nanoparticles into structured assemblies. This methodology allows monolayer-protected gold particles to self-assemble into structured aggregates while thermally controlling their size and morphology. Using 2-nm gold particles as building blocks, we show that spherical aggregates of size 97 +/- 17 nm can be produced at 23 degrees C, and that 0.5-1 microm spherical assemblies with (5-40) x 10(5) individual subunits form at -20 degrees C. Intriguingly, extended networks of approximately 50-nm subunits are formed at 10 degrees C, illustrating the potential of our approach for the formation of diverse structural motifs such as wires and rods. These findings demonstrate that the assembly process provides control over the resulting aggregates, while the modularity of the 'bricks and mortar' approach allows combinatorial control over the constituents, providing a versatile route to new materials systems.

Journal Article↗

The folding of hen lysozyme involves partially structured intermediates and multiple pathways.

Analysis of the folding of hen lysozyme shows that the protein does not become organized in a single cooperative event but that different parts of the structure become stabilized with very different kinetics. In particular, in most molecules the alpha-helical domain folds faster than the beta-sheet domain. Furthermore, different populations of molecules fold by kinetically distinct pathways. Thus, folding is not a simple sequential assembly process but involves parallel alternative pathways, some of which may involve substantial reorganization steps.

Amino Acid Sequence↗

A DNA-based method for rationally assembling nanoparticles into macroscopic materials.

Colloidal particles of metals and semiconductors have potentially useful optical, optoelectronic and material properties that derive from their small (nanoscopic) size. These properties might lead to applications including chemical sensors, spectroscopic enhancers, quantum dot and nanostructure fabrication, and microimaging methods. A great deal of control can now be exercised over the chemical composition, size and polydispersity of colloidal particles, and many methods have been developed for assembling them into useful aggregates and materials. Here we describe a method for assembling colloidal gold nanoparticles rationally and reversibly into macroscopic aggregates. The method involves attaching to the surfaces of two batches of 13-nm gold particles non-complementary DNA oligonucleotides capped with thiol groups, which bind to gold. When we add to the solution an oligonucleotide duplex with 'sticky ends' that are complementary to the two grafted sequences, the nanoparticles self-assemble into aggregates. This assembly process can be reversed by thermal denaturation. This strategy should now make it possible to tailor the optical, electronic and structural properties of the colloidal aggregates by using the specificity of DNA interactions to direct the interactions between particles of different size and composition.

Base Sequence↗

Nanotube electronics: large-scale assembly of carbon nanotubes.

Nanoscale electronic devices made from carbon nanotubes, such as transistors and sensors, are much smaller and more versatile than those that rely on conventional microelectronic chips, but their development for mass production has been thwarted by difficulties in aligning and integrating the millions of nanotubes required. Inspired by biomolecular self-assembly processes, we have created chemically functionalized patterns on a surface, to which pre-grown nanotubes in solution can align themselves in huge numbers. This method allows wafer-scale fabrication of millions of carbon-nanotube circuits with single-nanotube precision, and may enable nanotube-based devices, such as computer chips and high-density sensor arrays, to be produced industrially.

Journal Article↗

Folding intermediates of SNARE complex assembly.

SNARE (soluble NSF attachment protein receptor) proteins assemble into a stable complex essential for vesicle-membrane fusion. To further understand SNARE function we have used solution nuclear magnetic resonance (NMR) spectroscopy to characterize three assembly states of a yeast SNARE complex: first, the 'closed' conformation of Sso1; second, the binary complex of Sso1 and Sec9; and third, the ternary complex of Sso1, Sec9 and Snc1. Sec9 and Snc1 are unstructured in isolation. Sso1 likely consists of a four helix bundle formed by part of the C-terminal Hcore domain and the N-terminal H(A)H(B)H(C) domain, and this bundle is flanked on both sides by large flexible regions. Sso1 switches to an 'open' state when its Hcore domain binds Sec9. Conformational switching of the Hcore domain, via H(A)H(B)H(C), may provide a key regulatory mechanism in SNARE assembly. Formation of binary and ternary complexes induces additional alpha-helical structure in previously unstructured regions. Our data suggest a directed assembly process beginning distal to the membrane surfaces and proceeding toward them, bringing membranes into close proximity and possibly leading to membrane fusion.

Circular Dichroism↗

Assembly dynamics of microtubules at molecular resolution.

Microtubules are highly dynamic protein polymers that form a crucial part of the cytoskeleton in all eukaryotic cells. Although microtubules are known to self-assemble from tubulin dimers, information on the assembly dynamics of microtubules has been limited, both in vitro and in vivo, to measurements of average growth and shrinkage rates over several thousands of tubulin subunits. As a result there is a lack of information on the sequence of molecular events that leads to the growth and shrinkage of microtubule ends. Here we use optical tweezers to observe the assembly dynamics of individual microtubules at molecular resolution. We find that microtubules can increase their overall length almost instantaneously by amounts exceeding the size of individual dimers (8 nm). When the microtubule-associated protein XMAP215 (ref. 6) is added, this effect is markedly enhanced and fast increases in length of about 40-60 nm are observed. These observations suggest that small tubulin oligomers are able to add directly to growing microtubules and that XMAP215 speeds up microtubule growth by facilitating the addition of long oligomers. The achievement of molecular resolution on the microtubule assembly process opens the way to direct studies of the molecular mechanism by which the many recently discovered microtubule end-binding proteins regulate microtubule dynamics in living cells.

Algorithms↗

Long-range structuring of nanoparticles by mimicry of a cholesteric liquid crystal.

Patterning nano-objects is an exciting interdisciplinary research area in current materials science, arising from new optical and optoelectronic properties and the need to miniaturize electronic components. Many techniques have been developed for assembling nanoparticles into two- and three-dimensional arrays. Most studies involving liquid crystals as templates have dealt with colloidal particles and nematic and smectic phases. Here, we demonstrate the long-range ordering of nanoparticle assemblies that adopt the helical configuration of the cholesteric liquid crystalline phase. Because we used glass-forming cholesterics, the nanostructures could be examined by transmission electron microscopy. The platinum nanoparticles form periodic ribbons that mimic the well-known 'fingerprint' cholesteric texture. Surprisingly, the nanoparticles do not decorate the original cholesteric texture but create a novel helical structure with a larger helical pitch. By varying the molar fraction of cholesterol-containing mesogen in the liquid crystal host, we show that the distance between the ribbons is directly correlated to the pitch. Therefore this inherent lengthscale becomes a simple control parameter to tune the structuring of nanoparticles. These results demonstrate how such an assembly process could be modulated, providing a versatile route to new materials systems.

Crystallization↗

The type III secretion injectisome.

The type III secretion injectisome is a complex nanomachine that allows bacteria to deliver protein effectors across eukaryotic cellular membranes. In recent years, significant progress has been made in our understanding of its structure, assembly and mode of operation. The principal structural components of the injectisome, from the base located in the bacterial cytosol to the tip of the needle protruding from the cell surface, have been investigated in detail. The structures of several constituent proteins were solved at the atomic level and important insights into the assembly process have been gained. However, despite the ongoing concerted efforts of molecular and structural biologists, the role of many of the constituent components of this nanomachine remain unknown.

Bacteria↗

Early organization of pre-mRNA during spliceosome assembly.

Intron excision from precursor mRNAs (pre-mRNAs) in eukaryotes requires juxtaposition of reactive functionalities within the substrate at the heart of the spliceosome where the two chemical steps of splicing occur. Although a series of interactions between pre-mRNAs, pre-spliceosomal and spliceosomal factors is well established, the molecular mechanisms of splicing machinery assembly, as well as the temporal basis for organization of the substrate for splicing, remain poorly understood. Here we have used a directed hydroxyl radical probe tethered to pre-mRNA substrates to map the structure of the pre-mRNA substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly/recruitment and suggest a mechanism for the formation of the final active site of the mature spliceosome.

Adenosine Triphosphate↗

Nuclear speckles and nucleoli targeting by PIP2-PDZ domain interactions.

PDZ (Postsynaptic density protein, Disc large, Zona occludens) domains are protein-protein interaction modules that predominate in submembranous scaffolding proteins. Recently, we showed that the PDZ domains of syntenin-1 also interact with phosphatidylinositol 4,5-bisphosphate (PIP2) and that this interaction controls the recruitment of the protein to the plasma membrane. Here we evaluate the general importance of PIP2-PDZ domain interactions. We report that most PDZ proteins bind weakly to PIP2, but that syntenin-2, the closest homolog of syntenin-1, binds with high affinity to PIP2 via its PDZ domains. Surprisingly, these domains target syntenin-2 to nuclear PIP2 pools, in nuclear speckles and nucleoli. Targeting to these sites is abolished by treatments known to affect these PIP2 pools. Mutational and domain-swapping experiments indicate that high-affinity binding to PIP2 requires both PDZ domains of syntenin-2, but that its first PDZ domain contains the nuclear PIP2 targeting determinants. Depletion of syntenin-2 disrupts the nuclear speckles-PIP2 pattern and affects cell survival and cell division. These findings show that PIP2-PDZ domain interactions can directly contribute to subnuclear assembly processes.

Carrier Proteins↗

Are metastable, precrystallisation, density-fluctuations a universal phenomena?

In-situ observations of crystallisation in minerals and organic polymers have been made by simultaneous, time-resolved small angle X-ray scattering (SAXS) and wide angle X-ray scattering (WAXS) techniques. In isotactic polypropylene slow quiescent crystallisation shows the onset of large scale ordering prior to crystal growth. Rapid crystallisations studied by melt extrusion indicate the development of well resolved oriented SAXS patterns associated with long range order before the development of crystalline peaks in the WAXS region. Block copolymers self-assemble into mesophases in polymer melts above a critical chain length (or above a critical temperature) and this self-assembly process is shown to be susceptible to an incipient crystallisation. Mesophase formation is observed at anomalously high temperatures in ethylene-oxide containing block copolymers below the normal melting point of the polyoxy ethylene chains. Formation of calcium carbonate from aqueous solutions of sodium carbonate and calcium nitrate is observed to be a two-stage process and precipitation proceeds by the production of an amorphous metastable phase. This phase grows until it is volume filling and leads to the formation of the two polymorphs Calcite and Vaterite. These three sets of results suggest pre-nucleation density fluctuations, leading to a metastable phase, play an integral role in all three classes of crystallisation. In due course, this phase undergoes transformation to "normal" crystals.

Journal Article↗

Self-assembly of novel macrocyclic aminomethylphosphines with hydrophobic intramolecular cavities.

Novel macroheterocyclic tetraphosphines, namely, 1,1',5,5'-bis(arylene)-bis(1,5-diaza-3,7-diphosphacyclooctanes) 2-6, were obtained without the use of high-dilution techniques or any matrix by the reaction of bis(hydroxymethyl)organylphosphines with primary aromatic diamines containing two p-phenylene fragments linked by various one-atom bridges in a molecular self-assembly process. The structures of 4, 5 and 6 were investigated by X-ray crystal structure analyses. The macrocyclic cavities can be described as a truncated rhombohedral prism with side faces formed by phenylene rings and 1,5-diaza-3,7-diphosphacyclooctanes in the truncated acute angles. In the crystals of these macrocycles, solvating DMF molecules are present, and a methyl group from each of two DMF molecules penetrates the macrocyclic cavities of 4 and 5 from either side, whereas only one disordered molecule of DMF penetrates the cavity of macrocycle 6. Different types of crystal packing are observed for the P-benzyl-substituted compounds 4 and 5 and for the P-mesityl-substituted compound 6: for 4 and 5 the formation of alternating layers containing the macrocycles and the DMF molecules is observed, in which the cavities of the macrocyclic molecules form channels and the DMF molecules are located in the centers of the channels; in the crystal of 6, six molecules are arranged around the 3 axis in the fashion of a six-bladed propeller.

Crystallography, X-Ray↗

Crystal engineering of a versatile building block toward the design of novel inorganic-organic coordination architectures.

Six novel inorganic-organic coordination supramolecular networks based on a versatile linking unit 4-pyridylthioacetate (pyta) and inorganic Co(II), Cu(II), Ag(I), Zn(II), Mn(II) and Pb(II) salts have been prepared in water medium and structurally characterized by single-crystal X-ray diffraction analysis. Reaction of CoCl(2).6H(2)O with Hpyta afforded a neutral mononuclear complex [Co(pyta)(2)(H(2)O)(4)](1), which exhibits a two-dimensional (2-D) layered architecture through intermolecular O-HO interactions. Reaction of CuCl(2.2H(2)O with Hpyta yielded a neutral one-dimensional (1-D) coordination polymer [[Cu(pyta)(2)(H(2)O].0.5H(2)O](n)(2) consisting of rectangle molecular square units, which show a three-dimensional (3-D) supramolecular network through S...S and O-H...O weak interactions. However, when AgNO(3), Zn(OAc)(2).2H(2)O or MnCl(2).4H(2)O salts were used in the above self-assembled processes, the neutral 2-D coordination polymers [Ag(pyta)](n)(3), [[Zn(pyta)(2)].4H(2)O](n)(4) or [[Mn(pyta)(2)(H(2)O)]](n)(5) with different topologies were obtained, respectively. While substituting the transition metal ions used in 1-5 with Pb(OAc)(2).3H(2)O, a one-dimensional coordination polymer [Pb(pyta)(2)](n)(6), which shows a novel 2-fold interpenetrating 2-D supramolecular architecture through weak SS interactions, was isolated. It is interesting to note that the building block pyta anion exhibits different configurations and coordination modes in the solid structures of complexes 1-6. These results indicate that the versatile nature of this flexible ligand, together with the coordination preferences of the metal centers, play a critical role in construction of these novel coordination polymers or supramolecules. The spectral and thermal properties of these new materials have also been investigated.

Journal Article↗

Crystal engineering of porphyrin framework solids.

This article describes recent achievements made by us and other groups in targeted synthesis of porphyrin-based framework solids by various non-covalent mechanisms of molecular recognition. The self-assembly processes are effected in a tunable manner either by direct association of suitably designed porphyrin building blocks, or by their supramolecular aggregation through external linkers as metal ions and organic bi-dentate ligands. Many of these crystalline porphyrin materials exhibit open architectures and remarkable structural integrity, and their potential application for selective guest storage and molecular sieving is highlighted.

Journal Article↗