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 1,801 records · Page 100Linked to original sources
PubMed2004

Self-assembly of amphiphilic dendritic dipeptides into helical pores.

Natural pore-forming proteins act as viral helical coats and transmembrane channels, exhibit antibacterial activity and are used in synthetic systems, such as for reversible encapsulation or stochastic sensing. These diverse functions are intimately linked to protein structure. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state have not yet been realized. In the case of dendrimers, covalent and non-covalent coating and assembly of a range of different structures has only yielded closed columns. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.

Biological Transport↗
PubMed1989

Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus.

The three-dimensional structure of the Sabin strain of type 3 poliovirus has been determined at 2.4 A resolution. Significant structural differences with the Mahoney strain of type 1 poliovirus are confined to loops and terminal extensions of the capsid proteins, occur in all of the major antigenic sites of the virion and typically involve insertions, deletions or the replacement of prolines. Several newly identified components of the structure participate in assembly-dependent interactions which are relevant to the biologically important processes of viral assembly and uncoating. These include two sites of lipid substitution, two putative nucleotides and a beta sheet formed by the N-termini of capsid proteins VP4 and VP1. The structure provides an explanation for the temperature sensitive phenotype of the P3/Sabin strain. Amino acids that regulate temperature sensitivity in type 3 poliovirus are located in the interfaces between promoters, in the binding site for a lipid substituent and in an assembly-dependent extended beta sheet that stabilizes the association of pentamers. Several lines of evidence indicate that these structural components also control conformational transitions at various stages of the viral life cycle.

Antigens, Viral↗
PubMed2003

Establishing national goals for quality improvement.

BACKGROUND: For a number of reasons, it has been difficult to garner public interest in the need to improve the quality of care delivered nationally. One possible reason for this is that the concept of quality has different meanings for different stakeholders. To make the problems of suboptimal quality more concrete and potential solutions more compelling, the Strategic Framework Board (SFB) recommended developing a set of national goals for quality improvement. OBJECTIVES: To describe the criteria by which national goals should be selected, illustrate the analytic methods that should be used to support the development of such goals, and describe and illustrate a process by which national goals could be formulated. RESEARCH DESIGN: Targeted review of literature and discussions among members of the SFB. FINDINGS: National goals have played a key role in making progress under the Healthy People 2000 and Health People 2010 initiatives. The recommended process will involve assembling key evidence as well as engaging in a consensus process. CONCLUSIONS: Developing a set of national goals for quality improvement is a key activity for a national quality measurement and reporting system to undertake. The steps outlined here represent a feasible and productive method for accomplishing this objective.

Adult↗
PubMed2000

Fission yeast Rng3p: an UCS-domain protein that mediates myosin II assembly during cytokinesis.

Cell division in many eukaryotes, including the fission yeast Schizosaccharomyces pombe, utilizes a contractile actomyosin ring. In S. pombe, the actomyosin ring is assembled at the medial cortex upon entry into mitosis and constricts at the end of anaphase to guide the centripetal deposition of the septum. Despite identification of several structural components essential for actomyosin ring assembly, the interdependencies between these gene-products in the process of ring assembly are unknown. This study investigates the role of Rng3p, a member of the UCS-domain containing protein family (Unc-45p, Cro1p, She4p), in actomyosin ring assembly. Null mutants in rng3 resemble deletion mutants in the type II myosin heavy chain (myo2) and rng3(ts) mutants show strong negative interactions with the myo2-E1 mutant, suggesting that Rng3p is involved in modulating aspects of type II myosin function. Interestingly, a green fluorescent protein (GFP) tagged Rng3p fusion is detected at the division site in the myo2-E1 mutant, but not in other myo2-alleles, wild-type cells or in 18 other cytokinesis mutants. Assembly and maintenance of Rng3p at the division site in the myo2-E1 mutant requires F-actin. Rng3p is also required for the proper assembly of Myo2p and F-actin into a functional actomyosin ring but is not necessary for their accumulation at the division site. We conclude that Rng3p is a novel component of the F-actin cytoskeleton essential for a late step in actomyosin ring assembly and that it might monitor some aspect of type II myosin assembly during actomyosin ring construction.

Actomyosin↗
PubMed2003

Epitaxial self-assembly of block copolymers on lithographically defined nanopatterned substrates.

Parallel processes for patterning densely packed nanometre-scale structures are critical for many diverse areas of nanotechnology. Thin films of diblock copolymers can self-assemble into ordered periodic structures at the molecular scale (approximately 5 to 50 nm), and have been used as templates to fabricate quantum dots, nanowires, magnetic storage media, nanopores and silicon capacitors. Unfortunately, perfect periodic domain ordering can only be achieved over micrometre-scale areas at best and defects exist at the edges of grain boundaries. These limitations preclude the use of block-copolymer lithography for many advanced applications. Graphoepitaxy, in-plane electric fields, temperature gradients, and directional solidification have also been demonstrated to induce orientation or long-range order with varying degrees of success. Here we demonstrate the integration of thin films of block copolymer with advanced lithographic techniques to induce epitaxial self-assembly of domains. The resulting patterns are defect-free, are oriented and registered with the underlying substrate and can be created over arbitrarily large areas. These structures are determined by the size and quality of the lithographically defined surface pattern rather than by the inherent limitations of the self-assembly process. Our results illustrate how hybrid strategies to nanofabrication allow for molecular level control in existing manufacturing processes.

Journal Article↗
PubMed2000

Tracking sliding clamp opening and closing during bacteriophage T4 DNA polymerase holoenzyme assembly.

The bacteriophage T4 DNA polymerase holoenzyme, consisting of the DNA polymerase (gp43), the sliding clamp (gp45), and the clamp loader (gp44/62), is loaded onto DNA in an ATP-dependent, multistep reaction. The trimeric, ring-shaped gp45 is loaded onto DNA such that the DNA passes through the center of the ring. gp43 binds to this complex, thereby forming a topological link with the DNA and increasing its processivity. Using stopped-flow fluorescence-resonance energy transfer, we have investigated opening and closing of the gp45 ring during the holoenzyme assembly process. Two amino acids that lie on opposite sides of the gp45 subunit interface, W91 and V162C labeled with coumarin, were used as the fluorescence donor and acceptor, respectively. Free in solution, gp45 has two closed subunit interfaces with W91 to V162-coumarin distances of 19 A and one open subunit interface with a W91 to V162C-coumarin distance of 40 A. Making the assumption that the distance across the two closed subunit interfaces is unchanged during the holoenzyme assembly process, we have found that the distance across the open subunit interface is first increased to greater than 45 A and is then decreased to 30 A during a 10-step assembly mechanism. The gp45 ring is not completely closed in the holoenzyme complex, consistent with previous evidence suggesting that the C-terminus of gp43 is inserted into the gp45 subunit interface. Unexpectedly, ATP-hydrolysis events are coupled to only a fraction of the total distance change, with conformational changes linked to binding DNA and gp43 coupled to the majority of the total distance change. Using the nonhydrolyzable ATP analogue ATP-gamma-S results in formation of a nonproductive gp45 x gp44/62 complex; however, adding an excess of ATP to this nonproductive complex results in rapid ATP/ATP-gamma-S exchange to yield a productive gp45 x gp44/62 complex within seconds.

Adenosine Diphosphate↗
PubMed1994

The initiation of neurite outgrowth by sympathetic neurons grown in vitro does not depend on assembly of microtubules.

Neurite formation by dissociated chick sympathetic neurons in vitro begins when one of the many filopodia that emanate from the cell body of a neuron is invaded by cytoplasm containing microtubules and other components of axoplasm (Smith, 1994). This study was undertaken to determine whether this process depends on assembly of microtubules. To inhibit microtubule assembly, neurons were grown in medium containing nocodazole or colchicine. In one series of experiments, neurons first were exposed to the microtubule-stabilizing drug, taxol, so that existing microtubules would remain intact while assembly of new microtubules was inhibited. The ability of neurons to form neurites was assessed by time-lapse video microscopy. Neurons subsequently were stained with antibodies against the tyrosinated and acetylated forms of alpha-tubulin and examined by laser confocal microscopy to visualize microtubules. Neurons were able to form short processes despite inhibition of microtubule assembly and they did so in a way that closely resembled process formation in control medium. Processes formed by neurons that had not been pretreated with taxol were devoid of microtubules. However, microtubules were present in processes of taxol-pretreated neurons. These microtubules contained acetylated alpha-tubulin, as is typical of stable microtubules, but not tyrosinated alpha-tubulin, the form present in recently assembled microtubules. These findings show that the initial steps in neurite formation do not depend on microtubule assembly and suggest that microtubules assembled in the cell body can be translocated into developing neurites as they emerge. The results are compatible with models of neurite formation which postulate that cytoplasm from the cell body is transported into filopodia by actomyosin-based motility mechanisms.

Animals↗
PubMed1995

The intracellular assembly of antigenic-peptide-class II complexes.

The immune system employs remarkable strategies to ensure that foreign antigens, from the most complex pathogens to the simplest proteins, are displayed on the surfaces of cells which are targets of T lymphocyte recognition. At the heart of these strategies is the molecular transformation of a soluble protein antigen to a complex of a small peptide containing the antigenic determinant bound to a cell surface Major Histocompatibility Complex class I or class II protein. This process is termed antigen presentation. Progress in a variety of laboratories over the last several years has yielded a wealth of information about the molecular mechanisms underlying antigen presentation, providing potential new approaches to vaccine design. Here we describe recent studies in our laboratory aimed at elucidating the intracellular site in B lymphocytes in which antigenic peptide-class II complexes are assembled for recognition by helper T cells and the regulation of this assembly process. Our results suggest that processed antigen-class II complexes are assembled in a unique compartment in the endocytic route which contains all the necessary cellular and molecular machinery for assembly and that B cells regulate the assembly process in response to external and internal signals.

Antigen-Presenting Cells↗
PubMed1999

A human cell line constitutively expressing HIV-1 Gag and Gag-Pol gene products.

A human cell line constitutively expressing the HIV-1 gag and pol genes products was established. The cell line was established by stably transfecting 293 cells with a plasmid construct that expresses the HIV Gag and Pol and can confer the transfectants resistant to mycophenolic acid. Particles generated from transient expression of the plasmid construct were noninfectious when pseudotyped with HIV envelope or with amphotropic murine leukemia virus envelope proteins. However, virus-like Gag particles produced by the stable cell line were appropriately processed, exhibited a wild-type retrovirus particle density, and possessed significant reverse-transcriptase (RT) activities. Continuous passage of the cell line either in the presence or absence of mycophenolic acid had no major effects on the Gag processing efficiency, particle assembly, or RT activity release. It was also demonstrated that the proteolytic processing of the virus-like particles released from the cell line was inhibited by an HIV protease inhibitor, saquinavir. The establishment of a stable cell line producing noninfectious but proteolytically processed HIV Gag particles offers a safe, convenient tool for biochemical and immunological analysis of virus-like particle assembly and is very useful for the development of anti-HIV protease drugs.

Blotting, Western↗
PubMed2006

Biogenesis of functional antigenic peptide transporter TAP requires assembly of pre-existing TAP1 with newly synthesized TAP2.

The transporter associated with antigen processing (TAP) is essential for the delivery of antigenic peptides from the cytosol into the endoplasmic reticulum (ER), where they are loaded onto major histocompatibility complex class I molecules. TAP is a heterodimeric transmembrane protein that comprises the homologous subunits TAP1 and TAP2. As for many other oligomeric protein complexes, which are synthesized in the ER, the process of subunit assembly is essential for TAP to attain a native functional state. Here, we have analyzed the individual requirements of TAP1 and TAP2 for the formation of a functional TAP complex. Unlike TAP1, TAP2 is very unstable when expressed in isolation. We show that heterodimerization of TAP subunits is required for maintaining a stable level of TAP2. By using an in vitro expression system we demonstrate that the biogenesis of functional TAP depends on the assembly of preexisting TAP1 with newly synthesized TAP2, but not vice versa. The pore forming core transmembrane domain (core TMD) of in vitro expressed TAP2 is necessary and sufficient to allow functional complex formation with pre-existing TAP1. We propose that the observed assembly mechanism of TAP protects newly synthesized TAP2 from rapid degradation and controls the number of transport active transporter molecules. Our findings open up new possibilities to investigate functional and structural properties of TAP and provide a powerful model system to address the biosynthetic assembly of oligomeric transmembrane proteins in the ER.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1992

Self-assembly into fibrils of a homotrimer of type I collagen.

Type I collagen, the most abundant structural protein in vertebrates, is comprised of two alpha 1(I) chains and one alpha 2(I) chain. Fibroblasts from a proband with osteogenesis imperfecta, however, were shown to synthesize a type I procollagen that was a homotrimer of pro alpha 1(I) chains. The absence of pro alpha 2(I) chains in the procollagen provided a unique opportunity to assess the role of the alpha 2(I) chain in collagen fibrillogenesis by examining the self-assembly de novo of the homotrimeric collagen generated in vitro. The results demonstrated that the fibrils formed by the homotrimeric collagen had an asymmetric banding pattern similar to fibrils of normal heterotrimeric type I collagen. However, the efficiency for self-assembly of the homotrimer into fibrils was markedly reduced in that the critical concentration at 37 degrees C was 40-fold greater than for self-assembly of the heterotrimeric molecule. A van't Hoff-type plot of the data was used to determine values for delta G, delta H and delta S. The values indicated the self-assembly of the homotrimer is similar to self-assembly of the heterotrimer in that the process is entropy driven. The process is, however, less favorable in that the delta G value was 10 kJ/mol less negative. The results suggest that the presence of the alpha 2(I) chain in type I collagen helps drive the self-assembly process, probably because the alpha 2(I) chain is more hydrophobic than the alpha 1(I) chain and, therefore, smaller amounts of structured water may be lost during self-assembly of the homotrimer than during self-assembly of the heterotrimer.(ABSTRACT TRUNCATED AT 250 WORDS)

Cells, Cultured↗
PubMed1989

The assembly of regularly spaced nucleosomes in the Xenopus oocyte S-150 extract is accompanied by deacetylation of histone H4.

Histone proteins, which were assembled into chromatin using the Xenopus oocyte S-150 extract, were analyzed on acid-urea gels and Triton-acid-urea gels to determine their state of modification. We find that histone H4, which is present in a diacetylated form in the oocyte S-150, gradually loses its acetate groups as the DNA is packaged into chromatin. Thus, this process parallels the one observed in vivo during chromatin formation in growing eucaryotic cells. Histone H4 deacetylation in the oocyte S-150 is a DNA-dependent reaction. This reaction is blocked when butyrate (an inhibitor of histone deacetylase) is added at the onset of the chromatin assembly process. When butyrate is added at the end of the assembly process, no de novo acetylation of the nucleosomal histone H4 is observed. Chromatin with regularly spaced nucleosomes, displaying periodicities ranging from 160 to 220 base pairs, can be assembled in vitro with the oocyte S-150 (Rodríguez-Campos, A., Shimamura, A., and Worcel, A. (1989) J. Mol. Biol., in press). This chromatin may contain either deacetylated histone H4 when assembled under standard conditions or diacetylated H4 when assembled in the presence of butyrate. Both types of chromatin display identical structures upon digestion with nucleases. The potential applications of this system toward the study of the naturally occurring diacetylated histone H4 are discussed.

Acetylation↗
PubMed2000

In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element.

An unusual regulatory mechanism that controls transcription elongation in long fertility and virulence operons in bacteria is effected by two specialised components, the RfaH protein and the nucleic acid ops element. Without direct interaction, ops acts to reduce the concentration of RfaH required to stimulate distal gene transcription, and we have proposed that ops recruits RfaH to the transcription machinery. To provide direct experimental evidence for this view, we used gel fitration to identify potential RfaH complexes assembled in Escherichia coli cell extracts that carry out RfaH-dependent transcription. This novel molecular weight shift assay revealed that RfaH-dependent transcription elongation occurs concomitantly with recruitment of RfaH into a high molecular weight transcription complex, and that this recruitment is specifically directed by the ops element. Assembly of this complex required RNA polymerase and nucleotide hydrolysis, but not processive transcription. Neither assembly of the complex nor RfaH-dependent transcription was observed in in vitro reactions containing only ops, RfaH and purified core (alphabetabeta') RNA polymerase; both processes required the combination of subcellular fractions containing the RNA polymerase complex, the cytoplasmic membrane and ribosomes. The data confirm that the ops element directs recruitment of RfaH into a multi-component RNA polymerase complex that resists transcription termination.

Adenosine Triphosphate↗
PubMed1995

Self-assembly in vitro of purified CA-NC proteins from Rous sarcoma virus and human immunodeficiency virus type 1.

The internal structural proteins of retroviruses are proteolytically processed from the Gag polyprotein, which alone is able to assemble into virus-like particles when expressed in cells. All Gag proteins contain domains corresponding to the three structural proteins MA, CA, and NC. We have expressed the CA and NC domains together as a unit in Escherichia coli, both for Rous sarcoma virus (RSV) and for human immunodeficiency virus type 1 (HIV-1). We also expressed a similar HIV-1 protein carrying the C-terminal p6 domain. RSV CA-NC, HIV-1 CA-NC, and HIV-1 CA-NC-p6 were purified in native form by classic methods. After adjustment of the pH and salt concentration, each of these proteins was found to assemble at a low level of efficiency into structures that resembled circular sheets and roughly spherical particles. The presence of RNA dramatically increased the efficiency of assembly, and in this case all three proteins formed hollow, cylindrical particles whose lengths were determined by the size of the RNA. The optimal pH at which assembly occurred was 5.5 for the RSV protein and 8.0 for the HIV-1 proteins. The treatment of the RSV CA-NC cylindrical particles with nonionic detergent, with ribonuclease, or with viral protease caused disassembly. These results suggest that RNA plays an important structural role in the virion and that it may initiate and organize the assembly process. The in vitro system described should facilitate the dissection of assembly pathways in retroviruses.

Amino Acid Sequence↗
PubMed2005

Raspberry-like composite polymer particles by self-assemble heterocoagulation based on a charge compensation process.

Nano-sized poly(ethylene glycol dimethacrylate-co-acylic acid) (poly(EGDMA-co-AA)) were effectively self-assembled on poly(divinylbenzene-co-styryl methylpyridinium chloride) (poly(DVB-co-StMPyCl)) surfaces to form the raspberry-like composite by a charge compensation mechanism through the affinity complex between carboxylic group and pyridinium group. The effects of pH and salt electrolyte on the morphology of the self-assembled polymer composites were investigated. The resulting heterocoagulates were highly stable in water and acid solution. These heterocoagulates were reversible through the self-assembly in acidic or neutral media and the dissociation in the basic medium due to the charge compensation through the strong affinity complex between hydroxide anion and pyridinium group cation. The resulting heterocoagulates were characterized with scanning electron microscopy (SEM), field emission scanning electron microscopy (FESEM) and Fourier transform infrared spectroscopy (FTIR). As a result, a new method for tuning the structure of a charge compensation directed polymer composite was developed.

Composite Resins↗
PubMed1990

Spleen necrosis virus gag polyprotein is necessary for particle assembly and release but not for proteolytic processing.

The nature of spleen necrosis virus pol gene expression and the role of gag and gag-pol polyproteins in virion assembly was investigated. The DNA sequence of the gag-pol junction revealed that the two genes occupy the same open reading frame but are separated by an in-frame amber stop codon. Biochemical analysis of gag-pol translational readthrough in vitro and in Escherichia coli suggests that, in a manner similar to that in other mammalian type C retroviruses, amber stop codon suppression is required for pol gene expression. Removal of the gag stop codon had little or no effect on synthesis or cleavage of the polyprotein but interrupted particle assembly. This block could be overcome by complementation with wild-type gag protein.

Amino Acid Sequence↗
PubMed1996

Synthesis and assembly of retrovirus Gag precursors into immature capsids in vitro.

The assembly of retroviral particles is mediated by the product of the gag gene; no other retroviral gene products are necessary for this process. While most retroviruses assemble their capsids at the plasma membrane, viruses of the type D class preassemble immature capsids within the cytoplasm of infected cells. This has allowed us to determine whether immature capsids of the prototypical type D retrovirus, Mason-Pfizer monkey virus (M-PMV), can assemble in a cell-free protein synthesis system. We report here that assembly of M-PMV Gag precursor proteins can occur in this in vitro system. Synthesized particles sediment in isopycnic gradients to the appropriate density and in thin-section electron micrographs have a size and appearance consistent with those of immature retrovirus capsids. The in vitro system described in this report appears to faithfully mimic the process of assembly which occurs in the host cell cytoplasm, since M-PMV gag mutants defective in in vivo assembly also fail to assemble in vitro. Likewise, the Gag precursor proteins of retroviruses that undergo type C morphogenesis, Rous sarcoma virus and human immunodeficiency virus, which do not preassemble capsids in vivo, fail to assemble particles in this system. Additionally, we demonstrate, with the use of anti-Gag antibodies, that this cell-free system can be utilized for analysis in vitro of potential inhibitors of retrovirus assembly.

Animals↗
PubMed2005

Transcriptional analysis of Ralstonia eutropha genes related to poly-(R)-3-hydroxybutyrate homeostasis during batch fermentation.

Poly-(R)-3-hydroxybutyrate (PHB) homeostasis in Ralstonia eutropha takes place at the interface of the cytosol and the hydrophobic PHB granule. PHB synthesis and degradation are therefore intimately linked to the process of granule assembly and breakdown. Unraveling this time-dependent three-dimensional process requires an understanding of the kinetics of synthesis of relevant proteins. Reverse transcriptase quantitative PCR and quantitative Western blotting were carried out on batch cultures of R. eutropha H16 in order to gain insight into how expression of the PHB-related genes phaA, phaB, phaC, phaP, phaR, phaZ1a, phaZ1b, and phaZ1c changed during a cell growth phase, a PHB production phase, and a PHB utilization phase. phaA, phaB, phaC, phaR, and phaZ1a were transcribed throughout cell growth, PHB production, and PHB degradation. PHB-mediated induction of PhaP expression was shown to occur at the transcriptional level, with transcript levels increasing during PHB production and decreasing during PHB utilization. Levels of PhaP correlated strongly with levels of PHB. Levels of phaZ1b transcript and protein increased sharply during production and decreased during degradation, but transcript accumulation did not depend on PHB production as in the case of phaP. No evidence of phaZ1c expression was found under the experimental conditions used in this study.

Bacterial Proteins↗

Refine your search to explore more results.