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 1,261 records · Page 70Linked to original sources
PubMed1993

A candidate mammalian glycoinositol phospholipid precursor containing three phosphoethanolamines.

The glycoinositol phospholipid (GPI) anchors of mammalian proteins contain linear ethanolamine (EthN)-P-6ManManManGlcN glycan sequences that bear additional EthN-P substituents and in some cases include a fourth Man and a GalNAc or sialic acid-GalGalNAc. Precursors of these anchoring structures are preassembled in the endoplasmic reticulum by sequential glycosylation of inositol phospholipid. In previous studies (Hirose, S., Prince, G. M, Sevlever, D., Ravi, L., Rosenberry, T. L., Ueda, E., and Medof, M. E. (1992) J. Biol. Chem. 267, 16968-16974), a series of putative intermediates of this assembly process were isolated from human HeLa cells and murine lymphomas, and several of the more polar products were found to contain a second EthN-P attached to the Man residue (Man 1) proximal to GlcN. In this study, the most polar HeLa cell GPI species was purified by normal phase HeLa cell GPI species was purified by normal phase Iatrobead high performance liquid chromatography, and its glycan was characterized. Dionex anion exchange chromatographic analyses of fragments produced by nitrous acid deamination, hydrofluoric acid dephosphorylation, and trifluoroacetic acid hydrolysis in conjunction with biosynthetic labeling studies indicated a structure containing a third EthN-P substituent linked to the 6-position of Man 2. The polar GPI product exhibited a ManManManGlcN core lacking additional Man or GalNAc. The implications of the identification of this triply phosphoethanolamine-substituted species to mammalian GPI anchor biosynthesis are discussed.

Carbohydrate Sequence↗
PubMed1996

The assembly of human fibrinogen. The role of the amino-terminal and coiled-coil regions of the three chains in the formation of the alphagamma and betagamma heterodimers and alphabetagamma half-molecules.

Fibrinogen is a plasma protein consisting of six polypeptide chains which are linked by disulfide bonds. During protein synthesis, assembly of the molecule proceeds through the formation of alphagamma and betagamma heterodimers followed by the generation of alphabetagamma half-molecules and dimerizing to generate the mature six-chain molecule. In the present study, sequences required for the formation of the alphagamma and betagamma heterodimers were examined in stably transfected baby hamster kidney cells expressing combinations of normal as well as modified polypeptide chains. Deletion of the amino terminus and the proximal first half of the coiled-coil region of the three fibrinogen chains had little or no effect on heterodimer and half-molecule formation. These deletions, however, did prevent half-molecules from forming the six-chain molecule. Deletion of the distal second half of the coiled-coil region of each chain completely prevented the assembly process. Point mutations in the second half of the coiled-coil region also indicated that hydrophilic residues that form ion pairs between interacting chains were not critical in the formation of the heterodimeric complexes. These results suggest that the initial formation of the alphagamma and betagamma complexes depends primarily on hydrophobic interactions of amino acids located in the second half of the coiled-coil region of the molecule. These interactions occur in the rough endoplasmic reticulum in the presence of various chaperones such as BiP.

Amino Acid Sequence↗
PubMed1997

Immunocytochemical evidence for a stepwise assembly of Balbiani ring premessenger ribonucleoprotein particles.

In the active Balbiani ring (BR) genes of the dipteran Chironomus tentans, the assembly of a specific pre-mRNP particle can be analyzed in situ, and the incorporation of hnRNP proteins into the nascent pre-mRNP can be directly visualized by immunoelectron microscopy. In the present study we have shown that hrp36, one of the major hnRNP proteins in Chironomus tentans, is continuously added to the nascent BR pre-mRNP particle throughout transcription and is localized along the entire BR RNP fiber. Interestingly, hrp36 becomes concealed during the structural transition that occurs during the formation of the mature BR RNP particle. This conclusion is based on the observation that hrp36 can be revealed by a monoclonal antibody during the initial assembly of the BR RNP fiber but becomes almost undetectable in the final packaging stage. The hrp36 protein, however, is not removed from the BR RNP particle since the ability of the monoclonal antibody to reveal hrp36 is restored by artificial relaxation of mature BR RNP particles. Another major hnRNP protein, hrp45, is also incorporated in a continuous manner into the nascent pre-mRNP fiber but remains accessible in mature BR RNP particles. Our results provide immunocytochemical evidence for drastic structural changes occurring in the final stage of BR pre-mRNP packaging, and suggest that different hnRNP proteins might be differently involved in the pre-mRNP assembly process.

Animals↗
PubMed1981

Material self-assembly as a physicochemical process.

Material self-assembly as exemplified in protobiogeneses is shown to be result of molecular exchange interaction in reacting chemicals. Temporally and spatially correlated aggregates of reacting chemicals work as vertices of molecular exchange interaction. If the material accumulation rate at a locally correlated aggregate spontaneously happens to become positive at a certain time, the material accumulation due to self-assembly will increase with time afterward. A spontaneous formation of looped reaction at locally correlated aggregates of reacting chemicals can initiate a material self-assembly at succeeding times.

Mathematics↗
PubMed2002

Influence of ionic inorganic solutes on self-assembly and polymerization processes related to early forms of life: implications for a prebiotic aqueous medium.

A commonly accepted view is that life began in a marine environment, which would imply the presence of inorganic ions such as Na+, Cl-, Mg2+, Ca2+, and Fe2+. We have investigated two processes relevant to the origin of life--membrane self-assembly and RNA polymerization--and established that both are adversely affected by ionic solute concentrations much lower than those of contemporary oceans. In particular, monocarboxylic acid vesicles, which are plausible models of primitive membrane systems, are completely disrupted by low concentrations of divalent cations, such as magnesium and calcium, and by high sodium chloride concentrations as well. Similarly, a nonenzymatic, nontemplated polymerization of activated RNA monomers in ice/eutectic phases (in a solution of low initial ionic strength) yields oligomers with > 80% of the original monomers incorporated, but polymerization in initially higher ionic strength aqueous solutions is markedly inhibited. These observations suggest that cellular life may not have begun in a marine environment because the abundance of ionic inorganic solutes would have significantly inhibited the chemical and physical processes that lead to self-assembly of more complex molecular systems.

Calcium↗
PubMed2005

Evolution of multilevel order in supramolecular assemblies.

The process of self-assembly at multiple length scales of bis-urea substituted toluene on a Au(111) surface was studied by low temperature scanning tunneling microscopy. Pattern formation is controlled by specific hydrogen bonds between these molecules but also by significantly weaker lateral coupling between the resulting supramolecular polymers and a quasiepitaxial interlocking with the substrate. The ordered assemblies exhibit a tunnel transparency. Our experiments indicate the necessity of multiple interactions of different strengths for obtaining ordered structures with hierarchical levels of organization.

Journal Article↗
PubMed2002

Diffusion approximation of the stochastic process of microtubule assembly.

Microtubules are protein polymers that guide intracellular motility. Stochastic switching of a microtubule between states of elongation, shortening, and pause is described in detail by the dynamic instability (DI) model. Recently we have described the dynamics of microtubules phenomenologically as generalized diffusion of their ends. Genesis of the diffusion dynamics and accuracy of diffusion model are studied in this work. It is shown that wandering of the end of a microtubule undergoing DI asymptotically approaches the Wiener diffusion process. Accuracy of the diffusion approximation is evaluated by comparing its predictions with results of simulation of DI. Stationary distributions of microtubule length and life-time that are predicted by both models differ qualitatively between two cell types considered. However, predictions of the diffusion model are in each case practically identical to predictions of the DI model being also consistent with experimental data. The peculiar stochastic process of microtubule assembly thus converges at cell scale to a kind of widespread-in-nature diffusion process. This result is considered an example of qualitative change in dynamical properties in transition from the molecular to cellular level of biological organization. Additionally, it suggests employment of diffusion process theory in studying functions of microtubules in the cell.

Animals↗
PubMed2006

Amperometric glucose biosensor based on layer-by-layer assembly of multilayer films composed of chitosan, gold nanoparticles and glucose oxidase modified Pt electrode.

A new strategy for fabricating glucose biosensor was presented by layer-by-layer assembled chitosan (CS)/gold nanoparticles (GNp)/glucose oxidase (GOD) multilayer films modified Pt electrode. First, a cleaned Pt electrode was immersed in poly(allylamine) (PAA), and then transferred to GNp, followed by the adsorption of GOD (GOD/GNp/PAA/Pt). Second, the GOD/GNp/PAA/Pt electrode was immersed in CS, and then transferred to GNp, followed by the adsorption of GOD (GOD/GNp/CS/GOD/GNp/PAA/Pt). Third, different layers of multilayer films modified Pt electrodes were assembled by repeating the second process. Film assembling and characterization were studied by quart crystal microbalance, and properties of the resulting glucose biosensors were measured by electrochemical measurements. The results confirmed that the assembling process of multilayer films was simple to operate, the immobilized GOD displayed an excellent catalytic property to glucose, and GNp in the biosensing interface efficiently improved the electron transfer between analyte and electrode surface. The amperometric response of the biosensors uniformly increased from one to six layers of multilayer films, and then reached saturation after the seven layers. Among the resulting biosensors, the biosensor based on the six layers of multilayer films was best. It showed a wide linear range of 0.5-16 mM, with a detection limit of 7.0 microM estimated at a signal-to-noise ratio of 3, fast response time (within 8s). Moreover, it exhibited good reproducibility, long-term stability and interference free. This method can be used for constructing other thin films, which is a universal immobilization method for biosensor fabrication.

Biosensing Techniques↗
PubMed1994

Movement of axoplasmic organelles on actin filaments assembled on acrosomal processes: evidence for a barbed-end-directed organelle motor.

The directionality of the actin-dependent motors on squid axoplasmic organelles was determined using actin filaments assembled on the barbed ends of acrosomal processes. Acrosomal processes were isolated from Limulus polyphemus sperm and incubated in monomeric actin under conditions that promoted barbed end assembly only. Newly assembled actin was stabilized and stained with rhodamine-phalloidin and the presence of filaments at the barbed ends of the acrosomal processes was verified by fluorescence microscopy and negative contrast electron microscopy. Axoplasmic organelles that dissociated from extruded axoplasm were observed by video microscopy to move along the newly assembled actin filaments at an average velocity of 1.1 +/- 0.3 microns/second. All organelles moved in the direction away from the acrosomal fragment and towards the tip of the actin filaments. Therefore, the actin-dependent organelle motor on axoplasmic organelles is a barbed-end-directed motor like other myosins analyzed. These findings support the conclusions that axoplasmic organelles are driven by a myosin-like motor along actin filaments and that these filaments as well as microtubules function in fast axonal transport.

Acrosome↗
PubMed1988

Chloroplast ribosomal protein L-18 in Chlamydomonas reinhardtii is processed during ribosome assembly.

Chloroplast ribosomal protein L-18 is made in the cytoplasm as a precursor, imported into the chloroplast, and processed to the mature form in two steps. We report here that the intermediate produced following the first processing step associates specifically with a ribosomal complex migrating with the chloroplast ribosome large subunit peak in sucrose gradients, and is then processed into mature L-18. This processing event is slowed down in mutant cells deficient in synthesis of non-ribosomal proteins in the chloroplast. Thus the second processing step of L-18 occurs during ribosome assembly, depends on one or more nonribosomal proteins made in the chloroplast, and may be required for the maturation of the 50 S ribosome subunit. The mature L-18 protein shows extensive sequence homology at its amino-terminus to Escherichia coli ribosomal protein L27, which is located at the interface between 30 S and 50 S subunits and is involved in the formation of the peptidyl-tRNA binding site.

Amino Acid Sequence↗
PubMed1996

Effect of brefeldin A on rotavirus assembly and oligosaccharide processing.

Rotavirus is one of very few viruses that utilizes the endoplasmic reticulum (ER) for maturation. The maturation process is unique not only because it involves translocation of subviral particles across the ER membrane, but also because mature virus is thought to be retained in the ER until cell lysis. Brefeldin A (BFA) is a compound that blocks protein export from the ER to the Golgi complex and causes disruption of the Golgi complex with relocation of resident Golgi proteins to the ER. We found that BFA had a pronounced effect on rotavirus assembly and oligosaccharide processing. Single-step growth experiments demonstrated that BFA reduced infectious progeny rotavirus yield by 99.9%. Immunohistochemical staining with monoclonal antibodies showed that all examined VP4, VP6, VP7, and NS28 epitopes remained unaffected by BFA. A novel observation from pulse-chase experiments was that BFA-treatment rapidly increased the molecular weight of the ER-associated VP7 followed by endo-beta-N-acetylglucosaminidase H (endo H) resistance. A novel observation was also that the trans-ER NS28 protein remained endo H sensitive through the course of BFA-treatment, but that the molecular weight varied during chase. Electron microscopy analysis revealed that BFA interfered in the transition from the intermediate enveloped particle to the mature double-shelled virus.

Amino Acid Sequence↗
PubMed1991

Translocation of peptides through microsomal membranes is a rapid process and promotes assembly of HLA-B27 heavy chain and beta 2-microglobulin translated in vitro.

We have translated major histocompatibility complex (MHC) class I heavy chains and human beta 2-microglobulin in vitro in the presence of microsomal membranes and a peptide from the nucleoprotein of influenza A. This peptide stimulates assembly of HLA-B27 heavy chain and beta 2-microglobulin about fivefold. By modifying this peptide to contain biotin at its amino terminus, we could precipitate HLA-B27 heavy chains with immobilized streptavidin, thereby directly demonstrating class I heavy chain-peptide association under close to physiological conditions. The biotin-modified peptide stimulates assembly to the same extent as the unmodified peptide. Both peptides bind to the same site on the HLA-B27 molecule. Immediately after synthesis of the HLA-B27 heavy chain has been completed, it assembles with beta 2-microglobulin and peptide. These interactions occur in the lumen of the microsomes (endoplasmic reticulum), demonstrating that the peptide must cross the microsomal membrane in order to promote assembly. The transfer of peptide across the microsomal membrane is a rapid process, as peptide binding to heavy chain-beta 2-microglobulin complexes is observed in less than 1 min after addition of peptide. By using microsomes deficient of beta 2-microglobulin (from Daudi cells), we find a strict requirement of beta 2-microglobulin for detection of peptide interaction with the MHC class I heavy chain. Furthermore, we show that heavy chain interaction with beta 2-microglobulin is likely to precede peptide binding. Biotin-modified peptides are likely to become a valuable tool in studying MHC antigen interaction and assembly.

Amino Acid Sequence↗
PubMed1987

Gonadotropin beta subunits determine the rate of assembly and the oligosaccharide processing of hormone dimer in transfected cells.

The glycoprotein hormones lutropin (LH) and chorionic gonadotropin (CG) share a common structure consisting of an identical alpha subunit noncovalently linked to a hormone-specific beta subunit. While LH is produced in the anterior pituitary, CG is synthesized in placenta. To compare the assembly, processing, and secretion of human LH and CG in the same cell type, we have expressed their subunits, individually and together, in mouse C-127 mammary tumor cells. Analysis of transfected clones revealed an unexpected difference in the secretion of individually expressed subunits. Whereas alpha and CG beta subunits were rapidly and quantitatively secreted, only 10% of newly synthesized LH beta subunit reached the medium. The remaining subunit was found in an intracellular, endoglycosidase H (endo H)-sensitive pool that had a turnover rate of approximately 8 h. Coexpression with alpha subunit resulted in "rescue" of LH beta subunit by formation of LH dimer, which was efficiently secreted. However, combination of LH beta with alpha was slow, with an overall efficiency of only 50% despite the presence of excess alpha. In contrast, CG beta was rapidly assembled with the alpha subunit after synthesis. The two beta subunits also differed in their influence on the N-linked oligosaccharide processing of combined alpha. The oligosaccharides of LH dimer were endo H resistant, while those of CG dimer remained partially endo H sensitive. Thus, despite a high degree of homology between LH beta and CG beta, the two subunits differ in their secretion as free subunits, their rate of assembly with alpha subunit, and in their effect on the N-linked oligosaccharide processing of combined alpha.

Animals↗
PubMed2006

Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice.

Jawless vertebrates have acquired immunity but do not have immunoglobulin-type antigen receptors. Variable lymphocyte receptors (VLRs) have been identified in lamprey that consist of multiple leucine-rich repeat (LRR) modules. An active VLR gene is generated by the assembly of a series of variable gene segments, including many that encode LRRs. Stepwise assembly of the gene segments seems to occur by replacement of the intervening DNA between the 5' and 3' constant-region genes. Here we report that lamprey (Lethenteron japonicum) assemble their VLR genes by a process involving 'copy choice'. Regions of short homology seemed to prime copying of donor LRR-encoding sequences into the recipient gene. Those LRR-encoding germline sequences were abundant and shared extensive sequence homologies. Such genomic organization permits initiation of copying anywhere in an LRR-encoding module for the generation of various hybrid LRRs. Thus, a vast repertoire of recombinant VLR genes could be generated not only by copying of various LRR segments in diverse combinations but also by the use of multiple sites in an LRR gene segment for priming.

Alleles↗
PubMed1996

Hippocampal and neocortical cell assemblies encode memory processes for different types of stimuli in the rat.

The objective of this study was to determine whether each of several different memory processes is encoded exclusively by specific single neurons (single-neuron coding) or by overlapped groups of neurons (population coding by cell assembly). Single neuronal activity was recorded from the rat hippocampal formation (CA1, CA3, dentate gyrus) and temporal cortex during the performance of simple auditory, simple visual, and configural auditory-visual discrimination tasks. All the tasks employed the identical apparatus and time parameters and differed only in the type of stimuli to be processed for correct performance. Single neurons showing significantly differential activity among the discriminative stimuli in each task were judged to be task-related and involved in the memory process of the task. Of the total number of neurons recorded from the hippocampal formation and temporal cortex, 21-26% of the neurons showed task-related activity in only one task, in two tasks, or in all three tasks. This result indicates some overlapping among the neurons involved in each of teh different memory processes. A cross-correlation analysis tested activity correlations among the neurons recorded simultaneously. Most pairs of the hippocampal neurons related to the same tasks (same memory processes) showed correlations during performance of the related tasks. This result showing coactivation of the same types of task-related neurons, together with the result showing the overlapping of task-related neurons, supports the concept of population coding by cell assemblies specifically in the hippocampal formation during memory processing.

Acoustic Stimulation↗
PubMed2005

Assembly and infection process of bacteriophage T4.

Bacterophage T4 consists of three parts, namely, a head, a tail, and six tail fibers, each of which is assembled along an independent pathway and then joined. In contrast to simple plant viruses such as tobacco mosaic virus, disassembly and reassembly of the virion is not possible. This is due mainly to the fact that the assembly involves not only irreversible steps such as cleavage of covalent bonds of some constituent proteins, but also that it requires a scaffold and involves the inner membrane of the host cell. Another unique feature of the assembly as a biological nanomachine is the involvement of specific protein devices such as a "ruler molecule," which determines the length of the tail, an ATP-driven DNA packaging protein complex, and phage-encoded molecular chaperones. Recent structural biological studies of the phage started to unveil the molecular mechanics of structural transformation of the tail upon infection.

Animals↗
PubMed1997

Functional analysis of Rrp7p, an essential yeast protein involved in pre-rRNA processing and ribosome assembly.

During the functional analysis of open reading frames (ORFs) identified during the sequencing of chromosome III of Saccharomyces cerevisiae, the previously uncharacterized ORF YCL031C (now designated RRP7) was deleted. RRP7 is essential for cell viability, and a conditional null allele was therefore constructed, by placing its expression under the control of a regulated GAL promoter. Genetic depletion of Rrp7p inhibited the pre-rRNA processing steps that lead to the production of the 20S pre-rRNA, resulting in reduced synthesis of the 18S rRNA and a reduced ratio of 40S to 60S ribosomal subunits. A screen for multicopy suppressors of the lethality of the GAL::rrp7 allele isolated the two genes encoding a previously unidentified ribosomal protein (r-protein) that is highly homologous to the rat r-protein S27. When present in multiple copies, either gene can suppress the lethality of an RRP7 deletion mutation and can partially restore the ribosomal subunit ratio in Rrp7p-depleted cells. Deletion of both r-protein genes is lethal; deletion of either single gene has an effect on pre-rRNA processing similar to that of Rrp7p depletion. We believe that Rrp7p is required for correct assembly of rpS27 into the preribosomal particle, with the inhibition of pre-rRNA processing appearing as a consequence of this defect.

Alleles↗
PubMed2005

Characterization of conserved sequence elements in eukaryotic RNase P RNA reveals roles in holoenzyme assembly and tRNA processing.

RNase P is a ubiquitous endoribonuclease responsible for cleavage of the 5' leader of precursor tRNAs (pre-tRNAs). Although the protein composition of RNase P holoenzymes varies significantly among Bacteria, Archaea, and Eukarya, the holoenzymes have essential RNA subunits with several sequences and structural features that are common to all three kingdoms of life. Additional structural elements of the RNA subunits have been found that are conserved in eukaryotes, but not in bacteria, and might have functions specifically required by the more complex eukaryotic holoenzymes. In this study, we have mutated four eukaryotic-specific conserved regions in Saccharomyces cerevisiae nuclear RNase P RNA and characterized the effects of the mutations on cell growth, enzyme function, and biogenesis of RNase P. RNase P with mutations in each of the four regions tested is sufficiently functional to support life although growth of the resulting yeast strains was compromised to varying extents. Further analysis revealed that mutations in three different regions cause differential defects in holoenzyme assembly, localization, and pre-tRNA processing in vivo and in vitro. These data suggest that most, but not all, eukaryotic-specific conserved regions of RNase P RNA are important for the maturation and function of the holoenzyme.

Base Sequence↗