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.

SourceResearch connectionFrom yearThrough year

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

At least 577 records · Page 32Linked to original sources

PubMed1995

A domain sharing model for active site assembly within the Mu A tetramer during transposition: the enhancer may specify domain contributions.

The functional configuration of Mu transposase (A protein) is its tetrameric form. We present here a model for the organization of a functional Mu A tetramer. Within the tetramer, assembly of each of the two active sites for Mu end cleavage requires amino acid contributions from the central and C-terminal domains (domains II and III respectively) of at least two Mu A monomers in a trans configuration. The Mu enhancer is likely to function in this assembly process by specifying the two monomers that provide their C-terminal domains for strand cleavage. The Mu B protein is not required in this step. Each of the two active sites for the strand transfer reaction is also organized by domain sharing (but in the reverse mode) between Mu A monomers; i.e. a donor of domain II (also the recipient of domain III) during cleavage is a recipient of domain II (and the donor of domain III) during strand transfer. The function of the Mu B protein (which is required at the strand transfer step) and that of the enhancer element may be analogous in that their interactions with Mu A (domain III and domain I alpha respectively) promote conformations of Mu A conducive to strand cleavage or strand transfer.

Bacteriophage mu↗

PubMed1976

The oral apparatus of Tetrahymena pyriformis, strain WH-6. II. Cytochalasin B inhibition of oral apparatus morphogenesis.

The effects of cytochalasin B on oral apparatus morphogenesis and cell division were studied in synchronized Tetrahymena pyriformis, strain WH-6 syngen 1. Cytochalasin B brought about the rapid arrest of oral apparatus primordium development when added prior to the completion of oral apparatus membranelle differentiation. Cells arrested in development did not divide. When cytochalasin B was added after this transition point, oral apparatus morphogenesis and cell division were completed. The effects of cytochalasin B could be reversed by washing it from the medium. Even though cytochalasin B (at 400 mug/ml) reduced protein synthesis by 30%, the data are consistent with the interpretation that cytochalasin B prevents an assembly process during the membranelle differentiation phase of oral apparatus development.

Animals↗

PubMed1995

Reassembly of the 66 kD neurofilament protein in vitro following isolation and purification from bovine spinal cord.

NF-66, also known as alpha-internexin, has been characterized as a 66 kD mammalian neurofilament (NF) protein whose expression in developing rat brain precedes that of the low molecular weight NF protein (NF-L). NF-66 is thought to assemble into 10 nm diameter intermediate filaments in vitro, although the precise nature of the assembly process remains obscure. Likewise, the ability of NF-66 to polymerize with the low (NF-L), middle (NF-M), and high (NF-H) M(r)NF proteins has not been defined. This investigation describes the reassembly of bovine NF-66 regarding its formation into 10 nm diameter filaments as well as its potential for polymerization with other type IV intermediate filaments. NF-66 and the NF triplet proteins were isolated from bovine spinal cord using established biochemical extraction and isolation procedures (Balin et al., Brain Res 556:181-195, 1991), and purified by a combination of high performance liquid chromatography (HPLC) (DEAE anion exchange and hydroxylapatite column chromatography) and gel elution strategies. In vitro reassembly experiments revealed that NF-66 formed approximately 10 nm diameter filaments of varying length; immunoelectron microscopy demonstrated labeling of these filaments by a monoclonal antibody to intermediate filament antigen (IFA), a polyclonal antibody against rat NF-66 and by a monoclonal antibody generated against the core region of NF-M but cross-reactive with NF-66. This report is the first investigation to look at the in vitro interaction between NF-66 and other type IV intermediate filament proteins (NF-H, -M, and -L) and establishes that NF-66 forms heteropolymeric filaments with these other neurofilament proteins, as confirmed by double immunolabeling. These studies suggest that NF-66 could provide a nucleation site for the polymerization of later-expressed proteins during neuronal development.

Animals↗

PubMed1988

Comparison of the dynamics of the membrane-bound form of fd coat protein in micelles and in bilayers by solution and solid-state nitrogen-15 nuclear magnetic resonance spectroscopy.

Solid-state and solution 15N nuclear magnetic resonance experiments on uniformly and specifically 15N labeled coat protein in phospholipid bilayers and in detergent micelles are used to describe the dynamics of the membrane-bound form of the protein. The residues in the N- and C-terminal portions of the coat protein in both phospholipid bilayers and in detergent micelles are mobile, while those in the hydrophobic midsection are immobile. There is evidence for a gradient of mobility in the C-terminal region of the coat protein in micelles; at 25 degrees C only the last two residues are mobile on the 10(9)-Hz timescale, while the last six to eight residues appear to be mobile on slower timescales and highly mobile at higher temperatures. Since all of the C-terminal residues are immobile in the virus particles, the mobility of these residues in the membrane-bound form of the protein may be important for the formation of protein-DNA interactions in the assembly process.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2001

Consequence of beta 16 and beta 112 replacements on the kinetics of hemoglobin assembly.

The rates of alpha/beta monomer combination of four beta(A) variants (beta 112C --> S, beta 112C --> D, beta 112C --> T, and beta 112C --> V) in the presence and absence of beta 16G --> D (beta(J)) were measured in an attempt to assess the consequences of amino acid substitution at both a surface (beta 16) and an alpha(1)beta(1) interface (beta 112) residue on oxyhemoglobin assembly. Rates of alpha/beta monomer combination determined spectrally in 0.1 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA, pH 7.4, at 21.5 degrees C differed by over 40-fold (22 +/- 2.0 to 0.49 +/- 0.1 x 10(5) M(-1) s(-1)), and were in the order: HbA beta 112S = HbJ beta 16D, beta 112S > HbA beta 112D = HbJ beta 16D, beta 112D > HbA > Hb J > HbA beta 112T = HbJ beta 16D, beta 112T > HbJ beta 16D, beta 112V > HbA beta 112V. This extensive kinetic investigation of single/double amino acid-substituted recombinant hemoglobin molecules, in conjunction with molecular modeling studies, has allowed examination of an array of unique alpha/beta subunit interactions and assembly processes.

Amino Acid Substitution↗

PubMed1995

Redistribution of nuclear envelope associated antigen during the mitotic cycle.

Murine hybridomas were generated to DNA/tight binding proteins complex isolated from the residual nuclear structure following a procedure analogous to that yielding "empty" shells of nuclear envelope. A monoclonal antibody designated 2A8 was selected because of its differential immunostaining of mitotic cells of a synchronized mouse fibroblast cell culture L-929. The target antigen was rendered insoluble by a sequence of extractions of isolated nuclei of diverse cell types with detergents, urea, DNase I and alkali thus reproducing some solubility properties of proteins constituting an operationally defined residual nuclear matrix. The cognate polypeptide was localized on a subset of proteins of M(r) 58-65 kDa, 70 kDa in isolated fibroblast nuclear matrices. The functional implication of the antigen in mitosis-related disassembly-assembly process of the nuclear matrix/envelope was detected. At prophase the antibody decorated the nuclear periphery and nuclear envelope fixed inward filaments. A fibrous network of cytoplasmic localization was stained in metaphase. At anaphase the antigen was dispositioned into peripheral fibrogranular clusters of polar orientation predominantly on one side of the nucleus. Proceeding to telophase a spreading fluorescence was manifested over the entire contour of the nuclear periphery to delineate the reforming nucleus. By immunogold electron microscopy of interphase cells the antigen was identified as evenly distributed in chromatin and interchromatin regions. At initiation of chromosome condensation in mitosis the label was detected predominantly in the chromosomal area.

Animals↗

PubMed2002

Assembly of electroactive layer-by-layer films of myoglobin and ionomer poly(ester sulfonic acid).

Layer-by-layer films were assembled on solid substrates by alternate adsorption of negatively charged ionomer poly(ester sulfonic acid) or Eastman AQ55 from its aqueous dispersion and positively charged myoglobin (Mb) from its solution at pH 4.5. The film assembly process was monitored by cyclic voltammetry (CV), UV-vis spectroscopy, and quartz crystal microbalance (QCM). [AQ/Mb](n) films grown on pyrolytic graphite (PG) electrodes showed a pair of well-defined and nearly reversible CV peaks at about -0.20 V vs Ag/AgCl in pH 5.5 buffers, characteristic of the Mb heme Fe(III)/Fe(II) redox couple. Although the amount of Mb adsorbed in each bilayer was essentially the same, the fraction of electroactive Mb decreased dramatically with an increase of bilayer number (n). Soret absorption bands of [AQ/Mb](n) films on glass slides suggest that Mb in the films retains its native state in the medium pH range. Trichloroacetic acid, oxygen, and hydrogen peroxide were electrochemically catalyzed by [AQ/Mb](6) films with significant lowering of reduction overpotential.

Adsorption↗

PubMed1993

Two-dimensional crystallization of the light-harvesting complex from Rhodospirillum rubrum.

Homogeneous detergent-solubilized B873 light-harvesting complexes from a carotenoid-less mutant of the purple non-sulfur bacterium, Rhodospirillum rubrum G9, were reassembled spontaneously into two-dimensional (2D) hexagonal arrays during extensive and controlled dialysis. As the complexes contain only 1 to 2 mol phospholipid per mol alpha beta dimer, the arrays formed by a self assembly process are primary due to protein-protein interactions. The hexagonal lattices were analyzed by negative stain electron microscopy and digital image processing. They exhibited a unit cell size of 12.3 nm, in close agreement with the particle diameter of the active photo-unit in native chromatophore membranes. The unit cell contains a central 5 nm stain-filled depression, embraced by a ring with an outer diameter of 10 nm.

Crystallization↗

PubMed1994

DNA-protein cooperativity in the assembly and stabilization of mu strand transfer complex. Relevance of DNA phasing and att site cleavage.

The requirements for negatively supercoiled DNA substrates, the cis-acting transposition enhancer and the Escherichia coli HU protein during the phage Mu transposition reaction are relaxed under DMSO-assay conditions. We have used these modified assay conditions to extend studies on the transposition pathway. We show here that linear DNA fragments containing the right end of Mu (attR) and Mu A protein mutually promote the assembly of "high-order" complexes held together by non-covalent protein-DNA and protein-protein interactions. A large subset of these complexes is competent in mediating strand transfer. DNA fragments containing the left end of Mu (attL) as well as non-Mu DNA can be used as targets during strand transfer. The R1 and R2 subsites within attR are required, but R3 is dispensable, in the protein-DNA oligomerization steps as well as in the strand transfer reaction. Proper phasing and spacing between R1 and R2 are central to the reaction. A single base-pair change in the terminal nucleotide that renders attR non-cleavable prevents the assembly of stable high-order complexes, showing that strand cleavage and stabilization of high-order complexes are tightly coupled events. Conversely, pre-cleavage at the attL site allows it to function in the assembly process, albeit at a much lower efficiency than attR. In the presence of HU, the reactivity of pre-cleaved attL is enhanced significantly.

Attachment Sites, Microbiological↗

PubMed1995

The ribosomal DNA loci in Plasmodium falciparum accumulate mutations independently.

Homogeneity of rDNA sequence within a cell is maintained by mechanisms working at the DNA level. The imperative to maintain homogeneity is thought to result from pressure to maintain the sequence of the rRNA transcript. We have investigated the extent of sequence variation within and between members of a species that is unable to utilize some standard mechanisms of rDNA sequence correction. We have compared the sequence of the internal transcribed spacer (ITS1) located between the 18 S rRNA and 5.8 S rRNA genes of five different loci of a single Plasmodium falciparum genotype. The ITS1 sequences are identical at 80 to 91% of the positions among the three asexually expressed genes (A-types) and 75% between the two genes expressed during sporogony (S-types), with only 42 to 57% identity between the types. This is rather startling in that the differences described here for a single genome are greater than those normally seen when comparing rDNA units from distantly related organisms. We observe an apparent conservation of secondary structure within ITS1 sequences from the different transcription units, which would reflect a level of selection at the rRNA but the organism seems to be quite tolerant of primary sequence variation. Investigation of the mature coding region within the 18 S rRNA genes did not reveal sequence variation within A- and S-types from a single genotype. However, comparison of the 18 S rRNA coding region from 17 geographically distinct strains reveals up to 10% sequence variation within a 400 nucleotide region. Hence homogeneity of rRNA units within a species does not seem to be an imperative driven totally by selection at the RNA level. The extraordinary maintenance of homogeneity within rDNA units normally seen within a species appears to have significance beyond those that can be ascribed to the events involved in processing, assembly and function of the ribosome.

Animals↗

PubMed1996

The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains.

The vertebrate striated muscle protein titin is thought to play a critical rôle in myofibril assembly and passive tension. The recently determined complete primary structure of titin revealed a modular architecture that opens the way to a structural characterisation and the understanding of essential properties of this molecule through dissection into units that are structurally and/or functionally relevant. To understand the assembly process of titin, and ultimately the molecular basis of its elastic behaviour, we studied the thermodynamic properties of module pairs, the smallest structural unit that includes a module-module interface. Thus, selected module pairs and their component single modules from the I-band part of the titin molecule were expressed in Escherichia coli and their heat-induced and denaturant-induced unfolding was investigated with a combination of techniques (circular dichroism, fluorescence spectroscopy and nuclear magnetic resonance). The stabilities of single modules and pairs were determined from denaturation experiments. The module interface was also modelled on the basis of the sequence alignment of all approximately 40 immunoglobulin like modules from the I-band and the known structure of one of them. Our results show that all modules and module pairs examined are independently folded in solution. When covalently linked, although weakly interacting, they still behave as autonomous co-operative units upon unfolding. These observations lead us to suggest that folding of titin in vitro is a hierarchical event and that weak interactions between its adjacent modules must only partly account for its presumed elastic function.

Amino Acid Sequence↗

PubMed1997

Modeling supra-molecular helices: extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus.

Geometric matching of molecular surfaces appears to be essential for the formation of binary molecular complexes and of supra-molecular aggregates. The structure of a binary complex is characterized by the best geometric match, whereas the structure of an aggregate is characterized by the best combined match, i.e. the sum of all the internal matches in the system. We describe a method to identify and quantify the binary matches between molecules and then use them to form the supra-molecular helices and evaluate them. This method is applied to the single protein subunit of tobacco mosaic virus. It successfully predicts the structure of the helical protein coat of the virus and the structure of the disk that is formed as the initial step in the virus assembly process. It also predicts structural intermediates, between disk and helix, which explain how the disk can transform into a helix without dissociating into subunits.

Algorithms↗

PubMed2002

Stimulation of the weak ATPase activity of human hsp90 by a client protein.

Heat shock protein 90 (Hsp90) is a molecular chaperone involved in the folding and assembly of a limited set of "client" proteins, many of which are involved in signal transduction pathways. In vivo, it is found in complex with additional proteins, including the chaperones Hsp70, Hsp40, Hip and Hop (Hsp-interacting and Hsp-organising proteins, respectively), as well as high molecular mass immunophilins, such as FKBP59, and the small acidic protein p23. The role of these proteins in Hsp90-mediated assembly processes is poorly understood. It is known that ATP binding and hydrolysis are essential for Hsp90 function in vivo and in vitro. Here we show, for the first time, that human Hsp90 has ATPase activity in vitro. The ATPase activity is characterised using a sensitive assay based on a chemically modified form of the phosphate-binding protein from Escherichia coli. Human Hsp90 is a very weak ATPase, its activity is significantly lower than that of the yeast homologue, and it has a half-life of ATP hydrolysis of eight minutes at 37 degrees C. Using a physiological substrate of Hsp90, the ligand-binding domain of the glucocorticoid receptor, we show that this "client" protein can stimulate the ATPase activity up to 200-fold. This effect is highly specific and unfolded or partially folded proteins, which are known to bind to Hsp90, do not affect the ATPase activity. In addition, the peroxisome proliferator-activated receptor, which is related in both sequence and structure to the glucocorticoid receptor but which does not bind Hsp90, has no observable effect on the ATPase activity. We establish the effect of the co-chaperones Hop, FKBP59 and p23 on the basal ATPase activity as well as the client protein-stimulated ATPase activity of human Hsp90. In contrast with the yeast system, human Hop has little effect on the basal rate of ATP hydrolysis but significantly inhibits the client-protein stimulated rate. Similarly, FKBP59 has little effect on the basal rate but stimulates the client-protein stimulated rate further. In contrast, p23 inhibits both the basal and stimulated rates of ATP hydrolysis. Our results show that the ATPase activity of human Hsp90 is highly regulated by both client protein and co-chaperone binding. We suggest that the rate of ATP hydrolysis is critical to the mode of action of Hsp90, consistent with results that have shown that both over and under-active ATPase mutants of yeast Hsp90 have impaired function in vivo. We suggest that the tight regulation of the ATPase activity of Hsp90 is important and allows the client protein to remain bound to Hsp90 for sufficient time for activation to occur.

Adenosine Triphosphatases↗

PubMed2002

Tissue-specific co-expression and in vitro heteropolymer formation of the two small branchiostoma intermediate filament proteins A3 and B2.

The two small intermediate filament (IF) proteins A3 and B2 of the cephalochordate Amphioxus were investigated. Blot overlays indicated a heterotypic interaction pattern of the recombinant proteins. While the individual proteins formed only aggregates, the stoichiometric mixture formed obligatory heteropolymeric filaments. Mutant proteins with a single cysteine residue in equivalent positions gave rise to filaments that oxidize to the disulfide-linked heterodimer, which can again form IF. Thus the A3/B2 filaments, which are expressed in the intestinal epithelium, are based on a hetero coiled coil. This keratin-like assembly process of A3 plus B2 was unexpected, since previous evolutionary tree calculations performed by two laboratories on the various Amphioxus IF proteins identified keratin I and II orthologs but left the A/B group as a separate branch. We discuss obvious evolutionary aspects of the Amphioxus IF multigene family, including the previously made observation that B1, the closest relative of B2, forms homopolymeric IF in vitro and is, like vertebrate type III proteins, expressed in mesodermally derived tissues.

Aging↗

PubMed1995

A genetical theory of species selection.

Species selection, differential rates of speciation or extinction resulting from species level characters, is often invoked as the main mechanism of macroevolution that is not simply an extension of microevolutionary processes. So long as we are careful in defining "species", the logic of species selection is sound. This does not mean, however, that this process can influence evolutionary dynamics under realistic conditions. The principal challenge to the efficacy of species selection as an evolutionary mechanism is the idea that selection between individuals within species will be so much more efficient as to swamp out any effects of selection between species. To assess this, a genetic model is constructed that includes simultaneous selection within and between species, and this is used to ask: under what conditions could species selection influence evolutionary dynamics, even in the face of opposing selection between individuals? The model shows that the efficacy of species selection is strongly determined by the time between speciation events (measured in individual generations), the mutation rate of the character under consideration, and the initial size of a newly formed reproductively isolated population. Data indicate that a few studied lineages have shown sufficiently high speciation rates to make species selection an important mechanism in the evolution of characters with mutation rates on the order of 10(-6) per generation. Quantitative characters, such as body size, generally change too readily for species selection to be relevant to their evolution. Complex characters, however, may be good candidates to be influenced by species selection. The interaction of selection within and between species can be subtle, with individual selection looking, from the standpoint of a species, very much like development of an individual. Furthermore, selection between individuals may be the main process assembling complex adaptations, while species selection allows them to persist over long periods of time.

Animals↗

PubMed2001

The dynamics of SAP90/PSD-95 recruitment to new synaptic junctions.

SAP90/PSD-95 is thought to be a central organizer of the glutamatergic synapse postsynaptic reception apparatus. To assess its potential role during glutamatergic synapse formation, we used GFP-tagged SAP90/PSD-95, time lapse confocal microscopy, and cultured hippocampal neurons to determine its dynamic recruitment into new synaptic junctions. We report that new SAP90/PSD-95 clusters first appeared at new axodendritic contact sites within 20-60 min of contact establishment. SAP90/PSD-95 clustering was rapid, with kinetics that fit a single exponential with a mean time constant of approximately 23 min. Most new SAP90/PSD-95 clusters were found juxtaposed to functional presynaptic boutons as determined by labeling with FM 4-64. No evidence was found for the existence of discrete transport particles similar to those previously reported to mediate presynaptic active zone cytoskeleton assembly. Instead, we found that SAP90/PSD-95 is recruited to nascent synapses from a diffuse dendritic cytoplasmic pool. Our findings show that SAP90/PSD-95 is recruited to nascent synaptic junctions early during the assembly process and indicate that its assimilation is fundamentally different from that of presynaptic active zone components.

Animals↗

PubMed1994

Isoprenylation of large hepatitis delta antigen is necessary but not sufficient for hepatitis delta virus assembly.

Hepatitis delta virus (HDV) encodes two proteins, the small hepatitis delta antigen (SHDAg) and large hepatitis delta antigen (LHDAg). Both proteins are identical except for the presence of additional 19 amino acids at the C terminus of LHDAg. While SHDAg is required for HDV RNA replication, LHDAg inhibits replication and is required together with hepatitis B surface antigen for the assembly of HDV. The C-terminal last 4 amino acids of LHDAg (Cys-Arg-Pro-Gln) is an isoprenylation motif. It has previously been shown that the mutation of the Cys inhibited the assembly of HDV. In order to discern whether this effect is due to change of amino acid residue or abolition of isoprenylation, we constructed several LHDAg mutants of the terminal three amino acid residues and tested their abilities to be packaged with HBsAg by cotransfection experiments. We also made GST-fusion proteins of these mutants and tested their abilities to be isoprenylated in rabbit reticulocyte lysate system. We found that some, but not all, of the substitutions of the amino acid residues other than the Cys also inhibited isoprenylation and that the status of isoprenylation of these mutant proteins correlated well with their abilities to be packaged with HBsAg into virions. This result indicates that isoprenylation, rather than the primary amino acid sequence, is required for LHDAg packaging. Furthermore, we found that the attachment of an isoprenylation motif to SHDAg did not enable it to be packaged with HBsAg and that the deletions of any 5 amino acids in the last 15 amino acids (amino acids 196 to 210) unique to the LHDAg abolished the packaging ability. In contrast, the deletion of 33 amino acids (amino acids 163 to 195) upstream of the last C-terminal 19 amino acids of LHDAg did not interfere with its packaging ability. Therefore, we conclude that the 15 amino acids upstream of the isoprenylation site of LHDAg are also essential for HDV assembly, and a large portion of the alleged C-terminal Pro/Gly-rich region (amino acids 146 to 195) is not required for the assembly process.

Amino Acid Sequence↗

PubMed1994

Characterization of hepatitis B virus core mutants that inhibit viral replication.

We have generated and functionally characterized dominant negative core protein variants of the hepadnaviruses to determine their effects on "wild type" viral replication. Plasmids expressing these constructs were introduced into hepatoma cell lines by transient transfection and effects on wild type woodchuck hepatitis virus (WHV) and hepatitis B virus (HBV) replication were evaluated by Southern blot analysis of purified viral core particles. WHV and HBV constructs expressing a truncated core protein fused in frame with the C-terminus of the small surface protein were found to inhibit viral replication by 90-95% due to disruption of the viral nucleocapsid assembly process and preventing encapsidation of pregenomic RNA. The antiviral effects were found to be specific for the targeted virus. These results demonstrate that mutants of hepadnaviral core protein may represent a novel class of antiviral agents.

DNA Replication↗