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 1,153 records · Page 64Linked to original sources
PubMed1989

Role of the cell surface-exposed regions of outer membrane protein PhoE of Escherichia coli K12 in the biogenesis of the protein.

To investigate the role of the cell surface-exposed regions of outer membrane protein PhoE of Escherichia coli K12 in the biogenesis of the protein, deletions were generated in two presumed cell surface-exposed regions of the protein. Intact cells expressing these mutant proteins were recognized by PhoE-specific monoclonal antibodies, which recognize conformational epitopes on the cell surface-exposed parts of the protein and/or were sensitive to a PhoE-specific phage. This shows that the polypeptides were normally incorporated into the outer membrane. When the deletions extended four amino acid residues into the seventh presumed membrane-spanning segment, the polypeptides accumulated in the periplasm. In conclusion, exposed regions of PhoE protein apparently do not play an essential role in outer membrane localization, which is consistent with the observation that these regions are hypervariable when PhoE is compared to the related proteins OmpF and OmpC. In contrast, the membrane-spanning segments are essential for the assembly process.

Amino Acid Sequence↗
PubMed1992

Purification of assembly-competent tubulin from Saccharomyces cerevisiae.

We have developed a straightforward, two-step procedure to isolate highly purified yeast tubulin that reproducibly assembles into microtubules. The starting extracts are obtained from cells genetically engineered to overproduce both the alpha and beta subunits of tubulin, under control of the galactose promoter, to approximately 10-times wild-type levels. The first step of purification is carried out with the high-speed supernatant of lysed cells loaded onto a DEAE-Sephadex column; after this step the tubulin preparation is approximately 30% pure. In the second step, the tubulin fractions are loaded onto an immunoaffinity column prepared by coupling the anti-(alpha-tubulin) monoclonal antibody YL 1/2 to Sepharose-4B. Following elution with 0.8 M KCl, the tubulin present in the peak is 90% pure. Upon addition of porcine brain microtubule-associated proteins or DEAE-dextran, this tubulin preparation is functionally active for assembly into microtubules, as visualized by electron microscopy on negatively stained samples. Virtually identical microtubule structures are produced in parallel experiments on the assembly of yeast or porcine brain tubulin, with differences observed only at acidic pH values. Overall, this relatively simple procedure provides a useful tool for the production of functional tubulin suitable both for structural studies and for investigations of the assembly process.

Animals↗
PubMed1997

Cloning of an annelid fibrillar-collagen gene and phylogenetic analysis of vertebrate and invertebrate collagens.

Arenicola marina possesses cuticular and interstitial collagens, which are mostly synthesised by its epidermis. A cDNA library was constructed from the body wall. This annelid cDNA library was screened with a sea-urchin-collagen cDNA probe, and several overlapping clones were isolated. Nucleotide sequencing of these clones revealed an open reading frame of 2052 nucleotides. The translation product exhibits a triple helical domain of 138 Gly-Xaa-Yaa repeats followed by a 269-residue-long C-terminal non-collagenous domain (C-propeptide). The triple helical domain exhibits an imperfection that has been previously described in a peptide produced by cyanogen bromide digestion (CNBr peptide) of A. marina interstitial collagen. This imperfection occurs at the same place in the interstitial collagen of the vestimentiferan Riftia pachyptila. This identifies the clone as coding for the C-terminal part of a fibrillar collagen chain. It was called FAm1alpha, for fibrillar collagen 1alpha chain of A. marina. The non-collagenous domain possesses a structure similar to carboxy-terminal propeptides of fibrillar pro-alpha chains. Only six conserved cysteine residues are observed in A. marina compared with seven or eight in all other known C-propeptides. This provides information on the importance of disulfide bonds in C-propeptide interactions and in the collagen-assembly process. Phylogenetic studies indicate that the fibrillar collagen 1alpha chain of A. marina is homologous to the R. pachyptila interstitial collagen and that the FAm1alpha gene evolved independently from the other alpha-chain genes. Complementary analyses indicate that the vertebrate fibrillar collagen family is composed of two monophyletic subgroups with a specific position of the collagen type-V chains.

Amino Acid Sequence↗
PubMed1993

A tau fragment containing a repetitive sequence induces bundling of actin filaments.

Much indirect evidence suggests that the interconnections of actin microfilaments with the microtubule system are mediated by microtubule-associated proteins (MAPs). In this study we provide new data to support the interaction of a specific tubulin-binding domain on tau with actin in vitro. In actin polymerization assays, the synthetic peptide VRSKIGSTENLKHQPGGG, corresponding to the first repetitive sequence of tau protein, increased turbidity at 320 nm in a dose-dependent fashion. A salient feature of the tau peptide-induced assembly process is the formation of a large amount of actin filament bundles, as revealed by electron microscopic analysis. An increase in the tau peptide concentration resulted in a proportional increase in the bundling of actin filaments. It is interesting that a gradual decrease of pH within the range 7.6-4.7 resulted in a higher effect of tau peptide in promoting bundles of actin filaments. A similar pH-dependent effect was observed for tau protein-induced bundling. An analysis of the mechanisms that operate in the peptide induction of actin filament bundles suggests the involvement of electrostatic forces, because the neutralization of epsilon-aminolysyl residues by selective carbamoylation resulted in a complete loss of the peptide induction of actin bundles. The data suggest that a tau repetitive sequence (also found in MAP-2 and MAP-4) containing a common tubulin binding motif may constitute a functional domain on tau for the dynamics of the interconnections between actin filaments and microtubules.

Actins↗
PubMed1995

Bacteriophage HK97 head assembly.

The head assembly pathway of bacteriophage HK97 shares many features with head assembly pathways determined for other dsDNA phages, and it also provides examples of novel variations on the basic theme. We describe aspects of two specific steps in the assembly pathway, the covalent cross-linking among the assembled head protein subunits and the cleavage of those subunits that takes place earlier in the pathway. Comparisons of head assembly pathways among different phages, as well as comparisons of the organization of the genes that specify those pathways, suggest the range of different solutions phages have found to common assembly problems and give insight into the evolutionary histories of these assembly processes.

Bacteriophages↗
PubMed1998

Varied redox forms of teleost IgM: an alternative to isotypic diversity?

Teleosts (bony fish) are thought to primarily or exclusively possess a single structural form of immunoglobulin (Ig), a tetrameric IgM. However, in species wherein intact Ig has been electrophoretically analyzed under denaturing, non-reducing conditions, a significant degree of structural diversity has been revealed. This IgM molecule appears to be assembled with great latitude in the degree of disulfide crosslinking between monomeric or halfmer subunits composing the complete IgM molecule. This heterogeneity in the basic structure (herein referred to as redox forms) is not due to isotypic differences as each B cell produces this heterogeneity within its immunoglobulin product. Additionally, in the case of the catfish, a single fish/mouse chimeric Ig H gene is capable of producing IgM with a comparable amount of structural heterogeneity within the mouse cell. Thus, the piscine B lymphocyte routinely assembles a variety of redox forms from one IgM chain. This has both profound biosynthetic implications for macromolecular assembly processes as well as intriguing possibilities for the generation of teleost Ig functional diversity.

Animals↗
PubMed2006

On the formation of amelogenin microribbons.

We recently reported the remarkable spontaneous self-assembly and hierarchical organization of amelogenin 'microribbons' and their ability to facilitate oriented growth of apatite crystals in vitro. In a letter of correction we communicated the finding that the X-ray diffraction pattern reported in our original report was that of cellulose contaminant and not amelogenin microribbon. We have re-evaluated our data and confirmed the protein nature of the microribbons using Fourier transform infrared and Raman microspectroscopy. Some microribbons were remarkably similar in their morphology to that of cellulose fibers. The size distribution of amelogenin microribbons was wider, particularly in width and length, and generally smaller than those originally reported. Here we present additional detailed information on the formation of a series of intermediate hierarchical structures of amelogenin assemblies prior to the formation of microribbon. The most significant finding was that full-length amelogenin nanospheres had a tendency to assemble into collinear arrays whose function is assumed to be critical at the initial stage of enamel mineral deposition. The present data gives an insight into the step-by-step assembly process of amelogenin from nanometer scale molecules to micrometer scale organized structures that can be used as templates for controlled and oriented growth of apatite mineralization in vitro.

Amelogenesis↗
PubMed2006

Retrovirus RNA trafficking: from chromatin to invasive genomes.

Full-length retroviral RNA has three well-established functions: it constitutes the genomic RNA that is packaged into virions and is transmitted to target cells by infection, it is the messenger RNA (mRNA) template for viral Gag and Pol protein synthesis and it serves as the pre-mRNA for the production of subgenomic spliced mRNAs that encode additional viral proteins such as Env. More recent work indicates that these full-length RNAs also play important roles in the assembly of virus particles, not only as a structural scaffold that facilitates viral core formation but also as a potential regulator of the assembly process itself. Here, we discuss how these assorted activities may be coupled with each other, paying particular attention to the importance of RNA trafficking and subcellular localization in the cytoplasm, possible points of regulation, and the role(s) played by cellular RNA-binding proteins.

Active Transport, Cell Nucleus↗
PubMed2006

The minimal amyloid-forming fragment of the islet amyloid polypeptide is a glycolipid-binding domain.

Several proteins that interact with cell surface glycolipids share a common fold with a solvent-exposed aromatic residue that stacks onto a sugar ring of the glycolipid (CH-pi stacking interaction). Stacking interactions between aromatic residues (pi-pi stacking) also play a pivotal role in the assembly process, including many cases of amyloid fibril formation. We found a structural similarity between a typical glycolipid-binding domain (the V3 loop of HIV-1 gp120) and the minimal amyloid-forming fragment of the human islet amyloid polypeptide, i.e. the octapeptide core module NFGAILSS. In a monolayer assay at the air-water interface, the NFGAILSS peptide specifically interacted with the glycolipid lactosylceramide. The interaction appears to require an aromatic residue, as NLGAILSS was poorly recognized by lactosylceramide, whereas NYGAILSS behaved like NFGAILSS. In addition, we observed that the full-length human islet amyloid polypeptide (1-37) did interact with a monolayer of lactosylceramide, and that the glycolipid film significantly affected the aggregation process of the peptide. As glycolipid-V3 interactions are efficiently inhibited by suramin, a polyaromatic compound, we investigated the effects of suramin on amyloid formation by human islet amyloid polypeptide. We found that suramin inhibited amyloid fibril formation at low concentrations, but dramatically stimulated the process at high concentrations. Taken together, our results indicate that the minimal amyloid-forming fragment of human islet amyloid polypeptide is a glycolipid-binding domain, and provide further experimental support for the role of aromatic pi-pi and CH-pi stacking interactions in the molecular control of the amyloidogenesis process.

Amyloid↗
PubMed1991

Development of a treatment regimen for human cytomegalovirus (CMV) infection in bone marrow transplantation recipients by adoptive transfer of donor-derived CMV-specific T cell clones expanded in vitro.

CMV infection represents a major cause of morbidity and mortality in immunosuppressed bone marrow transplant (BMT) recipients. Life-threatening CMV infection was found to occur only in patients who did not develop a CMV-specific CD8+ Tc response. Therefore, methods to clone and expand CMV-specific Tc were developed to facilitate analysis of the specificity of the CD8+ Tc response to CMV responsible for protective immunity in seropositive donors, and to permit adoptive transfer of in vitro expanded CMV-specific Tc derived from bone marrow donors into immunocompetent HLA-matched BMT recipients to augment resistance to CMV. The immunodominant class I-restricted Tc response present in healthy seropositive individuals was found to be specific for a conserved CMV antigen introduced into the cytoplasm and presented shortly following viral penetration and uncoating, and did not require endogenous viral gene expression and protein synthesis. Thus, the protective immune response to CMV mediates lysis of virally-infected cells prior to virion assembly. Processing of viral proteins and access to presentation in the context of class I MHC molecules immediately following infection of target cells was selective for internal virion proteins, such as the tegument protein pp65. By contrast, presentation by infected cells of GB, the major CMV envelope protein, or IE, the major regulatory protein, was delayed due to a requirement for endogenous synthesis in infected cells, and CD8+ Tc specific for these proteins were detected in low frequency as compared to the immundominant response.

Antigens, Viral↗
PubMed2001

Molecular mechanisms of hypo- and afibrinogenemia.

Point mutations responsible for hypo- and afibrinogenemia are yielding new insights into amino acid side chains involved in the molecular processing, assembly, secretion, and domain stability of fibrinogen. Reverse phase chromatography, isoelectric focussing, electrospray mass spectrometry, and tryptic peptide mass mapping have shown that chains with heterozygous mutations of gamma 284 Gly-->Arg, B beta 316 Asp-->Tyr and gamma 371 Thr-->Ile are absent from plasma fibrinogen. The nonexpression of these mutations appears to result from perturbation of the five-stranded beta sheet of the D domain. We propose that this is due to retention of the variant in the endoplasmic reticulum and that in turn this leads to hypofibrinogenemia. Other mutations effect intracellular proteolysis and chain assembly. For example the mutation, A alpha 20 Val-->Asp, makes the protein a substrate for furin, which removes the first 19 residues of the A alpha chain as the mature molecule transits the trans golgi complex. Transient expression of gamma 153 Cys-->Arg chains together with A alpha and B beta chains suggests this mutation might perturb chain assembly, and the incorporation of mutations of B beta 353 Leu-->Arg or B beta 400 Gly-->Asp into intracellular fibrinogen precludes its subsequent export from host cells expressing fibrinogen genes. The graded severity of the hypo- and afibrinogenemias associated with homozygous A alpha chain truncations suggest the absolute minimal requirement for molecular assembly is the formation of the C terminal disulfide ring of the coiled coil.

Afibrinogenemia↗
PubMed1998

Mouse models of myelin diseases.

Dys- and demyelination are the common endpoints of several inherited diseases of glial cells, which elaborate myelin and which maintain the myelin sheath very much like an "external" cellular organelle. Whereas some of the genes that are affected by mutations appear to be glial-specific, other genes are expressed in many cell types but their defect is restricted to oligodendrocytes or Schwann cells. Many of the disease genes and their encoded proteins have been studied with the help of mouse models, and a number of different molecular pathomechanisms have emerged which have been summarized in Figure 8. Some of the new concepts in the field, which have been addressed in this review, have only emerged because similar pathomechanisms were discovered for different myelin proteins. Mouse models have clearly helped to address both, the molecular pathology of myelin diseases and the normal function of myelin genes, but as discussed in this review, these questions turned out to be very different. Despite the progress in understanding the role of the abundant myelin proteins, there also remain a number of open questions that concern, among other things, the initial axon-glia recognition, the assembly process of the myelin sheath, and the long-term interaction of axons with their myelinating glia. Finally, animal models of human neurological diseases should not be restricted to the study of pathology, but they should also contribute to the development of experimental treatments. It is encouraging that a few attempts have been made.

Animals↗
PubMed2001

Dielectrophoretic assembly of electrically functional microwires from nanoparticle suspensions.

A new class of microwires can be assembled by dielectrophoresis from suspensions of metallic nanoparticles. The wires are formed in the gaps between planar electrodes and can grow faster than 50 micrometers per second to lengths exceeding 5 millimeters. They have good ohmic conductance and automatically form electrical connections to conductive islands or particles. The thickness and the fractal dimension of the wires can be controlled, and composite wires with a metallic core surrounded by a latex shell can be assembled. The simple assembly process and their high surface-to-volume ratio make these structures promising for wet electronic and bioelectronic circuits.

Journal Article↗
PubMed2002

Surface stress and thermodynamic nanoscale size selection.

Using the Si(111) surface as an example, we show how temperature can be used to tune the size of domains during a surface phase transition. From analysis of the measured stable domain sizes, we determine key material parameters and clarify the close relationship between nucleation and thermodynamic size selection. More generally, the model we developed describes nanoscale self-assembly processes in contact with a reservoir (for example, liquid- or vapor-phase epitaxy).

Journal Article↗
PubMed2003

Heterochromatin and epigenetic control of gene expression.

Eukaryotic DNA is organized into structurally distinct domains that regulate gene expression and chromosome behavior. Epigenetically heritable domains of heterochromatin control the structure and expression of large chromosome domains and are required for proper chromosome segregation. Recent studies have identified many of the enzymes and structural proteins that work together to assemble heterochromatin. The assembly process appears to occur in a stepwise manner involving sequential rounds of histone modification by silencing complexes that spread along the chromatin fiber by self-oligomerization, as well as by association with specifically modified histone amino-terminal tails. Finally, an unexpected role for noncoding RNAs and RNA interference in the formation of epigenetic chromatin domains has been uncovered.

Animals↗
PubMed2004

Molecular borromean rings.

The realization of the Borromean link in a wholly synthetic molecular form is reported. The self-assembly of this link, which is topologically achiral, from 18 components by the template-directed formation of 12 imine and 30 dative bonds, associated with the coordination of three interlocked macrocycles, each tetranucleating and decadentate overall, to a total of six zinc(II) ions, is near quantitative. Three macrocycles present diagonally in pairs, six exo-bidentate bipyridyl and six endo-diiminopyridyl ligands to the six zinc(II) ions. The use, in concert, of coordination, supramolecular, and dynamic covalent chemistry allowed the highly efficient construction, by multiple cooperative self-assembly processes, of a nanoscale dodecacation with an approximate diameter of 2.5 nanometers and an inner chamber of volume 250 A(3), lined with 12 oxygen atoms.

Journal Article↗
PubMed2004

Building programmable jigsaw puzzles with RNA.

One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules.

Algorithms↗
PubMed2006

Structural basis for ribosome recruitment and manipulation by a viral IRES RNA.

Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domain from a Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing a view of the prefolded architecture of an all-RNA translation initiation apparatus. Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA.

Binding Sites↗