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 847 records · Page 47Linked to original sources

Partial biomimetic reconstitution of avian eggshell formation.

The avian eggshell is a biocomposite ceramic consisting of minute amounts of organic matrix and a crystalline calcium carbonate (calcite) filler. It is formed by a well regulated spatio-temporal assembling process, where extracellular matrix proteins, especially the sulfated glycosaminoglycan anionic sites of specific proteoglycans, have been involved in nucleation and growth of the inorganic crystalline phase. Together with such extracellular matrix molecules, the activity of carbonic anhydrase, is crucial for the normal eggshell formation. Here, we studied the effect of dermatan sulfate and carbonic anhydrase on the in vitro calcification of non-mineralized eggshell membrane-mammillae substrate at different pH and incubation times. Crystal morphology was analyzed by scanning electron microscopy. Crystal nucleation and growth was delayed at lower pH. Dermatan sulfate modified crystal morphology producing aggregates of large calcite crystals exhibiting a columnar morphology, contributing to the eggshell texture development. Carbonic anhydrase increased the velocity of crystal growth and eventually contributed to the fusion of the crystal aggregates to each other. Although, the effect of other macromolecules could not be ruled out, the combinatory effect of proteoglycans and carbonic anhydrase seems to be important for the control of eggshell formation.

Animals↗

Reassessment of effects on lignification and vascular development in the irx4 Arabidopsis mutant.

The Arabidopsis thaliana irregular xylem4 (irx4) cinnamoyl-CoA reductase 1 (CCR1) mutant was reassessed for its purported exclusive rate-limiting or key effects on lignification. Analyses of gross growth characteristics and stem cross-section anatomy, from seedling emergence to senescence, revealed that stunted irx4 mutant lines were developmentally delayed, which in turn indirectly but predictably led to modest reductions (ca. 10-15%) in overall lignin amounts. Such developmental changes are not generally observed in suppression of other monolignol pathway forming enzymes (e.g., 4-coumarate CoA ligase) even when accompanied by significant reductions in lignin amounts. With the greatly arrested development of the irx4 mutant, formation of the lignin-derived syringyl moieties was also predictably delayed (by about 1-2 weeks), although at maturation the final guaiacyl:syringyl ratios were essentially identical to wild-type. No evidence was obtained for so-called abnormal lignin precursors being incorporated into the lignin, as shown by solid-state 13C NMR spectroscopic analysis in contrast to a claim to the contrary [Jones, L., Ennos, A.R., Turner, S.R., 2001. Cloning and characterization of irregular xylem4 (irx4): a severely lignin-deficient mutant of Arabidopsis. Plant J. 26, 205-216]. A previous claim of an "abnormal" lignin present in stunted CCR downregulated tobacco was also not substantiated, with only trace differences being noted in the presumed cell-wall constituent levels. More importantly, a linear correlation between total lignin amounts and lignin-derived fragmentation products was observed at all stages of Arabidopsis growth/development in both wild-type and irx4 mutant lines, regardless of lignin content, i.e., in harmony with an exquisitely controlled and predictable macromolecular assembly process. Recombinant CCR1 displayed fairly broad substrate versatility for all phenylpropanoid CoA substrates, with both feruloyl and 5-hydroxyferuloyl CoA being the best substrates. Taken together, these data indicate that other CCR isoforms are apparently capable of generating monolignol-derived lignified elements in irx4 when CCR1 is impaired, i.e., indicative of a functionally redundant CCR metabolic network operative in Arabidopsis. Other dwarfed phenotypes have also been observed following downregulation/disruption of unrelated metabolic processes but which also involve CoA ester metabolism, i.e., with hydroxymethylglutaryl CoA reductases in Arabidopsis and a bacterial enoyl CoA hydratase/lyase overexpressed in tobacco. Although the reasons for dwarfing in each case are unknown, a common mechanism for the various pleiotropic effects is proposed through perturbation of CoASH pool levels. Finally, this study demonstrates the need for progressive analyses over the lifespan of an organism, rather than at a single time point which cannot reveal the progressive developmental changes occurring.

Aldehyde Oxidoreductases↗

Phospholipid molecular species profiles of tectiviruses infecting Gram-negative and Gram-positive hosts.

The phospholipid (PL) molecular species compositions of bacteriophages PRD1 and Bam35 as well as their respective hosts were determined quantitatively using liquid chromatography/electrospray ionization mass-spectrometry (LC-ESI-MS) and backed up by gas-chromatographic/mass-spectrometric (GC-MS) analysis of the total fatty acids (FAs). The results showed that both viruses contain significantly more phosphatidylglycerol (PG) and less phosphatidylethanolamine (PE) than the host membranes. Only modest differences in the molecular species composition of the viruses and their respective hosts were observed, indicating that the virus assembly process is relatively nonselective in respect of the fatty acid (FA) proportion of phospholipids (PL). These data indicate that the PL composition of these two viruses is largely, albeit not exclusively, determined by the availability of phospholipids in the host membrane.

Bacillus Phages↗

Steps of the tick-borne encephalitis virus replication cycle that affect neuropathogenesis.

Tick-borne encephalitis virus (TBEV) is an important human pathogen that causes severe neurological illness in large areas of Europe and Asia. The neuropathogenesis of this disease agent is determined by its capacity to enter the central nervous system (CNS) after peripheral inoculation ("neuroinvasiveness") and its ability to replicate and cause damage within the CNS ("neurovirulence"). TBEV is a small, enveloped flavivirus with an unsegmented, positive-stranded RNA genome. Mutations affecting various steps of its natural replication cycle were shown to influence its neuropathogenic properties. This review describes experimental approaches and summarizes results on molecular determinants of neurovirulence and neuroinvasiveness that have been identified for this virus. It focuses on molecular mechanisms of three particular steps of the viral life cycle that have been studied in some detail for TBEV and two closely related tick-borne flaviviruses (Louping ill virus (LIV) and Langat virus (LGTV)), namely (i) the envelope protein E and its role in viral attachment to the cell surface, (ii) the 3'-noncoding region of the genome and its importance for viral RNA replication, and (iii) the capsid protein C and its role in the assembly process of infectious virus particles. Mutations affecting each of these three molecular targets significantly influence neuropathogenesis of TBEV, particularly its neuroinvasiveness. The understanding of molecular determinants of TBEV neuropathogenesis is relevant for vaccine development, also against other flaviviruses.

Animals↗

The differential adhesion hypothesis: a direct evaluation.

The differential adhesion hypothesis (DAH), advanced in the 1960s, proposed that the liquid-like tissue-spreading and cell segregation phenomena of development arise from tissue surface tensions that in turn arise from differences in intercellular adhesiveness. Our earlier measurements of liquid-like cell aggregate surface tensions have shown that, without exception, a cell aggregate of lower surface tension tends to envelop one of higher surface tension to which it adheres. We here measure the surface tensions of L cell aggregates transfected to express N-, P- or E-cadherin in varied, measured amounts. We report that in these aggregates, in which cadherins are essentially the only cell-cell adhesion molecules, the aggregate surface tensions are a direct, linear function of cadherin expression level. Taken together with our earlier results, the conclusion follows that the liquid-like morphogenetic cell and tissue rearrangements of cell sorting, tissue spreading and segregation represent self-assembly processes guided by the diminution of adhesive-free energy as cells tend to maximize their mutual binding. This conclusion relates to the physics governing these morphogenetic phenomena and applies independently of issues such as the specificities of intercellular adhesives.

Animals↗

Xenopus fibrillin regulates directed convergence and extension.

Fibrillin-based human diseases such as Marfan syndrome and congenital contractural arachnodactyly implicate fibrillins in the function and homeostasis of multiple adult tissues. Fibrillins are also expressed in embryos, but no early developmental role has been described for these proteins. We use three independent methods to reveal a role for Xenopus fibrillin (XF) at gastrulation. First, expressing truncated forms of XF in the embryo leads to failure of gastrulation concomitant with a dominant-negative effect on native fibrillin fibril assembly. Expressing truncated XF also inhibits normal progression of the patterned, polarized cell motility that drives convergence and extension at gastrulation and perturbs directed extension in cultured explants of dorsal mesoderm. Second, injection of a synthetic peptide encoding a cell-binding domain of XF into midgastrula embryos causes acute failure of gastrulation associated with defective fibrillin fibril assembly. These injections also reveal a critical role for this peptide in the fibril assembly process. Third, morpholino-mediated knockdown of translation of XF in the embryo also perturbs normal gastrulation and directed extension. Together, these data show that native Xenopus fibrillin is essential for the process of directed convergent extension in presumptive notochord at gastrulation.

Amino Acid Sequence↗

Principles in the assembly of annelid erythrocruorins.

Erythrocruorins are giant extracellular respiratory proteins found freely dissolved in the blood of annelids. We present here results from our ultracentrifugation, electron microscopy, spectroscopy, and diffraction experiments on these erythrocruorins. These data are rationalized in terms of a three-dimensional model of the quaternary structure. The proposed structure is arranged in a hierarchy of symmetry. The implications of this structure for the assembly process are considered with special attention to uniqueness and self-limitation. The hypothesis is consistent with observations not used in its construction and it serves as a working hypothesis to focus further experimentation.

Animals↗

fc177, a minor dec-1 proprotein, is necessary to prevent ectopic aggregation of the endochorion during eggshell assembly in Drosophila.

The Drosophila eggshell is a highly specialized extracellular matrix that forms between the oocyte and the surrounding epithelial follicle cells during late oogenesis. The dec-1 gene, which is required for proper eggshell assembly, produces three proproteins that are cleaved within the vitelline membrane layer to multiple derivatives. The different spatial distributions of the cleaved derivatives suggest that they play distinct roles in eggshell assembly. Using extant dec-1 mutations in conjunction with genetically engineered dec-1 transgenes, we show that, although all three dec-1 proproteins, fc106, fc125, and fc177, are required for female fertility, gross morphological abnormalities in the eggshell are observed only in the absence of fc177. The coalescence of the roof, pillar, and floor substructures of the tripartite endochorion suggested that quantitatively minor fc177 derivatives are necessary to prevent ectopic aggregation of endochorion proteins during the assembly process. Expression of a fc177 cDNA in dec-1 null mutants was sufficient to restore spaces within the endochorion layer. Fc177 may function as a scaffolding protein akin to those utilized in viral morphogenesis.

Animals↗

Interaction of the disordered terminal regions of flagellin upon flagellar filament formation.

Helical filaments of bacterial flagella are built up by a self-assembly process from thousands of flagellin subunits. To clarify how the disordered terminal regions of flagellin interact upon filament formation, polymerization ability of various terminally truncated fragments was investigated. Fragments deprived of 19 N-terminal residues were able to bind to the end of filaments, however, only a single layer was formed. Removal of C-terminal segments or truncation at both ends resulted in the complete loss of binding ability. Our observations are consistent with the coiled-coil model of filament formation, which suggests that the alpha-helical N- and C-terminal regions of axially adjacent subunits form an interlocking pattern of helical bundles upon polymerization.

Bacterial Proteins↗

Ebola virus matrix protein VP40 interaction with human cellular factors Tsg101 and Nedd4.

The Ebola virus matrix protein VP40 is a major viral structural protein and plays a central role in virus assembly and budding at the plasma membrane of infected cells. For efficient budding, a full amino terminus of VP40 is required, which includes a PPXY and a PT/SAP motif, both of which have been proposed to interact with cellular proteins. Here, we report that Ebola VP40 can interact with cellular factors human Nedd4 and Tsg101 in vitro. We show that WW domain 3 of human Nedd4 is necessary and sufficient for binding to the PPXY motif of VP40, which requires an oligomeric conformation of VP40. Single particle electron microscopy reconstructions indicate that WW3 of Nedd4 is in close contact with the N-terminal domain of hexameric VP40. In contrast, the ubiquitin enzyme variant domain of Tsg101 was sufficient for binding to the PT/SAP motif of VP40, regardless of the oligomeric state of the matrix protein. These results suggest that hNedd4 and Tsg101 may play complimentary roles at a late stage of the assembly process, by recruiting cellular factors of two independent pathways to the site of budding at the plasma membrane.

Amino Acid Motifs↗

Clathrin lattice reorganization: theoretical considerations.

We wish to postulate a mechanism by which flat hexagonal lattices of clathrin trimers transform into coated pits. Using an established model for packing trimers into lattices, we explored the assembly process by single addition of trimers to form polygons. Subject to favorable conditions, removal of a single trimer from a hexagon could lead to the formation of a pentagon. Elimination of trimers from polygonal sheets can occur either at the center of the network or at the edges. Removal of a trimer from the center of these adjacent polygons, "hub transformation," is possible in very few instances, whereas removal from the edges of a polygonal sheet, "fringe transformation," is possible in a host of cases. These hypothetical constructs can be used effectively to explain intermediate structures actually observed in flat hexagonal lattices. The geometry of a purely hexagonal lattice seems to dictate that the first step in transformation must be a "fringe transformation," which then will allow subsequent "hub transformation" to take place leading to the introduction of pentagons into the center of the lattice and ultimately to the curvature of the clathrin lattice.

Biopolymers↗

The poly(phenolic) domain of potato suberin: a non-lignin cell wall bio-polymer.

Suberized plant cell walls have three distinguishing features: (1) tissue specificity, (2) a poly(aliphatic) domain and (3) a unique, "lignin-like" poly(phenolic) domain. With respect to the latter, comparisons have often been made to lignin, but the unique phenolic composition of suberized cells yields a unique polymer better designated as a poly(phenolic) domain. Potato tubers that have been induced to suberize through wounding make an excellent model system with which the chemistry, biochemistry and macromolecular assembly of the suberin poly(phenolic) domain can be monitored. For example, wound healing potato tubers have been used to determine the unique hydroxycinnamic acid nature of its poly(phenolic) domain using specific carbon-13 labeling studies and specific chemical degradation techniques (e.g. thioacidolysis). Furthermore, a suberization-associated anionic peroxidase has been purified from suberizing potato tubers and subsequently shown to oxidize hydroxycinnamic acids (and their derivatives) in preference to monolignols, as well as yield an unique polymer in vitro. We have since extended these studies to begin analyzing the macromolecular assembly process leading to the deposition of this suberized tissue specific domain. To this end we have begun to describe an H(2)O(2)-generating system with NAD(P)H-dependent oxidase-like properties that is temporally associated with the formation of potato suberin poly(phenolics) during suberization. Herein we describe our progress to date.

Biopolymers↗

Oligomerization and polymerization of the filovirus matrix protein VP40.

The matrix protein VP40 from Ebola virus plays an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. Here we show that the N-terminal domain of VP40 folds into a mixture of two different oligomeric states in vitro, namely hexameric and octameric ringlike structures, as detected by gel filtration chromatography, chemical cross-linking, and electron microscopy. Octamer formation depends largely on the interaction with nucleic acids, which in turn confers in vitro SDS resistance. Refolding experiments with a nucleic acid free N-terminal domain preparation reveal a mostly dimeric form of VP40, which is transformed into an SDS resistant octamer upon incubation with E. coli nucleic acids. In addition, we demonstrate that the N-terminal domain of Marburg virus VP40 also folds into ringlike structures, similar to Ebola virus VP40. Interestingly, Marburg virus VP40 rings reveal a high tendency to polymerize into rods composed of stacked rings. These results may suggest distinct roles for different oligomeric forms of VP40 in the filovirus life cycle.

Ebolavirus↗

Supramolecular architectures for the functionalization of solid surfaces.

Surface plasmon optical techniques are described as sensitive tools that allow for the on-line characterization of supramolecular biofunctional architectures at solid/solution interfaces. After a short introduction into the fundamentals of surface plasmon optics the observation of the build up of a functional bio-interface by the self-assembly process of long chain thiolates at an Au surface is described. Criteria are developed for tailoring the SAM architectures optimized for maximum protein binding from solution by specific bio-recognition reactions. SPM is employed to image the selective binding of streptavidin to a functionalized SAM laterally patterned by UV-photolithographic techniques.

Bacterial Proteins↗

Molecular fragment replacement approach to protein structure determination by chemical shift and dipolar homology database mining.

A novel approach is described for determining backbone structures of proteins that is based on finding fragments in the protein data bank (PDB). For each fragment in the target protein, usually chosen to be 7-10 residues in length, PDB fragments are selected that best fit to experimentally determined one-bond heteronuclear dipolar couplings and that show agreement between chemical shifts predicted for the PDB fragment and experimental values for the target fragment. These fragments are subsequently refined by simulated annealing to improve agreement with the experimental data. If the lowest-energy refined fragments form a unique structural cluster, this structure is accepted and side chains are added on the basis of a conformational database potential. The sequential backbone assembly process extends the chain by translating an accepted fragment onto it. For several small proteins, with extensive sets of dipolar couplings measured in two alignment media, a unique final structure is obtained that agrees well with structures previously solved by conventional methods. With less dipolar input data, large, oriented fragments of each protein are obtained, but their relative positioning requires either a small set of translationally restraining nuclear Overhauser enhancements (NOEs) or a protocol that optimizes burial of hydrophobic groups and pairing of beta-strands.

Computer Simulation↗

Conformation-dependent anti-amyloid oligomer antibodies.

Although abundant evidence suggests that amyloid accumulation plays a significant role in the pathogenesis of degenerative disease, the mechanism of amyloid formation and toxicity remains elusive. Early hypotheses for disease pathogenesis proposed that large amyloid deposits, which are composed primarily of 6-10-nm mature amyloid fibrils, were the primary causative agent in pathogenesis, but this hypothesis required modification to consider the central role of oligomers or aggregation intermediates, because the accumulation of these large aggregates does not correlate well with pathogenesis. Recent evidence supports the hypothesis that small soluble aggregates representing intermediates in the fibril assembly process may represent the primary culprits in a variety of amyloid-related degenerative diseases. Investigating the role of soluble amyloid oligomers in pathogenesis presents a problem for distinguishing these aggregates from the mature fibrils, soluble monomer, and natively folded precursor proteins, especially in vivo and in complex mixtures. Recently, we generated a conformation-specific antibody that recognizes soluble oligomers from many types of amyloid proteins, regardless of sequence. These results indicate that soluble oligomers have a common, generic structure that is distinct from both fibrils and low-molecular-weight soluble monomer/dimer. Conformation-dependent, oligomer-specific antibodies represent powerful tools for understanding the role of oligomers in pathogenesis. The purpose of this chapter is to review the methods for the production, characterization, and application of this antibody to understanding the contribution of amyloid oligomers to the disease process.

Amino Acid Sequence↗

Membrane domains in the secretory and endocytic pathways.

Progress in identifying, characterizing, and localizing the constituents of distinct membrane bound compartments has revealed a new level of intracellular subcompartmentation. Proteins and lipids are not uniformly distributed in a given organelle, and subdomains are formed by a combination of hierarchical assembly processes and protein exclusion. Thus, functionally distinct specializations of a given organelle are physically segregated to a greater extent than previously believed.

Animals↗

Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation.

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

Antigens, Bacterial↗