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Query: UMLS:C0344329 (collapse)
 28,634 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

High-molecular-weight DNA is known to collapse into very compact particles in a salt solution containing polymers like poly(ethylene oxide) [(EO)n] or polyacrylate. The biological relevance of this phenomenon is suggested by our recent finding that high concentrations of the highly acidic internal peptides found in the mature T4 bacteriophage head, as well as poly(glutamic acid) and poly(aspartic acid), can collapse DNA in a similar manner. The structure of DNAs collapsed by various methods has been studied with electron microscope. We find (EO)n collapses T4 or T7 bacteriophage DNA into compact particles only slightly larger than the size of the T4 and T7 head, respectively. In contrast, polylysine collapses DNA into different types of structures. Double-stranded DNA collapsed with (EO)n is cut by the single-strand specific Neurospora crassa endonuclease (EC 3.1.4.21) into small fragments. Extensive digestion only occurs above the critical concentration of polymer required for DNA collapse, demonstrating the (EO)n-collapsed DNA contains enzyme-vulnerable regions (probably at each fold), which are preferentially attacked. The size of the DNA fragments produced by limit-digestion with the nuclease ranges between 200 and 400 base pairs when DNA is collapsed by (EO)n. Only fragments of DNA which are larger than 600 base pairs are cut by the endonuclease in (EO)n-containing solution.
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PMID:Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine. 106 Jan 8

Receptor binding and biological activity properties of human interleukin-1 beta can be dissociated by mutating a single amino acid, arginine 127, to glycine (IL-1 beta R----G) [Gehrke et al. (1990) J. Biol. Chem. 265, 5922-5925]. The mechanism underlying the reduced biological activity has been examined by replacing arginine 127 with several other amino acids, followed by determination of biological activity using a T-helper cell proliferation assay. Mutant IL-1 beta proteins containing lysine, glutamic acid, tryptophan, or alanine in place of arginine 127 maintain biological activity. These data strongly suggest that IL-1 beta biological activity is not directly dependent upon the specific properties of charge, hydrophobicity/hydrophilicity, or side-chain group presented by the residue at position 127. Molecular modeling analyses indicate that the structural integrity of the antiparallel beta-strand 1/12 pair is disturbed in the glycine 127 mutant protein. Collapse of beta-strand 1 into a hydrated space between strands 1, 2, and 4 could structurally alter a cleft in IL-1 beta that contains a cluster of highly conserved amino acids, including a key aspartic acid residue [Ju et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2658-2662]. Mutagenesis data and the differential activities of the IL-1 beta R----G and IL-1 receptor antagonist proteins in stimulating early and late gene expression [Conca et al. (1991) J. Biol. Chem. 266, 16265-16268] suggest that multiple receptor-ligand contacts, exclusive of those required for receptor binding, are required for the stimulation of full IL-1 biological activity.
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PMID:Multiple amino acid substitutions suggest a structural basis for the separation of biological activity and receptor binding in a mutant interleukin-1 beta protein. 138 53

Nephrocalcin is a urinary glycopeptide that may be a physiological inhibitor of nephrolithiasis. Monomeric nephrocalcin purified from ethylenediaminetetracetic acid-treated urine is 14,000 daltons. Compositional analyses indicate that nephrocalcin is 10 per cent carbohydrate by weight and that 25 per cent of the amino acid residues are acidic (glutamic acid, aspartic acid and gamma-carboxyglutamic acid). Nephrocalcin binds reversibly to calcium oxalate crystals with a dissociation constant of about 0.5 microM. The high collapse pressure of nephrocalcin, 41.5 dynes per cm., measured for a monolayer at the air-water interface, suggests a highly organized structure in which hydrophilic and hydrophobic regions occupy separate regions on the surface of the inhibitor. Nephrocalcin contains the unusual amino acid, gamma-carboxyglutamic acid. Nephrocalcin isolated from urine of stone formers and from kidney stones does not contain gamma-carboxyglutamic acid and it has altered surface properties compared to normal nephrocalcin. The presence of the gamma-carboxyglutamic acid modification and the ability to form stable films with high collapse pressures may be important factors enabling nephrocalcin to prevent stone formation in vivo. The blood of cold water fishes contains antifreeze glycopeptides and/or peptides to prevent it from freezing. The structure of one such antifreeze peptide and its interactions with the crystal lattice of hexagonal ice are discussed as a model for how nephrocalcin might interact with calcium oxalate crystals and arrest their growth in urine.
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PMID:Protein inhibitors of crystal growth. 264 34

Studies are made of the pH-induced intramolecular structuring of such random copolymers as glutamic acid with leucine. It is shown that these copolymers, consisting of hydrophobic and hydrophilic residues, contain large amounts of fractions capable of acquiring non-aggregating compact structures in aqueous medium. These fractions have an approximately similar amino acid composition which does not almost depend on the composition of the initial copolymers. A decrease in the degree of ionization of side groups of glutamic acid promotes a formation of helical regions in the molecules of these fractions. At a further deionization, the helical regions collapse into compact structures stabilized by hydrophobic interactions of side groups of leucine. The compactness of the obtained structures is close to that of protein globules.
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PMID:[Compact structure of random copolymers of hydrophobic and hydrophilic amino acid residues]. 738 26

Poly-glutamic acid, a polyanion, has been shown to induce the all-or-none collapse transition in individual duplex DNAs from an elongated coil into a collapsed compact state, through the observation of single chains by fluorescence microscopy. This experimental finding is discussed in relation to the change in the higher-order structure of DNAs in the cytoplasmic space induced by a change in the concentration of polyanions, such as mRNA, as a possible route for feedback in gene expression.
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PMID:Single chain observation on collapse transition in giant DNA induced by negatively-charged polymer. 944 14

Prothymosin alpha has previously been shown to be unfolded at neutral pH, thus belonging to a growing family of "natively unfolded" proteins. The structural properties and conformational stability of recombinant human prothymosin alpha were characterized at neutral and acidic pH by gel filtration, SAXS, circular dichroism, ANS fluorescence, (1)H NMR, and resistance to urea-induced unfolding. Interestingly, prothymosin alpha underwent a cooperative transition from the unfolded state into a partially folded conformation on lowering the pH. This conformation of prothymosin alpha is a compact denatured state, with structural properties different from those of the molten globule. The formation of alpha-helical structure by the glutamic acid-rich elements of the protein accompanied by the partial hydrophobic collapse is expected at lower pH due to the neutralization of the negatively charged residues. It is possible that such conformational changes may be associated with the protein function.
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PMID:Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH. 1055 83

Elastin undergoes an inverse temperature transition and collapses at high temperatures in both simulation and experiment. We investigated a pH-dependent modification of this transition by simulating a glutamic acid (Glu)-substituted elastin at varying pHs and temperatures. The Glu-substituted peptide collapsed at higher temperature than the unsubstituted elastin when Glu was charged. The charge effects could be reversed by neutralization of the Glu carboxyl groups at low pH, and in that case the peptide collapsed at a lower temperature. The collapse was accompanied by the formation of beta-turns and short distorted beta-sheets. Formation of contacts between hydrophobic side chains drives the collapse at high temperature, but interactions between water and polar groups (Glu and main chain) can attenuate this effect at high pH. The overall competition and balance of the polar and nonpolar groups determined the conformational states of the peptide. Water hydration contributed to the conformational transition, and the peptide and its hydration shell must be considered. Structurally, waters near polar residues mainly formed hydrogen bonds with the protein atoms, while waters around the hydrophobic side chains tended to be parallel to the peptide groups to maximize water-water interactions.
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PMID:The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides. 1257 84

Specific allergy vaccination is an efficient treatment for allergic disease; however, the development of safer vaccines would enable a more general use of the treatment. Determination of molecular structures of allergens and allergen-Ab complexes facilitates epitope mapping and enables a rational approach to the engineering of allergen molecules with reduced IgE binding. In this study, we describe the identification and modification of a human IgE-binding epitope based on the crystal structure of Bet v 1 in complex with the BV16 Fab' fragment. The epitope occupies approximately 10% of the molecular surface area of Bet v 1 and is clearly conformational. A synthetic peptide representing a sequential motif in the epitope (11 of 16 residues) did not inhibit the binding of mAb BV16 to Bet v 1, illustrating limitations in the use of peptides for B cell epitope characterization. The single amino acid substitution, Glu(45)-Ser, was introduced in the epitope and completely abolished the binding of mAb BV16 to the Bet v 1 mutant within a concentration range 1000-fold higher than wild type. The mutant also showed up to 50% reduction in the binding of human polyclonal IgE, demonstrating that glutamic acid 45 is a critical amino acid also in a major human IgE-binding epitope. By solving the three-dimensional crystal structure of the Bet v 1 Glu(45)-Ser mutant, it was shown that the change in immunochemical activity is directly related to the Glu(45)-Ser substitution and not to long-range structural alterations or collapse of the Bet v 1 mutant tertiary structure.
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PMID:Dominating IgE-binding epitope of Bet v 1, the major allergen of birch pollen, characterized by X-ray crystallography and site-directed mutagenesis. 1296 Mar 34

The stability and properties of dilute solution hydrogels, synthesized by transition metal mediated polymerization of amino acid N-carboxyanhydrides (NCAs), have been studied in deionized (DI) water as well as various ionic media. These hydrogels are diblock amphiphilic copolymers of hydrophilic, charged segments of poly(l-lysine HBr) or poly(l-glutamic acid sodium salt), and helical, hydrophobic segments of poly(l-leucine). While many of these samples are able to form strong gels in deionized water at polymer concentrations as low as 0.25 wt %, stability in salt or buffer solutions was found to be only achieved at moderately higher polymer concentrations ( approximately 3.0 wt %). We have adjusted relative copolymer compositions and molecular weights to optimize hydrogel strength and polymer solubility in salt concentrations up to 0.5 M NaCl, as well as in cell growth media and aqueous buffers of varying pH. These materials are unique since they do not collapse in high ionic strength media, even though gel formation is contingent upon the presence of highly charged polyelectrolyte segments. The remarkable properties of these hydrogels make them excellent candidates for use as scaffolds in biomedical applications, such as tissue regeneration.
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PMID:Unusual salt stability in highly charged diblock co-polypeptide hydrogels. 1466 16

Fungicidic Bacillus amyloliquefaciens strains isolated from the indoor environment of moisture-damaged buildings contained heat-stable, methanol-soluble substances that inhibited motility of boar spermatozoa within 15 min of exposure and killed feline lung cells in high dilution in 1 day. Boar sperm cells lost motility, cellular ATP, and NADH upon contact to the bacterial extract (0.2 microg dry wt/ml). Two bioactive substances were purified from biomass of the fungicidal isolates. One partially characterized substance, 1,197 Da, was moderately hydrophobic and contained leucine, proline, serine, aspartic acid, glutamic acid and tyrosine, in addition to chromophore(s) absorbing at 365 nm. In boar sperm and human neural cells (Paju), the compound depolarized the transmembrane potentials of mitochondria (Delta Psi(m)) and the plasma membrane (Delta Psi(p)) after a 20-min exposure and formed cation-selective channels in lipid membranes, with a selectivity K(+):Na(+):Ca(2+) of 26:15:3.5. The other substance was identified as a plasma-membrane-damaging lipopeptide surfactin. Plate-grown biomass of indoor Bacillus amyloliquefaciens contained ca. 7% of dry weight of the two substances, 1,197 Da and surfactin, in a ratio of 1:6 (w:w). The in vitro observed simultaneous collapse of both cytosolic and mitochondrial ATP in the affected mammalian cell, induced by the 1,197-Da cation channel, suggests potential health risks for occupants of buildings contaminated with such toxins.
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PMID:Bacillus amyloliquefaciens strains isolated from moisture-damaged buildings produced surfactin and a substance toxic to mammalian cells. 1501 30


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