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PubMed2004

Mercury(II) binding to metallothioneins. Variables governing the formation and structural features of the mammalian Hg-MT species.

With the aim of extending our knowledge on the reaction pathways of Zn-metallothionein (MT) and apo-MT species in the presence of Hg(II), we monitored the titration of Zn7-MT, Zn4-alphaMT and Zn3-betaMT proteins, at pH 7 and 3, with either HgCl2 or Hg(ClO4)2 by CD and UV-vis spectroscopy. Detailed analysis of the optical data revealed that standard variables, such as the pH of the solution, the binding ability of the counter-ion (chloride or perchlorate), and the time elapsed between subsequent additions of Hg(II) to the protein, play a determinant role in the stoichiometry, stereochemistry and degree of folding of the Hg-MT species. Despite the fact that the effect of these variables is unquestionable, it is difficult to generalize. Overall, it can be concluded that the reaction conditions [pH, time elapsed between subsequent additions of Hg(II) to the protein] affect the structural properties more substantially than the stoichiometry of the Hg-MT species, and that the role of the counter-ion becomes particularly apparent on the structure of overloaded Hg-MT.

Animals↗
PubMed2001

Isolation, purification and some structural features of the mucilaginous exudate from Musa paradisiaca.

The water-soluble polysaccharides isolated from the vascular gel of Musa paradisiaca, were fractionated via anion exchange chromatography into four fractions. Fractionated polymers contained arabinose, xylose and galacturonic acid as major sugars, together with traces of galactose, rhamnose, mannose and glucose residues. Methylation analysis revealed the presence of a highly branched arabinoxylan with a significant amount of terminal arabinopyranosyl units and an arabinogalactan type I pectin. Periodate oxidation studies supported the results of methylation analysis.

Humans↗
PubMed2001

Structural features of the Abeta amyloid fibril elucidated by limited proteolysis.

Although the gross morphology of amyloid fibrils is fairly well understood, very little is known about how the constituent polypeptides fold within the amyloid folding motif. In the experiments reported here, we used trypsin and chymotrypsin to conduct limited proteolysis studies on synthetic amyloid fibrils composed of the Alzheimer's disease peptide Abeta(1-40). In both reactions, the extreme N-terminal proteolytic fragment is released from fibrils as rapidly as it is from the Abeta monomer, while other proteolytic fragments are generated much more slowly. Furthermore, aggregated material isolated by centrifugation of intermediate digestion time points from both proteases contains, in addition to full-length material, peptides that possess mature C-termini but truncated N-termini. These data strongly suggest that the N-terminal region of Abeta is not involved in the beta-sheet network of the amyloid fibril, while the C-terminus is essentially completely engaged in protective-presumably beta-sheet-structure. In both digests, release of the extreme N-terminal fragments of Abeta(1-40) reaches plateau values corresponding to about 80% of the total available Abeta. This suggests that there are two classes of peptides in the fibril: while the majority of Abeta molecules have an exposed N-terminus, about 20% of the peptides have an N-terminus that is protected from proteolysis within the fibril structure. The most likely cause of this heterogeneity is the lateral association of protofilaments into the fibril structure, which would be expected to generate a unique environment for those Abeta N-termini located at protofilament packing interfaces and/or in the interior core region between the packed protofilaments. This suggests that the N-terminal region of Abeta, while not directly involved in the beta-sheet network of the fibril, may contribute to fibril stability by participating in protofilament packing.

Amino Acid Sequence↗
PubMed2001

The human isolate of Brachiola algerae (Phylum Microspora): development in SCID mice and description of its fine structure features.

Ocular, peroral, intraperitoneal, intramuscular, and subcutaneous inoculation of severe combined immunodeficient (SCID) mice with spores of the human isolate (CDC: V404) of Brachiola algerae (syn. Nosema algerae) (Phylum Microspora) revealed that the microsporidium develops in viscera of the immunodeficient mouse host, but only after the ocular administration of spores. It is hypothesized that the physico-chemical milieu of the conjunctiva and cornea helped to adapt the originally 'poikilothermic microsporidian' to the conditions within the homoiothermic organism. Ocular application of spores caused no clinical signs of disease at the application site. However, severe infection in the liver was found 60 days after infection, manifested as hepatosplenomegaly and multifocal miliary necroses and granulomas containing parasites. No microsporidia were found in any other tissues. Transmission electron microscopy revealed characteristic tubulovesicular 'secretory materials' on the plasma membrane of all developmental stages of B. algerae except sporoblasts and spores. These formations increase the parasite surface and allow more efficient metabolic communication of the parasite with the host cell. It is hypothesized that the presence of these structures is a factor helping the parasite to grow in a variety of hosts and tissues. Ultrastructural characters support the likelihood that B. algerae and B. vesicularum are conspecific, and that there exists a relationship between species of the genera Brachiola and Anncaliia.

Aged↗
PubMed2001

Cyclodextrin complexes of salts of acidic drugs. Thermodynamic properties, structural features, and pharmaceutical applications.

The objective of this mini-review is to summarize the findings concerning the physicochemical properties and the pharmaceutical applications of acidic drugs whose performances have been modified by simultaneous complexation with cyclodextrins and salt formation. Particular attention is paid to the approaches undertaken for increasing the solubility of the drugs by proper choice of the type of counterion analogously to what has been reported for complexes of basic drugs in the presence of hydroxy acids.

Acids↗
PubMed1993

Gross structural features of myosin head during sliding movement of actin as studied by quick-freeze deep-etch electron microscopy.

With quick-freeze deep-etch electron microscopy coupled with mica-flake technique, I showed previously that myosin subfragment-1 (S1) attached to F-actin in the presence of ATP is short and rounded, in contrast to its elongated and tilted appearance under rigor condition [J. Biochem. 106, 751-770 (1989)]. I further indicated that each head of heavy meromyosin (HMM) changes its configuration in a likely manner as above by the addition of various nucleotides, i.e. heads were pear-shaped in the absence of nucleotide, in a ball-on-a-stick appearance when complexed with ADP and strongly kinked to the particular direction in the presence of ATP or ADP.Vi [J. Muscle Res. Cell Motility 12, 313 (1991)]. Such morphological data not only corroborates the independent biophysical evidences suggesting gross conformational changes of myosin head upon binding ATP or ADP.Vi, but also provide strong evidence for the distinct polarity in the structure of each myosin head. Negatively stained image of chemically cross-linked acto-S1 also included cross-bridges sharply kinked to the same direction, confirming the above observation. Attempts were made to examine if such conformational change of myosin cross-bridge occurs during actomyosin superprecipitation. Samples were quick-frozen during rapid turbidity-increasing phase where actin filaments actively slide past myosin heads. The resultant image included actin-attached myosin heads all in a kinked configuration with the same polarity as observed for HMM. Several heads associated with a single actin filament were bent to the same direction suggesting that myosin heads might be in a kinked configuration with distinct polarity during contraction.

Actins↗
PubMed1985

Fractionation and structural features of two heparin families with high antithrombotic, antilipemic and anticoagulant activities.

15 heparin preparations from bovine intestine, pancreas and lung and hog intestine were fractionated in two main components by selective barium precipitation. The ones that precipitated at room temperature with barium (slow moving (SM)-heparins) had a high anticoagulant activity measured by the USP and APTT (activated partial thromboplastin time) assay and low antithrombotic activity by the Yin and Wessler method. The fractions precipitated at 5 degrees C with barium (fast moving (FM)-heparins) had a low anticoagulant action and high antithrombotic activity. The maximum anti-Xa activity (chromogenic method) was present in heparins with molecular weights around 12-15 X 10(3) daltons whereas high APTT and LPL releasing activities were present in SM-heparins with molecular weights of 30-40 X 10(3) and 15-25 X 10(3) daltons, respectively. FM-heparins had a higher anti-Xa activity and lower lipoprotein lipase (LPL)-releasing activity when compared with the SM-heparins with the same molecular weights. Significant structural differences were observed between SM- and FM-heparins by 13C-NMR spectra and enzymatic degradation with heparinase and heparitinase from Flavobacterium heparinum. Also, significant differences were observed for anti-Xa and anticoagulant activities for the two types of heparins depending on the pharmacological assay used.

Animals↗
PubMed2004

Structural features of the interleukin-10 family of cytokines.

The interleukin-10 (IL-10) family of cytokines includes IL-10, a number of its viral gene homologs, and eight recently discovered cellular cytokines (IL-19, IL-20, IL-22, IL-24, IL-26, IFN-lambda1, IFN-lambda2, IFN-lambda3). IL-10 is an intercalated dimer consisting of two six-helix bundle domains. Signal transduction occurs when each domain of IL-10 binds to two receptor chains, IL-10R1 and IL-10R2. Viral homologs use the same IL-10 receptor system, while cellular homologs use their own receptors: three long receptor chains (IL-20R1, IL-22R1 and IFN-lambda1R1) and two short receptor chains (IL-20R2 and IL-10R2). Most of the cellular homologs belong to the IL-19 subfamily of cytokines including IL-19, IL-20, IL-22 and IL-24. It is likely that IFN-lambda1, IFN-lambda2, and IFN-lambda3 also belong to the same subfamily. All these proteins are monomers in solution. Crystal structures of IL-19 and IL-22 show that the molecules consist of seven helices (A-G) forming a seven-helix bundle with compact hydrophobic core inside. Structures of complexes of IL-10 and CMVIL-10 with an extracellular domain of high affinity receptor IL-10R1 (sIL-10R1) showed that ligand/receptor interactions are of mostly polar nature, with two hydrophobic patches around receptor residues Tyr43 and Phe143 at the top and bottom of the interface. The location and structure of the binding site for the second receptor chain are still unknown. It has also been shown that in the case of IL-19 and IL-20, IL-20R2 rather than IL-20R1 is a high-affinity receptor chain. This review summarizes all published three-dimensional structures of the cytokines representing the IL-10 family of homologs, including the IL-19 subfamily and their interaction with appropriate receptors.

Cytokines↗
PubMed2001

Structural features of procyanidin interactions with salivary proteins.

Procyanidin dimers and trimer C1 were synthesized, whereas (-)-epicatechin O-gallate and B2-3"-O-gallate were isolated from grape seeds. Human saliva was separated into two fractions. One of these was mainly alpha-amylase and the other mainly proline-rich proteins (PRPs). The procyanidin compounds were combined with each of the saliva protein fractions and with bovine serum albumin. The protein-polyphenol interactions were observed using nephelometry. (+)-Catechin had a higher tannin specific activity (TSA) for PRPs than (-)-epicatechin (1.45 versus 0.65 nephelos turbidity units/mg of polyphenol). This indicated the effect of the stereochemistry of flavan-3-ols on their interaction with proteins. Procyanidin dimers linked through a C(4)-C(8) interflavanoid bond had consistently greater TSA than their counterparts with a C(4)-C(6) linkage. Esterification of a galloyl group to the C(3) hydroxyl function of (-)-epicatechin or to the epicatechin moiety of procyanidin dimer B2 increased TSA. This was not as strong an effect for the dimer, probably as a result of the expected "closed" structure of B2-3"-O-gallate.

Animals↗
PubMed1998

Structural features of helical aggregates of antibacterial peptides via simulated annealing and molecular modeling.

A 27-residue stretch of amino acids encompassing two putative 13-residue amphiphilic helical segments is an important determinant of activity in the 47-residue antibacterial peptide bovine seminalplasmin. Synthetic peptides corresponding to the 27-residue stretch (P27) SLSRYAKLANRLANPKLLETFLSKWIG as well as the 13-residue segments PKLLETFLSKWIG (SPF),exhibit antimicrobial activity. An analog of SPF where E has been replaced by K(SPFK) showed improved antimicrobial properties as compared to SPF. The peptides have the ability to bind and permeabilize membranes. We have modeled helical bundles of P27 and the two 13-residue peptides SPF and SPFK using simulated annealing via molecular dynamics. Octameric but not hexameric aggregates of P27 can form channels which would allow the passage of ions. In the case of 13-residue peptides, aggregates formed by 6 monomers can conceivably form ion conducting channels. Since the ability to form channels which would allow the passage of ions across the membranes is an important determinant of the biological activities of these peptides, knowledge of the pore forming structures should help in the design of analogs with improved activities.

Amino Acid Sequence↗
PubMed1993

Axonal glycoproteins with immunoglobulin- and fibronectin type III-related domains in vertebrates: structural features, binding activities, and signal transduction.

The L1- and F11-like axonal glycoproteins, implicated in neurite outgrowth and fasciculation, are members of the Ig superfamily comprising multiple fibronectin type III-like domains. Their Ig-like and fibronectin type III-related domains are likely to be composed of seven beta-strands arranged in two opposing beta-sheets of highly similar topology. Whereas the F11-like molecules lack a transmembrane sequence and are anchored in the plasma membrane by a glycosylphosphatidylinositol, the L1-like molecules comprise cytoplasmic domains with highly conserved sequence motifs. Most of the latter proteins occur in different isoforms generated by alternative pre-mRNA splicing, which has not been documented for molecules of the F11 subgroup. L1-like proteins undergo heterophilic as well as homophilic interactions, whereas only the former mode of binding was observed for F11-like proteins. Evidence is accumulating that these Ig superfamily molecules with fibronectin type III-like domains are interacting in a complex manner with each other and molecules of the extracellular matrix. Investigations assigning structure to function reveal that their individual extracellular domains serve distinct binding activities. Recent studies also suggest that L1 and NCAM are implicated in the transduction of transmembrane signals.

Animals↗
PubMed1975

Structural features determining the antibiotic potencies of natural and synthetic hop bitter resins, their precursors and derivatives.

Twenty-six hop bitter resins, some hitherto not investigated, were tested for antimicrobial activities. Gram-positive bacteria were much more sensitive than Gram-negative ones. The inhibitory effect against Bacillus subtilis 168 was measured by several methods and the general rule could be established that the antibiotic properties are mainly dependent on the hydrophobic parts of the molecules. Thus the acyl-lupuphenones (2-acyl-3,5-4,4',6-tri(3-methyl-2-butenyl)-cyclohexane-triones (1, 3, 5) having three prenyl and one acyl side chain are the most active substances. Their minimum inhibitory concentration (MIC) increases from the capro (0.5 muM) to the aceto derivative (11 muM). Any substitution with hydrophilic functions or loss of hydrophobic groups causes reductions in biological activity. This is most evident with the corresponding acyl-phloroglucine precursors (2-acyl-1,3,5-trihydroxybenzenes) which lack the three prenyl side chains (MIC, 110 to 5050 muM respectively). Conversion of the central six-membered ring structure into a five-membered one results in additional losses of antimicrobial activity. These findings support the proposal that the lipophilic region of the cell membrane represents the target site for the hop bitter resins.

Anti-Bacterial Agents↗
PubMed1997

Structural features of the gene encoding human muscle type carnitine palmitoyltransferase I.

We isolated a human muscle type of carnitine palmitoyltransferase I (CPTI-M) genomic clone and determined its entire nucleotide sequence. By comparison of the nucleotide sequence of the genomic clone with that of cDNA, we determined the intron/exon junctions. For detection of the exon(s) in the 5'-region of the CPTI-M gene, we isolated cDNA clones corresponding to the 5'-region of its transcript by 5'-rapid amplification of cDNA ends (5'-RACE method). Results showed two alternative exons, 1A and 1B, that do not encode amino acids in the 5'-region of the human CPTI-M gene. The gene encoding human CPTI-M was found to consist of two 5'-non-coding exons, 18 coding exons and one 3'-non-coding exon spanning approximately 10 kbp. Furthermore, on analysis of the 5'-flanking region, a putative gene encoding a 'choline kinase homologue' was found to be located only about 300 bp upstream from exon 1A of the human CPTI-M gene. Comparison of the gene structure of human CPTI-M with the reported partial gene structure of human liver type CPTI (CPTI-L) showed that the intron insertion sites were completely conserved in these two genes.

Amino Acid Sequence↗
PubMed2004

Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns.

The J4/5 loop of group I introns has tertiary interactions with the P1 helix that position the P1 substrate for the self-splicing reaction. The J4/5 loop of Candida albicans and Candida dubliniensis, 5'GAAGG3'/3'UAAUU5', potentially contains two A.A pairs flanked by one G.U pair on one side and two G.U pairs on the other side. Results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments with a mimic of the C. albicans and C. dubliniensis J4/5 loop are consistent with the adenosines forming tandem sheared A.A pairs with a cross-strand stack and only the G.U pair not adjacent to an A.A pair forming a static wobble G.U pair. The two G.U pairs adjacent to the tandem A.A pairs are likely in a dynamic equilibrium between multiple conformations. Although Co(NH(3))(6)(3+) stabilizes the loop by several kilocalories per mole at 37 degrees C, addition of Mg(2+) or Co(NH(3))(6)(3+) has no effect on the structure of the loop. The tandem G.U pairs provide a pocket of negative charge for Co(NH(3))(6)(3+) to bind. The results contribute to understanding the structure and dynamics of purine-rich internal loops and potential G.U pairs adjacent to internal loops.

Base Pairing↗
PubMed1976

Structural features and biologic properties of fragments obtained by limited proteolysis of C3.

Limited proteolysis of the third component of human complement (C3) was performed by using trypsin and streptococcal proteinase and the digests were analyzed for biologic activity. Incubation of C3 with trypsin for 1 min yielded a peptide with smooth muscle-contracting activity but no chemotactic activity, whereas the digest obtained after 15 min of incubation had only chemotactic activity. The conversion of muscle contracting to chemotactic activity could be correlated with the time course of trypsin hydrolysis. Hydrolysis of C3 with streptococcal proteinase gave a digest demonstrating only chemotactic activity. Each digest was resolved on a Sephadex G-100 column and the fractions containing biologic activities were characterized. The amino acid composition of the trypsin fragments, despite having different biologic activities, was remarkably similar, although differences in NH2-terminal amino acids were demonstrable. The fragments obtained by digestion of C3 with the streptococcal proteinase had an amino acid composition different from the trypsin fragments and displayed marked heterogeneity of NH2-terminal residues. These results suggest that slight alterations in the primary structure of C3 fragments may yield significant changes in their biologic activities and that the structural requirements for chemotactic activity are not confined to a single peptide species.

Amino Acid Sequence↗
PubMed1999

Structural features and light-dependent changes in the sequence 59-75 connecting helices I and II in rhodopsin: a site-directed spin-labeling study.

Twenty-one single-cysteine substitution mutants were prepared in the sequence 56-75 between transmembrane helices I and II at the cytoplasmic surface of bovine rhodopsin. Each mutant was reacted with a sulfhydryl-specific reagent to produce a nitroxide side chain. The electron paramagnetic resonance of the labeled proteins in dodecyl maltoside solution was analyzed to provide the relative mobility and accessibility of the nitroxide side chain to both polar and nonpolar paramagnetic reagents. The results indicate that the hydrophobic-water interface of the micelle intersects helices I and II near residues 64 and 71, respectively. Thus, the sequence 64-71 is in the aqueous phase, while 56-63 and 72-75 lie in the transmembrane helices I and II, respectively. The lipid-facing surfaces on transmembrane helices I and II near the cytoplasmic surface correspond to approximately 180 degrees and 90 degrees of arc on the helical surfaces, respectively. Photoactivation of rhodopsin produced changes in structure in the region investigated, primarily around helix II. However, these changes are much smaller than those noted by spin labels in helix VI (Altenbach, C., Yang, K., Farrens, D., Farahbakhsh, Z., Khorana, H. G., and Hubbell, W. L. (1996) Biochemistry 35, 12470).

Amino Acid Sequence↗
PubMed1995

Structural features of the reactions between antibodies and protein antigens.

Antibodies bind protein antigens over large sterically and electrostatically complementary surfaces. Van der Waals forces, hydrogen bonds, and occasionally ion pairs provide stability to antibody-antigen complexes. In addition, water molecules contribute hydrogen bonds linking antigen and antibody, and increase the complementarity of antigen-antibody interfaces. In qualification to a strict 'lock and key' mechanism, evidence of conformational changes between free and complexed antibodies indicate some accommodation to the antigen. Antibody-protein antigen reactions are enthalpically driven with varying degrees of entropic compensation, often dependent on the magnitude of the enthalpy of the reaction. In the case of two antibody-combining sites studied by X-ray diffraction, the relative arrangements of the variable domains of the light and heavy chains of the antibody change slightly from the free to the antigen-bound state. Furthermore, the contacting residues of both antibodies exhibit similar reduced mobilities when complexed to antigen, suggesting that differences in 'solvent entropy' rather than in conformational freedom may be the source of different entropic compensation factors. In concert, data from structural studies, reaction rates, calorimetric measurements, molecular dynamics simulations, and site-directed mutagenesis are beginning to detail the nature of antibody-protein antigen interactions.

Animals↗