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PubMed1995

Structural features of the precursor to mitochondrial aspartate aminotransferase responsible for binding to hsp70.

The precursor (pmAspAT) and mature (mAspAT) forms of mitochondrial aspartate aminotransferase interact with hsp70 very early during translation when synthesized in either rabbit reticulocyte lysate or wheat germ extract (Lain, B., Iriarte, A., and Martinez-Carrion. (1994) J. Biol. Chem. 269, 15588-15596). The nature of the structural elements responsible for recognition and binding of this protein to hsp70 has been studied by examining the folding and potential association with the chaperone of several engineered forms of this enzyme. Whereas pmAspAT and mAspAT bind hsp70 very early during translation, the cytosolic form of this enzyme (cAspAT) does not interact with hsp70. A fusion protein consisting of the mitochondrial presequence peptide attached to the amino terminus of cAspAT associates with hsp70 only after the protein has acquired its native-like conformation, apparently through binding to the presequence exposed on the surface of the folded protein. Deletion of the amino-terminal segment of mAspAT or its replacement with the corresponding domain from the cytosolic isozyme eliminates the cotranslational binding of hsp70 to the mitochondrial protein. We conclude that both the presequence and NH2-terminal region of pmAspAT represent recognition signals for binding of hsp70 to the newly synthesized mitochondrial precursor. Results from competition studies with synthetic peptides support this conclusion. The ability of hsp70 to discriminate between these two highly homologous proteins probably involves the recognition of specific sequence elements in the NH2-terminal portion of the mitochondrial protein and may relate to their separate localization in the cell. A slower folding rate and higher affinity for cytosolic chaperones may represent evolutionary adaptations of translocated mitochondrial proteins to ensure their efficient importation into the organelle.

Amino Acid Sequence↗
PubMed1987

Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features.

The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by 1H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and 1H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only 1H NMR clearly distinguishes all three ferric isomers. The ring current shifts in the carbonyl complexes of reduced sulf-Mb complexes support saturation for a pyrrole in each isomer. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first 1H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albeit to a smaller extent.

Animals↗
PubMed1993

Predicted common structural features of DNA-binding domains from Ets, Myb and HMG transcription factors.

The Ets family of transcription factors shares a 85 amino acid domain, named the ETS domain, which appears responsible for their DNA binding activity. This domain did not show any clear similarity with already known DNA binding motifs. Hydrophobic Cluster Analysis (HCA), a sensitive method able to detect protein structural relationships even at low sequence identity, was chosen in order to compare the ETS domain with other conventional DNA binding motifs. HCA analysis combined with known three-dimensional NMR data, suggests that the ETS domain may be structurally related to the Myb DNA binding domain and possibly to the HMG one. Indeed, the ETS domain is likely to contain two helix-loop-helix motifs.

Amino Acid Sequence↗
PubMed1987

Structural features of cartilage matrix protein deduced from cDNA.

cDNAs encoding the Mr 54,000 chicken cartilage matrix protein (CMP) were selected from a cartilage cDNA expression library by immunological means. Antibodies elicited against insert-encoded protein purified from one of the clones reacted specifically with chicken CMP in immunoblots of total cartilage extract, providing positive identification of the cDNA clones isolated. The cDNAs detect a 3.4-kilobase transcript that was present in sternal cartilage and in cartilaginous but not in precartilaginous embryonic limb tissues. The cDNAs code for 416 amino acids of the chicken CMP, including its COOH terminus. There are two striking features in the deduced CMP amino acid sequence: first, it contains a region with significant homologies to repeat sequences in the precursor for epidermal growth factor; and second, it is made up of two large homologous repeat sequences. These results provide the first detailed structural information on the CMP and establish it as a developmentally regulated marker of cartilage differentiation.

Amino Acid Sequence↗
PubMed1980

The inverted repeat as a recognizable structural feature in supercoiled DNA molecules.

The single-strand-specific endonuclease S1 from Aspergillus oryzae introduces highly selective cleavages into supercoiled covalently closed circular DNA molecules, but not into their previously linearized counterparts. The cleavage sites are inverted repeats of unit length between 9 and 13 base pairs, separated by a nonrepetitious 2-6 base pairs. Such regions may adopt hairpin or similar structures stabilized by the negative superhelix density and may constitute recognition sites for cellular proteins.

Bacteriocin Plasmids↗
PubMed1978

The packaging unit: a basic structural feature for the condensation of late cricket spermatid nuclei.

The alignment, folding and packaging of cricket chromatin was examined during late spermiogenesis by an electron-microscope study of nuclei dispersed by air--liquid surface tension forces after detergent treatment. Late developing spermatid genomes arrange themselves in multiple packaging units in a stepwise process which includes: (1) a loss of the beaded repeating structure of chromatin as nucleoprotein fibres become smooth and gradually assume a uniform diameter; (2) a side-by--side alignment of structurally modified chromatin fibres; and (3) a regular folding into packaging units. Alignment and folding of chromatin fibres are presumably mediated by intermolecular bonds easily disrupted by spreading forces. In very late spermatids, interfibre binding forces are difficult to overrride by spreading alone, indicating a stronger cross-linking of increasingly coalescent packaging units. 'Unit to unit' coalescence stabilizes the nuclear structure, first limiting and afterwards denying penetration of phosphotungstic acid, as displayed in thin sections of extremely cricket spermatid nuclei. Binding of phosphotungstate by nuclear basic proteins can be facilitated by limited protein solubilization after disulphide reduction of unfixed cricket tests with sodium dodecyl sulphate and dithiothreitol. Results of this study permit the proposal of model experiments useful for clarifying the organization of highly condensed spermatid genomes and for evaluating the structure of genome segments in systems wherein changes of chromatin-associated protein occur.

Animals↗
PubMed1992

Polysaccharides in fungi. XXIX. Structural features of two antitumor polysaccharides from the fruiting bodies of Armillariella tabescens.

An antitumor polysaccharide containing peptide moieties AT-HW ([alpha]D + 31 degrees in water) and an antitumor polysaccharide AT-AL ([alpha]D + 209 degrees in 1 M sodium hydroxide) were isolated from hot-water extract and the alkaline extract of the fruiting bodies of Armillariella tabescens, respectively. Chemical structures of AT-HW and AT-AL were investigated by a combination of chemical and spectroscopic methods. The results indicate that the major constituent of AT-HW (molecular weight, 105000), a heteroglycan, is composed primarily of beta-(1----6)-linked D-glucopyranosyl and D-galactopyranosyl residues, and contains their branched residues and terminal sugar (gluco-, manno-, and fucopyranose) residues, in addition to beta-(1----3)-linked D-glucopyranosyl residues, while AT-AL (molecular weight, 93000) is chiefly composed of alpha-(1----3)-linked D-glucopyranosyl residues.

Antineoplastic Agents↗
PubMed1981

[Structural features of the elementary bodies of bacterial L-forms].

Elementary bodies have been detected in the L-forms of various bacteria, irrespective of their strain, the phase of development and stabilization of their culture. Elementary bodies have been found to have all organoids peculiar to other L-culture cells (the unit membrane, the nucleoid, ribosomes, more seldom mesosome-like structures and the outer membrane of the cell wall), which is indirectly indicative of their possible viability. The cytoplasmic membrane of elementary bodies contains dehydrogenases (detected in the NBT test), has the hydrophobic layer structure typical of bacterial membranes and, judging by the results of the ferritin test, possesses the same antigenic properties as the cytoplasmic membrane of other L-culture cells. Nevertheless, the above-mentioned properties are far from being the attribute of every elementary body, and the completeness of their manifestation is not directly related with the size of elementary bodies.

Cell Membrane↗
PubMed1995

Structural features of the uniporter/symporter/antiporter superfamily.

The uniporter/symporter/antiporter superfamily is an evolutionarily related group of solute transporters. For the entire superfamily, we have used a new predictive program to identify the transmembrane domains. These transmembrane domains were then analyzed with regard to their overall hydrophobicity and amphipathicity. In addition, the lengths of the hydrophilic loops connecting the transmembrane domains were calculated. These data, together with structural information in the literature, were collectively used to produce a general model for the three-dimensional arrangement of the transmembrane domains.

Antiporters↗
PubMed1981

Structural features associated with movement and 'catch' of sea-urchin spines.

Spine catch ligaments of a sea urchin Arbacia punctulata were extended under constant load. Ligaments from an undisturbed animal may show any extension rate from zero (catch state) to rapid extension to failure. Replacing the preparation bath with CA(2)- and Mg(2+)-free sea water reversibly abolishes the catch state. The fine structure of the outermuscle layer and inner ligament cone associated with the spine base is described. The unstriated paramyosin muscles bear thin flanges and form compact interlocking rows. Subsurface cisternae are associated with the plasma membrane. The muscles are innervated by glia-free axons ending in bulbous terminals containing lucent synaptic vesicles. The ligament comprises cylindrical bundles of collagen fibrils: one or more minute muscle fibers (paramyosin) lie parallel with and closely adjoining each bundle. The mean diameter of these muscles is 0.3 micrometers and they occupy 2-3% of the ligament's cross-sectional area. Axons containing electron-opaque secretory droplets accompany the muscles between the collagen bundles: the cell bodies of these neurones generally lie on the outer surface of the ligament. When an urchin points a spine, the ligament on the side of the contracting spine muscle shortens but does not buckle. A function of the intraligamental muscles is to effect this non-buckled shortening. The catch mechanism (which reside entirely within the ligament) may be due either to the intraligamental muscles and/or to a locked polymer mechanism in which matrix molecules between collagen fibrils are reversibly cross-linked by divalent cations.

Animals↗
PubMed2002

Towards a new T-fold protein?: the coproporphyrinogen III oxidase sequence matches many structural features from urate oxidase.

Urate oxidase (UOX) and coproporphyrinogen III oxidase (CPO) are two unusual oxidases as they accomplish their catalytic act with no co-factor nor metal ion. They both require molecular oxygen, and lead to hydrogen peroxide in addition to the product. UOX is composed of two contiguous Tunneling-fold domains and CPO appears to be also divided into two structurally equivalent domains. Moreover, each of these putative domains can be coherently aligned on UOX domains. Although their sequences are very distant, we therefore suggest that functional CPO dimer is built around a tunnel, with the substrate sitting above it, on the N- and C-terminal side. This overall model is supported by mutation data and is coherent with the chemical events expected for substrate processing by CPO.

Amino Acid Sequence↗
PubMed1998

Structural features of tannic acid important for DNA degradation in the presence of Cu(II).

Tannic acid has numerous food and pharmacological applications. It is an additive in medicinal products and is used as a flavouring agent and as an antioxidant in various foods and beverages. However, there are reports of its mutagenicity and carcinogenicity in bacterial and animal test systems. Tannic acid and its structural monomer gallic acid are also capable of inducing apoptosis in animal cells. We have earlier shown that tannic acid in the presence of Cu(II) causes DNA degradation through generation of reactive oxygen species such as hydroxyl radicals. In order to understand the chemical basis of the various biological properties of tannic acid we have studied the structure-activity relationship between tannic acid and gallic acid using the DNA cleavage assay. Results in the present paper indicate that gallic acid is considerably more active than tannic acid. However, if two of the three hydroxyl groups of gallic acid are methylated (syringic acid) the DNA degrading capacity declines sharply. Further, decarboxylation of gallic acid (pyrogallol) leads to enhancement of its activity. In conclusion, the results indicate that the DNA cleavage activity of tannic acid is due to its digalloyl moeity and that free hydroxyl groups are essential for cleavage.

Animals↗
PubMed2000

8-Difluoromethoxy-4-quinolone derivatives as anti-feline immunodeficiency virus (FIV) agents: important structural features for inhibitory activity of FIV replication.

The inhibitory activities of various 8-difluoromethoxy-4-quinolone derivatives against feline immunodeficiency virus (FIV) replication in the chronically infected cell line P-CrFK were investigated. Certain derivatives were found to inhibit FIV production from P-CrFK cells in a dose-dependent manner without exhibiting cytotoxic effects at inhibitory concentrations. Based on this study, the structures important for anti-FIV activity are suggested to be (i) a carboxyl group at position C-3, and (ii) an aromatic modification at position 4 of the C-7 piperazinyl moiety.

Animals↗
PubMed2005

Small molecule p38 inhibitors: novel structural features and advances from 2002-2005.

The discovery and development of selective, efficacious, and safe small molecule p38 mitogen-activated protein kinase inhibitors for the treatment of inflammatory diseases remains the focus of many pharmaceutical research programs. Advances in small molecule p38 inhibitor design in potency and oral efficacy have been accelerated with the large number of available inhibitor-enzyme x-ray structures. These advances have allowed for the discovery of diverse sets of inhibitors with the opportunity to map inhibitor interactions and design selective inhibitors. This review covers recent compound disclosures in the patent and published literature over the last three years. Many disclosures represent new chemotypes as well as creative modifications of known structures.

Drug Design↗