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PubMed1991

Analysis of conserved domains identifies a unique structural feature of a chloroplast heat shock protein.

A low molecular weight heat shock protein which localizes to chloroplasts has been identified in several plant species. This protein belongs to a eukaryotic superfamily of small HSPs, all of which contain a conserved carboxyl-terminal domain. To investigate further the structure of this HSP, we isolated and sequenced cDNA clones for the chloroplast LMW HSPs from Petunia hybrida and Arabidopsis thaliana. The cloning of chloroplast HSPs from these two species enabled us to compare the amino acid sequences of this protein from plant species (petunia, Arabidopsis, pea, soybean and maize) that represent evolutionarily divergent taxonomic subclasses. Three conserved regions were identified, which are designated as regions I, II and III. Regions I and II are also shared by cytoplasmic LMW HSPs and therefore are likely to have functional roles common to all eukaryotic LMW HSPs. In contrast, consensus region III is not found in other LMW HSPs. Secondary structure analysis predicts that this region forms an amphipathic alpha-helix with high conservation of methionine residues on the hydrophobic face and 100% conservation of residues on the hydrophilic face. This structure is similar to three helices, termed "methionine bristles", which are found in a methionine-rich domain of a 54 kDa protein component of signal recognition particle (SRP54). The conservation of regions I and II among LMW cytoplasmic and chloroplast HSPs suggests that these HSPs perform related functions in different cellular compartments. However, identification of the methionine bristle domain suggests that chloroplast HSPs also have unique functions or substrates within the special environment of the chloroplast or other plastids.

Amino Acid Sequence↗
PubMed1993

Cloning, sequence and structural features of a lipase from the antarctic facultative psychrophile Psychrobacter immobilis B10.

A lipase gene (lip1) from the facultative psychrophilic strain Psychrobacter immobilis B10 has been cloned and sequenced. The deduced preprotein sequence is composed of 317 amino acids with a predicted M(r) of 35,288. A primary structure alignment of lipases including lip1 shows conserved elements for which a structural role is proposed in the light of recent crystallographic studies. The analysis of the psychrophilic enzyme sequence suggests characteristics in relation with the adaptation to cold.

Amino Acid Sequence↗
PubMed2002

Proteolysis of bovine beta-lactoglobulin during thermal treatment in subdenaturing conditions highlights some structural features of the temperature-modified protein and yields fragments with low immunoreactivity.

Bovine beta-lactoglobulin was hydrolyzed with trypsin or chymotrypsin in the course of heat treatment at 55, 60 and 65 degrees C at neutral pH. At these temperatures beta-lactoglobulin undergoes significant but reversible structural changes. In the conditions used in the present study, beta-lactoglobulin was virtually insensitive to proteolysis by either enzyme at room temperature, but underwent extensive proteolysis when either protease was present during the heat treatment. High-temperature proteolysis occurs in a progressive manner. Mass spectrometry analysis of some large-sized breakdown intermediates formed in the early steps of hydrolysis indicated that both enzymes effectively hydrolyzed some regions of beta-lactoglobulin that were transiently exposed during the physical treatments and that were not accessible in the native protein. The immunochemical properties of the products of beta-lactoglobulin hydrolysis were assessed by using various beta-lactoglobulin-specific antibodies, and most epitopic sites were no longer present after attack of the partially unfolded protein by the two proteases.

Animals↗
PubMed1996

Structural features of the central cannabinoid CB1 receptor involved in the binding of the specific CB1 antagonist SR 141716A.

The antagonist SR 141716A has a high specificity for the central CB1 cannabinoid receptor and negligeable affinity for the peripheral CB2 receptor, making it an excellent tool for probing receptor structure-activity relationships. From binding experiments with mutated CB1 and with chimeric CB1/CB2 receptors we have begun to identify the domains of CB1 implicated in the recognition of SR 141716A. Receptors were transiently expressed in COS-3 cells, and their binding characteristics were studied with SR 141716A and with CP 55,940, an agonist recognized equally well by the two receptors. The region delineated by the fourth and fifth transmembrane helices of CB1 proved to be crucial for high affinity binding of SR 141716A. The CB1 and CB2 second extracellular loops, e2, were exchanged, modifications that had no effect on SR 141716A binding in the CB1 variant but that eliminated CP 55,940 binding in both mutants. The replacement of the conserved cysteine residues in e2 of CB2 by serine also eliminated CP 55,940 binding, but replacement of those in CB1 resulted in the sequestration of the mutated receptors in the cell cytoplasm. The e2 domain thus plays some role in CP 55,940 binding but none in SR 141716A recognition, binding of the latter clearly implicating residues in the adjoining transmembrane helices.

Amino Acid Sequence↗
PubMed1994

Structural features of adenovirus 2 virus-associated RNA required for binding to the protein kinase DAI.

The double-stranded RNA activated protein kinase DAI contains an RNA binding domain consisting of two copies of a double-stranded RNA binding motif. We have investigated the role of RNA structure in the interaction between DAI and the structured single-stranded RNA, adenovirus VA RNAI, which inhibits DAI activation. Mutations in the apical stem, terminal stem, and central domain of the RNA were tested to assess the contribution of these elements to DAI binding in vitro. The data demonstrate that over half a turn of intact apical stem is required for the interaction and that there is a correlation between the binding of apical stem mutants and their ability to function both in vivo and in vitro. There was also evidence of preference for GC-rich sequence in the proximal region of the apical stem. In the central domain the correlation between binding and function of mutant RNAs was poor, suggesting that at least some of this region plays no direct role in binding to DAI, despite its functional importance. Exceptionally, central domain mutations that encroached on the phylogenetically conserved stem 4 of VA RNA disrupted binding, and complementary mutations in this sequence partially restored binding. Measurement of the binding of wild-type VA RNAI to DAI and p20, a truncated form of the protein containing the RNA binding domains alone, under various ionic conditions imply that the major interactions are electrostatic and occur via the protein's RNA binding domain. However, differences between full-length DAI and p20 in their binding to mutants in the conserved stem suggest that regions outside the RNA binding domain also participate in the binding. The additional interactions are likely to be non-ionic, and may be important for preventing DAI activation during virus infection.

Adenoviruses, Human↗
PubMedDate not supplied

Structural features correlated with the extreme thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima.

Understanding the molecular mechanisms behind extreme temperature stability is of relevance for the protein folding problem and for designing proteins for industrial and medical applications. A powerful approach for understanding the structural basis of thermostability is the comparison of high resolution structures of homologous proteins from mesophiles and thermophiles. The 1.75 A crystal structure of Thermotoga maritima 1[4Fe-4S] ferredoxin was compared with those of mesophilic ferredoxins. Detailed analysis of structural differences reveals that thermostability is achieved without large changes of the overall polypeptide chain folding. The most striking differences include the formation of additional hydrogen bonding networks involving both side-chain and main-chain atoms. These networks are mainly connecting turns and strongly fix the N-terminus to the central core of the protein, increasing the overall rigidity of Thermotoga maritima ferredoxin. Other possibly stabilizing factors are the shortening of a solvent exposed surface loop, the increased content of alanines in the second alpha-helix, and the replacement of three residues close to the iron-sulfur cluster, which are in energetically unfavourable conformations in other ferredoxins, by glycines.

Amino Acid Sequence↗
PubMed2007

Abeta(25-35) and its C- and/or N-blocked derivatives: copper driven structural features and neurotoxicity.

The toxic properties of beta-amyloid protein, Abeta(1-42), the major component of senile plaques in Alzheimer's disease, depend on nucleation-dependent oligomerization and aggregation. In addition, Abeta(1-42) toxicity is favored by the presence of trace metals, which affect the secondary structure of the peptide. A peptide comprising 11 residues within Abeta(1-42) [Abeta(25-35)] aggregates and retains the neurotoxic activity of Abeta(1-42). We have used both Abeta(25-35) and its C-amidated or N-acetylated/C-amidated derivatives to investigate the role of copper(II) in modulating the conformation and aggregation state as well as the neurotoxic properties of amyloid peptides. Electrospray ionization mass spectrometry (ESI-MS) and electron paramagnetic resonance (EPR) measurements were performed to verify the formation of copper(II)/Abeta(25-35) complexes and to determine the coordination mode, respectively. Abeta(25-35) and its derivatives were analyzed by circular dichroism spectroscopy to assess their secondary structure, subjected to thioflavine-T (Th-T) binding assay to reveal beta-sheet structured aggregates formation, and imaged by scanning force microscopy. Toxicity was assessed on mature cultures of rat cortical neurons. We found that beta-sheet-structured species of Abeta(25-35) were neurotoxic, whereas the random-coil-structured derivatives were devoid of effect. Interestingly, copper promoted the random-coil/beta-sheet transition of Abeta(25-35), with ensuing peptide toxicity, but it induced the toxicity of the N-acetylated/C-amidated derivative without affecting peptide folding. Moreover, copper did not influence either the folding or the activity of the C-amidated Abeta(25-35), suggesting that blockade of the C-terminus of Abeta peptides might be sufficient to prevent Abeta toxicity.

Amyloid beta-Peptides↗
PubMed1991

Protein motifs that recognize structural features of DNA.

Many proteins have the ability to bind to a variety of DNA sequences, the recognition of which depends on some general rather than specific feature of the DNA. Some of the protein motifs that are responsible for this type of recognition have been identified in transcription factors and chromosomal proteins. These motifs consist of sequences capable of forming a structural framework in which positively charged residues can be arranged so that binding to a particular DNA structure is preferred.

Amino Acid Sequence↗
PubMed1999

Common structural features of MAPEG -- a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism.

A novel superfamily designated MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism), including members of widespread origin with diversified biological functions is defined according to enzymatic activities, sequence motifs, and structural properties. Two of the members are crucial for leukotriene biosynthesis, and three are cytoprotective exhibiting glutathione S-transferase and peroxidase activities. Expression of the most recently recognized member is strongly induced by p53, and may therefore play a role in apoptosis or cancer development. In spite of the different biological functions, all six proteins demonstrate common structural characteristics typical of membrane proteins. In addition, homologues are identified in plants, fungi, and bacteria, demonstrating this superfamily to be generally occurring.

Amino Acid Sequence↗
PubMed1995

Digestion of raw banana starch in the small intestine of healthy humans: structural features of resistant starch.

The digestion of freeze-dried green banana flour in the upper gut was studied by an intubation technique in six healthy subjects over a 14 h period. Of alpha-glucans ingested, 83.7% reached the terminal ileum but were almost totally fermented in the colon. Structural study of the resistant fraction showed that a small part of the alpha-glucans which escaped digestion in the small intestine was composed of oligosaccharides from starch hydrolysis, whereas the rest was insoluble starch in granule form with physical characteristics similar to those of raw banana starch. Passage through the small intestine altered granule structure by increasing susceptibility to further alpha-amylase hydrolysis. Compared with resistant starch values in vivo, those obtained with the in vitro methods tested were inadequate to estimate the whole fraction of starch reaching the terminal ileum.

Adult↗
PubMed1991

Structural features of the arabinan component of the lipoarabinomannan of Mycobacterium tuberculosis.

The recent availability of pure lipoarabinomannan (LAM) from Mycobacterium spp. has resulted in its implication in host-parasite interaction, which events may be mediated by the presence of a phosphatidylinositol unit at the reducing end of LAM. Herein we address the structure of the antigenic, nonreducing end of the molecule. Through the process of 13C NMR analysis of the whole molecule and gas chromatography/mass spectrometry of alditol acetates derived from the differential per-O-alkylated lipopolysaccharide, the majority of the arabinosyl residues were recognized as furanosides. Second, through analysis of per-O-alkylated oligoarabinosyl arabinitol fragments of partially hydrolyzed LAM, it was established that the internal segments of the arabinan component consists of branched 3,5-linked alpha-D-arabinofuranosyl (Araf) units with stretches of linear 5-linked alpha-D-Araf residues attached at both branch positions, whereas the nonreducing terminal segments of LAM consist of either of the two arrangements, beta-D-Araf-(1----2)-alpha-D-Araf-(1----5)- alpha-D-Araf---- or [beta-D-Araf-(1----2)-alpha-D-Araf-(1----]2---- (3 and 5)-alpha-D-Araf----. Since this latter arrangement also characterizes the terminal segments of the peptidoglycan-bound arabinogalactan of Mycobacterium spp., we propose that mycobacteria elaborate unique terminal arabinan motifs in two distinct settings. In the case of the bound arabinogalactan, these motifs provide the nucleus for the esterified mycolic acids, entities which dominate the physicochemical features of mycobacteria and their peculiar pathogenesis. In the case of LAM, these motifs, non-mycolylated, are the dominant B-cell antigens responsible for the majority of the copious antibody response evident in most mycobacterial infections.

Antigens, Bacterial↗
PubMed1994

Structural features and hypoglycemic activities of two polysaccharides from a hot-water extract of Agrocybe cylindracea.

A glucan (AG-HN1, [alpha]D +24 degrees) and a heteroglycan (AG-HN2, [alpha]D +26 degrees) were isolated from a hot-water extract of the fruiting bodies of Agrocybe cylindracea. The structures were investigated by a combination of chemical and spectroscopic methods. The results indicated that high molecular weight glucan AG-HN1 is primarily a beta-(1-->6)-branched (1-->3)-beta-D-glucan containing small amounts of (1-->4)-linked and (1-->6)-linked glucopyranosyl residues. Low molecular weight heteroglycan AG-HN2 gives galactose, glucose, fucose, and mannose on hydrolysis and appears to be chiefly composed of (1-->6)-linked gluco- and galacto-pyranosyl residues, many of them branched, and various nonreducing terminal residues. AG-HN1 showed a remarkable hypoglycemic activity in both normal and streptozotocin-induced diabetic mice by ip administration, and its activity was higher than that of AG-HN2.

Animals↗
PubMed1995

Structural features of the epsilon subunit of the Escherichia coli ATP synthase determined by NMR spectroscopy.

The tertiary fold of the epsilon subunit of the Escherichia coli F1F0 ATPsynthase (ECF1F0) has been determined by two- and three-dimensional heteronuclear (13C, 15N) NMR spectroscopy. The epsilon subunit exhibits a distinct two domain structure, with the N-terminal 84 residues of the protein forming a 10-stranded beta-structure, and with the C-terminal 48 amino acids arranged as two alpha-helices running antiparallel to one another (two helix hairpin). The beta-domain folds as a beta-sandwich with a hydrophobic interior between the two layers of the sandwich. The C-terminal two-helix hairpin folds back to the N-terminal domain and interacts with one side of the beta-domain. The arrangement of the epsilon subunit in the intact F1F0 ATP synthase involves interaction of the two helix hairpin with the F1 part, and binding of the open side of the beta-sandwich to the c subunits of the membrane-embedded F0 part.

Amino Acid Sequence↗
PubMed2000

Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards.

DNA sequences from 195 squamate reptiles indicate that mitochondrial gene order is the most reliable phylogenetic character establishing monophyly of acrodont lizards and of the snake families Boidae, Colubridae, and Viperidae. Gene order shows no evidence of evolutionary parallelisms or reversals in these taxa. Derived secondary structures of mitochondrial tRNAs also prove to be useful phylogenetic characters showing no reversals. Parallelisms for secondary structures of tRNAs are restricted to deep lineages that are separated by at least 200 million years of independent evolution. Presence of a stem-and-loop structure between the genes encoding tRNA(Asn) and tRNA(Cys), where the replication origin for light-strand synthesis is typically located in vertebrate mitochondrial genomes, is found to undergo at least three and possibly as many as seven evolutionary shifts, most likely parallel losses. This character is therefore a less desirable phylogenetic marker than the other structural changes examined. Sequencing regions that contain multiple genes, including tRNA genes, may be preferable to the common practice of obtaining single-gene fragments for phylogenetic inference because it permits observation of major structural changes in the mitochondrial genome. Such characters may occasionally provide phylogenetic information on relatively short internal branches for which base substitutional changes are expected to be relatively uninformative.

Animals↗