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PubMed1986

Structural features in the 3'-terminal region of polyribosome-bound rabbit globin messenger RNAs.

A nuclease S1 mapping procedure was used to identify sites accessible to nucleases in the 3'-noncoding region of the rabbit globin mRNAs. A complex structure was evident in the alpha-globin species, with one highly accessible single-stranded site, large portions in an accessible double-stranded configuration, and a portion not accessible to any of the nucleases. In the beta-globin mRNA, the region was more uniformly accessible to RNase T1 and to a cobra venom enzyme specific for double-stranded RNA, but it had only a single site highly accessible to a bulkier Neurospora endonuclease. The patterns of cleavage were nearly identical in the deproteinized mRNAs and in the mRNAs associated with polyribosomes in reticulocyte extracts. In both species, a zone of secondary structure occurred around the poly(A) junction. In each species, virtually all the molecules had a poly(A) sequence of at least 20-25 AMP residues. A periodicity in poly(A) size distribution was observed. These results indicate that the beginning of this sequence is well protected against degradation inside the cell and that zones of partial protection occur at measured intervals. In crude extracts, where the poly(A) is covered with proteins, this sequence was protected against nuclease digestion.

Animals↗
PubMed2001

Structural features and methylation patterns associated with paramutation at the r1 locus of Zea mays.

In paramutation, two alleles of a gene interact and, during the interaction, one of them becomes epigenetically silenced. The various paramutation systems that have been studied to date exhibit intriguing differences in the physical complexity of the loci involved. B and Pl alleles that participate in paramutation are simple, single genes, while the R haplotypes that participate in paramutation contain multiple gene copies and often include rearrangements. The number and arrangement of the sequences in particular complex R haplotypes have been correlated with paramutation behavior. Here, the physical structures of 28 additional haplotypes of R were examined. A specific set of physical features is associated with paramutability (the ability to be silenced). However, no physical features were strongly correlated with paramutagenicity (the ability to cause silencing) or neutrality (the inability to participate in paramutation). Instead, paramutagenic haplotypes were distinguished by high levels of cytosine methylation over certain regions of the genes while neutral haplotypes were distinguished by lack of C-methylation over these regions. These findings suggest that paramutability of r1 is determined by the genetic structure of particular haplotypes, while paramutagenicity is determined by the epigenetic state.

Alleles↗
PubMed1996

Vitrified articular cartilage reveals novel ultra-structural features respecting extracellular matrix architecture.

The quality of cryosections prepared from high pressure frozen bovine articular cartilage has been recently evaluated by systematic electron diffraction analysis, and vitrification found to be zone-dependent. The lower radial layer was optimally frozen throughout the entire section thickness (150 microns), whereas in the upper radial, transitional and superficial layers this was achieved down to a depth of only approximately 5-50 microns. These differences were found to correlate proportionally with proteoglycan concentration and inversely with water content. In the current investigation, extracellular matrix ultrastructure was examined in high pressure frozen material (derived from the lower radial zone of young adult bovine articular cartilage), by both cryoelectron microscopy of cryosections and by conventional transmission electron microscopy of freeze-substituted and embedded samples. Several novel features were revealed, in particular, the existence of a fine filamentous network; this consisted of elements 10-15 nm in diameter and with a regular cross-banded structure similar to that characterising collagen fibrils. These filaments were encountered throughout the entire extracellular space, even within the pericellular region, which is generally believed to be free of filamentous or fibrillar components. The proteoglycan-rich interfibrillar/filamentous space manifested a fine granular appearance, there being no evidence of the reticular network previously seen in suboptimally frozen material.

Animals↗
PubMed1998

Freeze tolerance in the wood frog Rana sylvatica is associated with unusual structural features in insulin but not in glucagon.

The wood frog Rana sylvatica utilises glucose, derived from hepatic glycogen, as a cryoprotectant in order to survive freezing during winter hibernation, and glycogenolysis is initiated by hormonal and/or neural stimuli. The primary structure of insulin was determined from R. sylvatica and from two species of freeze-intolerant Ranid frogs R. catesbeiana (American bullfrog) and R. ridibunda (European green frog). All three insulins contain a dipeptide (Lys-Pro) extension to the N-terminus of the A-chain. The amino acid sequences of insulins from R. catesbeiana and R. ridibunda differ by only one residue (Asp for Glu at B21) but R. sylvatica insulin differs from R. catesbeiana insulin at A12 (Thr-->Met), A23 (Asn-->Ser), B5 (Tyr-->His) and B13 (Glu-->Asp). The residue at A23 (corresponding to A21 in human insulin) has been otherwise fully conserved during evolution and the residue at B13 has been strongly conserved in tetrapods. Insulin isolated from specimens of R. sylvatica that had been frozen for 24 h and from control animals that had not been frozen had the same structure, showing that freezing did not alter the pathway of post-translational processing of proinsulin. R. sylvatica glucagon was isolated in two molecular forms. Glucagon-29 was identical to R. catesbeiana glucagon-29 and contains only one amino acid substitution (Thr-->Ser) compared with human glucagon. Glucagon-36 represents glucagon-29 extended from its C-terminus by Lys-Arg-Ser-Gly-Gly-Ile-Ser and is identical to R. catesbeiana glucagon-36. We speculate that selective changes in the structure of the insulin molecule may contribute to the anomalous regulation of glycogen phosphorylase in the wood frog.

Adaptation, Physiological↗
PubMed1998

Structural features determining differential receptor regulation of neuronal Ca channels.

Dihydropyridine-insensitive Ca channels are subject to direct receptor G-protein-mediated inhibition to differing extents. alpha1B channels are much more strongly modulated than alpha1E channels. To understand the structural basis for this difference, we have constructed and expressed various alpha1B and alpha1E chimeric Ca channels and examined their regulation by kappa-opioid receptors. Replacement of the first membrane-spanning domain of alpha1E with the corresponding region of alpha1B resulted in a chimeric Ca channel that was modulated by kappa-opioid receptors to a significantly greater extent than alpha1E. Transfer of the N terminus and I/II loop from alpha1B in addition to domain I resulted in a chimeric channel that was modulated to the same extent as alpha1B. Other regions of the molecule do not appear to contribute significantly to the degree of inhibition obtained, although the C terminus may contribute to facilitation.

Analgesics↗
PubMed2005

Song types and their structural features are associated with specific contexts in the banded wren.

We studied the use of song types and their acoustic features in different social contexts in the banded wren (Thryothorus pleurostictus), a resident tropical songbird in which males possess about 20 distinctive song types varying in duration, bandwidth, note composition, and trill structure. We recorded six focal males intensively for four days each while we observed context information such as during versus after dawn chorus, presence of the female, counter-versus solo-singing, location at the edge versus centre of the territory, and proximity to the nest. All males used at least some song types differentially during each of these pairs of alternative contexts. Males also preferentially used the song types they shared with a given neighbour when interacting with that bird. Songs delivered during dawn chorus were significantly longer, wider in bandwidth, often compound (double songs), and more likely to contain a rattle or buzz and an up-sweeping trill, compared to songs delivered after dawn chorus. Similar features were also more commonly observed when birds were engaged in intense male-male interactions and boundary disputes after dawn chorus, especially when countersinging at the edge of the territory. The presence of the female caused the male to deliver song types with narrower whole-song and trill bandwidth and fewer rattles and buzzes, and song-type diversity and fraction of compound songs were higher when the female was present. Thus, in addition to using type matching and variations in song-type switching and diversity to signal different levels of aggressive intention, male banded wrens also select song types based on their acoustic structure in different social contexts.

Journal Article↗
PubMed1990

A gene for cytochrome c oxidase subunit III (COXIII) in broad bean mitochondrial DNA: structural features and sequence evolution.

A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains the coxIII gene is presented, and compared to corresponding sequences of Oenothera and corn mtDNAs. Upstream from the broad bean coxIII gene are three potential secondary structures: a single stem and loop (hairpin) that is conserved in the Oenothera and corn sequences; a second single stem and loop; and a double stem and loop. The rate of evolution of the coxIII gene has been slower in plants than in mammals. Constraints on the fixation of at least some kinds of mutations in silent (synonymous) third position nucleotides, as well as of mutations that cause amino acid replacements, seem to have contributed to this slower rate.

Amino Acid Sequence↗
PubMed1991

Structural features of dermatan sulfates and their relationship to anticoagulant and antithrombotic activities.

Dermatan sulfate is a polydisperse, microheterogeneous sufated copolymer of N-acetyl-D-galactopyranose and idopyranosyluronic acid that is currently under clinical investigation as a new antithrombotic agent. The structure and activity of two pairs of dermatan sulfates, isolated from bovine and porcine mucosa, were studied. One dermatan sulfate from each species demonstrated high in vivo antithrombotic activity in the rat vena cava assay. The in vitro anticoagulant activity of each dermatan sulfate was determined using activated partial thromboplastin time (APTT), thrombin time (TT) (5 units), calcium thrombin time (CaTT) (5 units), Heptest, anti-factor Xa and anti-factor IIa antithrombin assays and heparin cofactor II amidolytic assays. The coagulation-based assays gave the best correlation to in vivo antithrombotic activity. The physical and chemical properties of each dermatan sulfate were determined using 1H-NMR and 13C-NMR spectroscopy, molecular weight determination, potentiometric titration, chemical degradative analysis, chondroitin lyase degradative analysis and oligosaccharide mapping. These analyses indicated that the major difference between dermatan sulfates from a particular species having high and low in vivo antithrombotic activity was their iduronic acid content. The relation between increased iduronic acid content and increased in vivo antithrombotic activity may be the result of the conformational flexibility of this residue.

Animals↗
PubMed2002

Direct high-performance liquid chromatographic separation of peptide enantiomers: study on chiral recognition by systematic evaluation of the influence of structural features of the chiral selectors on enantioselectivity.

All-R/all-S enantiomers of oligoalanines (Ala(n), n = 1-10) with N-terminal protection group have been separated by HPLC on chiral stationary phases based on various cinchona alkaloid selectors. Structure-enantioselectivity relationships derived by extensive selector structure optimization provided insights into binding mechanisms and chiral recognition. Their interpretation was supported by X-ray crystal structures of amino acid and dipeptide, respectively, in complex with chiral selector. Optimized selectors have bulky elements representing steric barriers and deep binding pockets that afforded very high enantioselectivities; e.g., for the all-R and all-S enantiomers of N-(3,5-dinitrobenzoyl)alanylalanine, an alpha-value of 20.0 (corresponding to deltadeltaG of -7.43 kJ/mol) was obtained with a chiral stationary phase based on 6'-(neopentoxy)-9-O-tert-butylcarbamoylcinchonidine. Further, a chiral stationary phase based on 1,4-bis(9-O-quinidinyl)phthalazine was able to distinguish between the all-R and all-S enantiomers of hepta- to decaalanine peptides with enantioselectivity values between 1.8 and 1.9, corresponding to deltadeltaG of -1.46 and -1.59 kJ/mol, respectively.

Chromatography, High Pressure Liquid↗
PubMed2002

Structural features of the cytochrome C molten globule revealed by fluorescence energy transfer kinetics.

Nonnative states of proteins are involved in a variety of cellular processes, including translocation of proteins across membranes and formation of amyloid fibrils. Probes that report on the structural heterogeneity of a polypeptide ensemble could resolve ambiguities in the classification of these states. Employing fluorescence energy transfer kinetics, we have shown that added anions shift the equilibrium between the compact and extended polypeptide structures that are present during refolding of Saccaromyces cerevisiae iso-1 cytochrome c. Specifically, at high salt concentrations (>/=700 mM), all of the polypeptides are compact with a mean C-terminal fluorophore-heme separation quite close to that in the native protein (25 A).

Circular Dichroism↗
PubMed1994

Unique structural features and differential phosphorylation of the 280-kDa component (isozyme) of rat liver acetyl-CoA carboxylase.

Rat liver acetyl-CoA carboxylase (ACC, EC 6.4.1.2) exhibits major and minor subunits (M(r) of 265,000 and 280,000 respectively), the structure and function of which are compared in this study. The two subunits copurified and each contained biotin as demonstrated by avidin reactivity and direct determination of biocytin. In agreement with previous studies, the ACC subunits could be distinguished with specific monoclonal antibodies and differential tissue expression. We now report extensive differences in primary structure revealed by peptide mapping, mass spectrometric analysis of peptides following reverse phase high performance liquid chromatography, and microsequencing of selected peptides. Four peptides derived from the 265-kDa subunit were sequenced and matched sequences within the predicted structure of rat 265-kDa ACC. Although one identical peptide sequence was detected within both subunits (residues 2009-2024 of the 265-kDa subunit), 12 peptides derived from the 280-kDa subunit exhibited entirely novel sequences or matched partially (average 70% identity) with sequences within the 265-kDa subunit. The 280-kDa subunit may also exhibit distinct functional properties, since the initial rate of phosphorylation was at least 10-fold greater than that of the 265-kDa subunit in the presence of cAMP-dependent protein kinase. Two-dimensional mapping demonstrated that the tryptic phosphopeptides released from the two ACC subunits are distinct. These structural studies suggest that the 265- and 280-kDa components (isozymes) of ACC are so distinct they may be encoded by separate genes, while the differential phosphorylation observed in vitro suggests a key role for the 280-kDa subunit in regulating enzyme activity within intact cells.

Acetyl-CoA Carboxylase↗
PubMed1993

Cloning and expression of a spinal cord- and brain-specific glycine transporter with novel structural features.

A novel glycine transporter (GLYT2) was cloned from a rat brain cDNA library. GLYT2 is about 48 and 50% homologous to the previously cloned mouse glycine transporter (GLYT1) and rat proline transporter (PROT), respectively. GLYT2 differs from GLYT1 in molecular structure, tissue specificity, and pharmacological properties. The cDNA of GLYT2 encodes for 799 amino acid residues with an extended amino-terminal peptide containing 200 amino acids before the first transmembrane domain. Potential phosphorylation sites for protein kinase C, cAMP-dependent kinase, and calmodulin-dependent kinase were identified in the amino-terminal region. GLYT2 mRNA was shown to be specifically localized in spinal cord, brain stem, and to a lesser extent in the cerebellum. In contrast, GLYT1 mRNA distribution in the brain has been found previously to be more ubiquitous. Xenopus oocytes injected with GLYT2 cRNA transport glycine with a Km of 17 microM, and the uptake of glycine is resistant to inhibition by sarcosine. The experimental data suggests GLYT2 might play a major role in the termination of the inhibitory effect of glycine in the brain stem and spinal cord of vertebrates. On the other hand, the main function of GLYT1 may be in the modulation of excitatory nerve terminals. Two types of GLYT1 cDNA, GLYT1a and GLYT1b, were cloned from the mouse brain library. They differ only at their amino-terminal sequences, and GLYT1b contains two additional potential phosphorylation sites for proline-dependent kinase. Cloning of the gene encoding the GLYT1 revealed that the two variants resulted from a differential splicing.

Amino Acid Sequence↗
PubMed1994

Structural and electrophysiological analysis of annexin V mutants. Mutagenesis of human annexin V, an in vitro voltage-gated calcium channel, provides information about the structural features of the ion pathway, the voltage sensor and the ion selectivity filter.

Annexin V binds to phospholipids in a calcium-dependent manner and exhibits calcium channel activity in vitro. We prepared a variety of mutants yielding information about the structure-function relationship of the ion channel activity. All mutants were characterized by X-ray crystallography, electron microscopy and electrophysiological measurements. Their structures are insignificantly changed whereas their electrophysiological properties are drastically different. Glu95, located in the central hydrophilic pore of the molecule, is crucial for the ion selectivity filter as its exchange leads to reduced calcium and increased sodium conductance. The removal of Glu17, located on the protein surface and far from the ion conduction pathway, leads to the appearance of a second conductance level of 9 pS in addition to the conductance level of about 30 pS in the wild-type molecule. This was also the case for Glu78, which is part of a weak calcium binding site. The exchange of Glu17 and Glu78 produced a mutant retaining only the smaller conductance level. We conclude that these two residues influence the angle between the two halves of the molecule, which determines the diameter of the ion conduction pathway, thereby leading to the occurrence of a second conductance level.

Amino Acid Sequence↗
PubMed1997

Functional and structural features of the holin HOL protein of the Lactobacillus plantarum phage phi gle: analysis in Escherichia coli system.

Lactobacillus plantarum phage phi gle has two consecutive cell lysis genes hol-lys (Oki et al., 1996b). In the present study, functional and structural properties of the hol protein (Hol) were characterized in Escherichia coli. Electron microscopic examinations showed that hol under plac in E. coli XL1-Blue injured the inner membrane to yield empty ghost cells with the bulk of the cell wall undisturbed. Northern blot analysis indicated that hol-lys genes under plac were co-transcribed, although the amount of hol transcript was larger than that of lys, ceasing via an apparently rho-independent terminator just downstream of hol. However, deletion and/or fusion experiments suggested that: (1) the N-terminal half of phi gle Hol composed of three putative transmembrane domains may be responsible for interaction with membrane; (2) the N-terminal end (five amino acids) seems nonessential; and (3) the C-terminal half containing charged amino acids appears to be involved in proper hol function. These results suggest that phi gle Hol is a member of the lambdoid holin family, but divergent in several properties from lambda holin.

Amino Acid Sequence↗
PubMed1993

Interaction of calf-thymus DNA with trivalent La, Eu, and Tb ions. Metal ion binding, DNA condensation and structural features.

The interaction of calf-thymus DNA with La3+, Eu3+ and Tb3+ has been investigated in aqueous solution at pH 6.5, using metal/DNA(P) molar ratios(r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2. Correlations between FTIR spectral changes and DNA structural properties have been established. At low metal/DNA(P) (r) 1/80, the metal ions bind mainly to the PO2- groups of the backbone, resulting in increased base-stacking interaction and duplex stability. At (r) 1/40 and 1/20, metal ion binding to the PO2- and the guanine N-7 site (chelation) predominates with minor perturbations of the A-T base pairs. Evidence for this comes from the displacement of the band at 1712 cm-1 (T,G) towards a lower frequency and the PO2- antisymmetric band at 1222 cm-1 towards a higher frequency. At higher metal/DNA(P) ratio, r > 1/20, DNA begins to condensate and drastic structural changes occur, which are accompanied by the shift and intensity changes of several G-C and A-T absorption bands. No major departure from B-DNA conformation was observed before and after DNA condensation even though some local structural modifications were observed. A comparison with the Cu-DNA complexes (denaturated DNA) shows some degree of helical destabilization of the biopolymer in the presence of lanthanide ions.

Animals↗
PubMed1990

Structural features of neutral protease from Bacillus subtilis deduced from model-building and limited proteolysis experiments.

The overall folding of neutral protease from Bacillus subtilis has been predicted by computer-aided modelling, taking as a basis the known three-dimensional structure of thermolysin. As expected from the 50% similarity of sequence between the two proteins, the structure of B. subtilis protease is similar to that of thermolysin, including the two-domain topology and location of elements of regular secondary structure (helices and strands), whereas specific differences were predicted in loop regions. A protruding and loose loop predicted in B. subtilis has been detected also experimentally by a limited proteolysis approach. Incubation of B. subtilis protease at pH 9.0 for 24 h at room temperature with trypsin at 20:1 ratio (by mass) leads to a specific and almost quantitative fission of the Arg214-Asn215 peptide bond located in a highly exposed, and thus probably flexible, loop of the protease. On the other hand, thermolysin was completely resistant to tryptic hydrolysis when reacted under identical conditions. The 'nicked' B. subtilis protease can be isolated by gel filtration chromatography at neutral pH, whereas the two constituting fragments 1-214 and 215-300 are separated under protein-denaturing conditions. Overall, these results indicate that the limited proteolysis approach can pinpoint a peculiar difference in surface structure between the two similar protein molecules of B. subtilis neutral protease and thermolysin and emphasize the potential use of proteolytic enzymes as structural probes of globular proteins.

Amino Acid Sequence↗