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PubMed1997

Characterisation of structural changes in the arterial elastic matrix by a new fractal feature: directional fractal curve.

A new fractal feature, the Directional Fractal Curve (DFC), defined over an arc of 180 and composed of 90 fractal dimensions determined at intervals of arc of 2, is developed to account for the anisotropic property of a fractal texture. The DFC algorithm is first applied to two images with different textural patterns, one without directional preference and one with a well-organised texture. The DFC of these images shows different patterns. The technique is then applied to quantify the structure of the elastic texture in the arterial wall where the elastic network was imaged by scanning electron microscopy following selective tissue digestion. The results suggest: (i) that images of the elastin matrix of the arterial wall exhibit fractal properties with directional preference, (ii) the DFC gives quantitative parameters which allow characterisation of structural changes in the elastin matrix of the arterial wall in terms of disorganisation and fragmentation of elastin fibres-conditions which are associated with medial degeneration due to normal ageing or presence of arterial disease.

Algorithms↗

PubMed1996

Structural changes in factor VIIa induced by Ca2+ and tissue factor studied using circular dichroism spectroscopy.

Factor VIIa (fVIIa) is composed of four discrete domains, a gamma-carboxyglutamic acid (Gla)-containing domain, two epidermal growth factor (EGF)-like domains, and a serine protease domain, all of which appear to be involved, to different extents, in an optimal interaction with tissue factor (TF). All except the second EGF-like domain contain at least one Ca2+ binding site and many properties of fVIIa, e.g., TF and phospholipid binding and amidolytic activity, are Ca(2+)-dependent. A CD study was performed to characterize and locate the conformational changes in fVIIa induced by Ca2+ and TF binding. In addition to intact fVIIa, derivatives lacking the Gla domain or the protease domain were used. Assignment of the Ca(2+)-induced changes in the far-UV region of the fVIIa spectrum to the Gla domain could be made by comparing the CD spectra obtained with these fVIIa derivatives. The changes primarily appeared to reflect a Ca(2+)-induced ordering of alpha-helices existing in the apo state of fVIIa. This was corroborated by models of the apo and Ca2+ forms of fVIIa, obtained as difference spectra between fVIIa derivatives, were very similar to those of isolated Gla peptides from other vitamin K-dependent plasma proteins. The near-UV CD spectrum of fVIIa was dominated by aromatic residues residing in the protease domain and specific bands affected by Ca2+ were indicative of tertiary structural alterations. The formation of a fVIIa:TF complex led to secondary structural changes that appeared to be restricted to the catalytic domain, possibly shedding light on the mechanism by which TF induces an enhancement of fVIIa catalytic activity.

Calcium↗

PubMed2001

Structural changes in the neck linker of kinesin explain the load dependence of the motor's mechanical cycle.

The two-headed motor protein kinesin hydrolyzes ATP and moves on microtubule tracks towards the plus end. The motor develops speeds and forces of the order of hundreds of nanometers per second and piconewtons, respectively. Recently, the dependence of the velocity, the dissociation rate and the displacement variance on the load and the ATP concentration were measured in vitro for individual kinesin molecules (Coppin et al., 1997; Visscher et al., 1999) over a wide range of forces. The structural changes in the kinesin motor that drive motility were discovered by Rice et al. (1999). Here we present a phenomenological model for force generation in kinesin based on the bi-stable, nucleotide-dependent behavior of the neck linker. We demonstrate that the model explains the mechanical, kinetic and statistical (experimental) data of Coppin et al. (1997). We also discuss the relationship between the model results and experimental data of Visscher et al. (1999).

Adenosine Diphosphate↗

PubMed1986

Structural changes in the nucleoid of Bacillus subtilis at low temperature.

The external shape of the nucleoid of Bacillus subtilis strain w23 was examined with a new electron microscopic technique, the rapid freezing and substitution fixation method. The nucleoid of the log and stationary phase cells was recognized as an area devoid of ribosomes and widely dispersed in the cytoplasm, which was different from that observed in OsO4-fixed cells. If the bacteria were exposed to low temperatures (0 to 10 C), the nucleoid showed a highly concentrated shape in the middle of the cytoplasm. These structural changes were observed only when the bacteria were maintained in a high-salt buffer. The results are discussed in relation to the membrane fluidity at low temperature.

Bacillus subtilis↗

PubMed2003

Analysis of large structural changes of the factor VIII gene, involving intron 1 and 22, in severe hemophilia A.

BACKGROUND AND OBJECTIVES: Hemophilia A (HA), the deficiency of coagulation factor VIII (FVIII), is the most common, sex-linked inherited bleeding disorder. The disease is caused by FVIII gene intron 22 inversion in approximately 50% of the patients, and by intron 1 inversion in 5% of the patients with severe HA. Both inversions occur as a result of intrachromosomal recombination between homologous regions, in intron 1 or 22, and their extragenic copy located telomeric to the FVIII gene. The goal of the present study was to analyze the presence of large structural changes in the FVIII gene in patients with severe hemophilia A. DESIGN AND METHODS: We studied 104 unrelated, severe HA-patients or obligate carriers for the presence of intron 22 and intron 1 inversions by Southern blotting, long-distance polymerase chain reaction (PCR), and simple PCR. RESULTS: We found altered intron 22 restriction profiles by Southern analyses in 58 cases: 43 type 1, 11 type 2 inversions and 4 unusual patterns. Upon further examination of the last 4 cases, large deletions involving intron 22 were demonstrated in two cases. In the remaining two patients extra homologous regions were detected by Southern analysis, and long-distance PCR showed the presence of unaltered intra- and extragenic copies together with one inversion-affected copy, suggesting that an additional intronic fragment participated in the inversion process and was inserted in the genome. During screening for intron 1 inversion among 43 patients, who were intron 22 inversion negative, we identified only wild type individuals. INTERPRETATION AND CONCLUSIONS: The relatively large proportion of unusual patterns further supports the observation that the structure of FVIII intron 22 represents a hot spot for large gene rearrangements with various mechanisms, while intron 1 inversion seems to be not common in Hungary.

Adolescent↗

PubMed1999

Minor structural changes in nicotinoid insecticides confer differential subtype selectivity for mammalian nicotinic acetylcholine receptors.

The major nitroimine insecticide imidacloprid (IMI) and the nicotinic analgesics epibatidine and ABT-594 contain the 6-chloro-3-pyridinyl moiety important for high activity and/or selectivity. ABT-594 has considerable nicotinic acetylcholine receptor (AChR) subtype specificity which might carry over to the chloropyridinyl insecticides. This study considers nine IMI analogues for selectivity in binding to immuno-isolated alpha1, alpha3 and alpha7 containing nicotinic AChRs and to purported alpha4beta2 nicotinic AChRs. Alpha1- and alpha3-containing nicotinic AChRs (both immuno-isolated by mAb 35, from Torpedo and human neuroblastoma SH-SY5Y cells, respectively) are between two and four times more sensitive to DN-IMI than to (-)-nicotine. With immuno-isolated alpha3 nicotinic AChRs, the tetrahydropyrimidine analogues of IMI with imine or nitromethylene substituents are 3-4 fold less active than (-)-nicotine. The structure-activity profile with alpha3 nicotinic AChRs from binding assays is faithfully reproduced in agonist potency as induction of 86rubidium ion efflux in intact cells. Alpha7-containing nicotinic AChRs of SH-SY5Y cells (immuno-isolated by mAb 306) and rat brain membranes show maximum sensitivity to the tetrahydropyrimidine analogue of IMI with the nitromethylene substituent. The purported alpha4beta2 nicotinic AChRs [mouse (Chao & Casida, 1997) and rat brain] are similar in sensitivity to DN-IMI, the tetrahydropyrimidine nitromethylene and nicotine. The commercial insecticides (IMI, acetamiprid and nitenpyram) have low to moderate potency at the alpha3 and purported alpha4beta2 nicotinic AChRs and are essentially inactive at alpha1 and alpha7 nicotinic AChRs. In conclusion, the toxicity of the analogues and metabolites of nicotinoid insecticides in mammals may involve action at multiple receptor subtypes with selectivity conferred by minor structural changes.

Animals↗

PubMed2001

ATP-induced structural change of the thermosome is temperature-dependent.

Protein folding by chaperonins is powered by ATP binding and hydrolysis. ATPase activity drives the folding machine through a series of conformational rearrangements, extensively described for the group I chaperonin GroEL from Escherichia coli but still poorly understood for the group II chaperonins. The latter--archaeal thermosome and eukaryotic TRiC/CCT--function independently of a GroES-like cochaperonin and are proposed to rely on protrusions of their own apical domains for opening and closure in an ATP-controlled fashion. Here we use small-angle neutron scattering to analyze structural changes of the recombinant alpha-only and the native alphabeta-thermosome from Thermoplasma acidophilum upon their ATPase cycling in solution. We show that specific high-salt conditions, but not the presence of MgATP alone, induce formation of higher order thermosome aggregates. The mechanism of the open-closed transition of the thermosome is strongly temperature-dependent. ATP binding to the chaperonin appears to be a two-step process: at lower temperatures an open state of the ATP-thermosome is predominant, whereas heating to physiological temperatures induces its switching to a closed state. Our data reveal an analogy between the ATPase cycles of the two groups of chaperonins and enable us to put forward a model of thermosome action.

Adenosine Triphosphatases↗

PubMed2005

Cooperative structural change of actin filaments interacting with activated myosin motor domain, detected with copolymers of pyrene-labeled actin and acto-S1 chimera protein.

Acto-S1 chimera proteins CP24 and CP18 carry the entire actin sequence, inserted in loop 2 of the motor domain of Dictyostelium myosin II, and have MgATPase activity close to that of natural Dictyostelium actomyosin [M.S.P. Siddique, T. Miyazaki, E. Katayama, T.Q.P. Uyeda, M. Suzuki, Evidence against essential roles of subdomain 1 of actin in actomyosin sliding movements, Biochem. Biophys. Res. Commun. 332 (2005) 474-481]. Here, we examined and detected cooperative structural change of actin filaments accompanying interaction with myosin motor domain in the presence of ATP using copolymer filaments consisting of pyrene-labeled skeletal actin (SA) and either CP24 or CP18. Upon addition of ATP, the fluorescence intensity increased over the range from 380 to 480nm using 365-nm excitation. The relative increases of fluorescence intensity at 390nm were 14%, 46%, and 77% for the copolymer filaments with the CP24 to actin molar ratios of 0.0625, 0.143, and 0.333, respectively, and demonstrated a sigmoid behavior. Stoichiometric analysis indicates that each CP24 molecule appears to affect four actin molecules, on average, in SA-CP24 copolymers, and each CP18 molecule appears to affect three actin molecules in SA-CP18 copolymers.

Actin Cytoskeleton↗

PubMed2000

Evidence for major structural changes in the Manduca sexta midgut V1 ATPase due to redox modulation. A small angle X-ray scattering study.

The shape and overall dimensions of the oxidized and reduced form of the V(1) ATPase from Manduca sexta were investigated by synchrotron radiation x-ray solution scattering. The radius of gyration of the oxidized and reduced complex differ noticeably, with dimensions of 6. 20 +/- 0.06 and 5.84 +/- 0.06 nm, respectively, whereas the maximum dimensions remain constant at 22.0 +/- 0.1 nm. Comparison of the low resolution shapes of both forms, determined ab initio, indicates that the main structural alteration occurs in the head piece, where the major subunits A and B are located, and at the bottom of the stalk. In conjunction with the solution scattering data, decreased susceptibility to tryptic digestion and tryptophan fluorescence of the reduced V(1) molecule provide the first strong evidence for major structural changes in the V(1) ATPase because of redox modulation.

Animals↗

PubMed1983

Effects of inhibiting hepatocarcinogenesis upon the early fine structural changes induced in rat hepatocytes by 3'-methyl-4-dimethylaminoazobenzene.

Young adult male Leeds strain rats were fed for up to 10 weeks on diets containing either 0.06% 3'-methyl-4-dimethylaminoazobenzene (3'-MeDAB) or 0.06% 3'-MeDAB together with 0.0067% 3-methylcholanthrene (MeCh), which is known to inhibit the induction of hepatocarcinogenesis by the azo dye. Controls received either MeCh alone or a normal diet. Animals were killed at 10 days, 4 weeks and 10 weeks and their liver tissues examined by electron microscopy. Although MeCh did not prevent the induction of some non-specific fine structural changes such as glycogen depletion and proliferation of the smooth endoplasmic reticulum (ER), it did prevent the early dislocation and dispersal of the rough ER that was elicited by 3'-MeDAB. This provides further evidence indicating the importance to liver tumorigenesis of this rough ER change, which appears to be induced by all classes of chemical hepatocarcinogens and which, in comparative studies with carcinogen/non-carcinogen pairs of related chemicals, also appears to be specific to carcinogens.

Animals↗

PubMed2002

Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clusters.

Proteins containing Rieske-type [2Fe-2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe-2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X-ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron-histidine bond length of at least 0.1 A upon reduction of two distantly related Rieske-type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P-1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox-dependent structural change may fine tune the protein-protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske-type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells.

Acinetobacter↗

PubMed1989

Common structural changes accompany the functional inactivation of HPr by seryl phosphorylation or by serine to aspartate substitution.

Although many proteins are known to be regulated via reversible phosphorylation, little is known about the mechanism by which the covalent modification of seryl, threonyl, or tyrosyl residues alters the activities of the target systems. To address this question, modified versions of Bacillus subtilus HPr, a protein component of the bacterial phosphotransferase system, have been studied by 1H NMR spectroscopy. Phosphorylation at Ser46 or a Ser to Asp substitution at this position inactivates HPr [Reizer, J., Sutrina, S. L., Saier, M. H., Stewart, G. C., Peterkofsky, A., & Reddy, P. (1989) EMBO J. 8, 2111-2120]. Two-dimensional spectra of these two modified proteins display nearly identical proton chemical shifts that differ significantly from those observed in the spectra of the unphosphorylated, wild-type protein and of functionally active HPr mutants. The results demonstrate that the functional inactivation of HPr brought about by the serine to aspartate mutation is accompanied by the same structural changes that occur when HPr is phosphorylated at Ser46.

Aspartic Acid↗

PubMed1989

Structural changes in the thin filament during activation studied by X-ray diffraction of highly stretched skeletal muscle.

The actin layer-lines were recorded from a frog semitendinosus muscle stretched to a sarcomere length greater than 4.4 microM. On activation of the muscle, the equator, the second layer-line at 1/18 nm-1 and the 5.9 nm layer-line increased in integrated intensity. On the other hand, the integrated intensity of the first layer-line at 1/36 nm-1 decreased markedly on activation. This decrease was not fully attributable to shifts of tropomyosin strands and therefore suggested a structural change in the actin subunit. The decrease may account for the apparent lack of an intensity increase of this layer-line on activation at normal muscle lengths where attachment of myosin heads to actin increases the intensities of other layer-lines.

Actins↗

PubMed2005

LOXL null mice demonstrate selective dentate structural changes but maintain dentate granule cell and CA1 pyramidal cell potentiation in the hippocampus.

Lysyl oxidase-like protein (LOXL), part of the lysyl oxidase copper-dependent amine oxidase family, is expressed in the extracellular matrix and in the nucleus. It likely plays a role in cross-linking collagen and elastin, possibly modulating cellular functions. Immunohistochemical studies show the presence of LOXL in the pyramidal cell layer of the hippocampus; and in this study, we report that cells in the granule cell layer have significantly smaller somas in LOXL -/- compared to LOXL +/+ mice. In addition we tested the hypothesis that these structural alterations in the dentate granule layer were associated with synaptic efficacy and thus muted long-term potentiation in mice lacking the protein. Electrical recordings were obtained in 300-mum hippocampal slices in dentate and CA1 pyramidal cell layers in age-matched wild type and LOXL null mice. Potentiation in the CA1 cell layer of 10 LOXL -/- and 8 LOXL +/+ mice was 191.0+/-9.3% and 181.6+/-9.1%, respectively (mean+/-S.E.M.). Dentate potentiation was 120.8+/-7.0% and 121.0+/-3.4% in 11 LOXL -/- and 11 LOXL +/+ mice, respectively. No phenotypic difference in potentiation of population spike amplitude (or in EPSP slope) in either layer was observed. Thus, contrary to expectation, structural changes in the hippocampus of LOXL -/- mice did not affect synaptic remodeling in a manner that impaired the establishment of LTP.

Amino Acid Oxidoreductases↗

PubMed1976

Ligand-induced structural changes in amylose partially complexed with iodine.

The influence of complexing agents such as methanol, ethanol, 1-propanol, 1-butanol, 1-pentanol, 1-hexanol, cyclohexanol and 2-octanol on the formation of a blue coloured amylose - iodine complex (pH 4.8), under suboptimum concentrations of iodine and in the absence of potassium iodide, is studied by recording the absorbance at 640 nm. A drop in absorbance at 640 nm accompanied by a blue shift in the spectrum (640-580 nm) was observed at higher concentrations of the complexing agents. This behaviour of amylose partially complexed with iodine appears to be due to ligand-induced structural changes in the amylose chain. The fall in absorbance at 640 nm observed when the temperature of amylose - iodine complex in the presence of complexing agents is raised, and the subsequent regeneration of the absorbance on cooling, indicates the possible helix to random coil transition of the amylose chain in an aqueous system.

Alcohols↗

PubMed2004

Structural changes and viscoplastic behavior of a generic embedded-atom model metal in steady shear flow.

We study equilibrium and nonequilibrium properties of a simple "generic embedded-atom model" (GEAM) for metals. The model allows to derive simple analytical expressions for several zero-temperature constitutive properties--in overall agreement with real metals. The model metal is then subjected to shear deformation and strong flow via nonequilibrium molecular dynamics simulation in order to discuss the origins of some qualitative properties observed using more specific embedded-atom potentials. The "common neighbor analysis," based on planar graphs is used to obtain information about the transient structures accompanying viscoplastic behavior on an atomic level. In particular, pressure tensor components and plastic yield are investigated and correlated with underlying structural changes. A simple analytical expression for the isotropic pressure at finite temperatures is proposed. A nonequilibrium phase diagram is obtained by semianalytic calculation.

Journal Article↗

PubMed1990

Single site proteolysis in silkworm antitrypsin causes structural changes in behavior against denaturing reagents.

Silkworm antitrypsin (sw-AT), which was thought to belong to serpin family, changed its behavior against denaturation after chymotryptic cleavage of a single peptide bond (Tyr-Val) two amino acids away from the reactive site for trypsin (Lys-Val). This chymotrypsin-modified sw-AT became resistant to denaturation by heat, sodium dodecyl sulfate, or guanidine hydrochloride, and this characteristic was evident in its circular dichroism spectrum. The modified sw-AT was also indigestible by S. aureus V8 protease. These facts should indicate a structural change from a stressed, unstable state to a stable one accompanying the cleavage of the single peptide bond in sw-AT. The stabilizing factor was in part attributed to the interaction of a COOH-terminal fragment (5 kDa) and an NH2-terminal one (36 kDa) in modified sw-AT.

Animals↗

PubMed1979

Structural changes for speech improvement in complete upper denture fabrication.

In the absence of any clearly identifiable pathologic condition, the prosthodontic patient demonstrating speech problems after insertion of complete dentures is having difficulty with loss of turbulence, because of the diminution of tactile location skills in speaking, or both. Potential aids to speech improvement are a nonanatomic papilla placed on the oral surface of the denture just posterior to the location of the incisive papilla, a transversely elongated rugae-like papilla at about the same location, a roughened region at that spot, or an identation sufficient for the patient's tongue to identify. The location and effectiveness of such structural changes can be planned and judged with the cooperation of a qualified speech pathologist.

Alveolar Process↗