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PubMed2004

Structural changes in the midbrain with aging and Parkinson's disease: an MRI study.

We measured midbrain structures of 59 subjects with Parkinson's disease (PD) and 140 age- and gender-matched normal subjects without neurological disorders by using T2-weighted MR imaging. There is a significant increase in the maximum distance of the substantia nigra (SND) and a significant decrease in the average distance from the substantia nigra to the red nucleus (SNRND) in patients with PD compared with normal subjects in the 70 years old or less group. These findings may reflect the pathologic increase of iron concentration and the neuronal loss in the region. However, it is difficult to find differences between normal subjects and patients with PD in the greater than 70 years old group in the midbrain structures. These findings based on a large-scale morphometric study provide essential information to evaluate conventional MR images of PD.

Adult↗

PubMed1986

Structural changes in lipid bilayers and biological membranes caused hydrostatic pressure.

By use of neutron diffraction, the structural parameters of oriented multilayers of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine with deuteriocarbon chains/cholesterol (molar ratio 70:30), multilamellar lipid vesicles composed of pure lipids and lipid/cholesterol mixtures, and crystalline purple membrane patches from Halobacterium halobium have been measured at pressures up to 2 kbar. Pressurization of the oriented 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine/cholesterol multilayers results in an in-plane compression with the mean deuteriocarbon chain spacing of 4.44 A obtained under ambient conditions decreasing by 3-7% at 1.9 kbar. The thickness for this bilayer increases by approximately equal to 1.5 A, but the net bilayer volume decreases and the isothermal compressibility is estimated to be in the range (-0.1 to -0.6) X 10(-4)/bar at 19.0 degrees C. The d spacings for multilamellar vesicles composed of lipids in the liquid crystalline state and lipid/cholesterol mixtures increase linearly as a function of pressure, suggesting that these bilayers are also compressed in the membrane plane. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine and 1,2-distearoyl-sn-glycero-3-phosphatidylcholine MLVs in the gel state, the d spacing decreases with pressure. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine, the hexagonally packed chains are anisotropically compressed in the bilayer plane, resulting in a pseudohexagonal chain packing at 1.9 kbar. The bilayer compressibility is (-0.4 or -0.5) X 10(-4)/bar depending on whether the chain tilt increases with pressure or terminal methyl groups of apposing lipid monolayers approach each other.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriorhodopsins↗

PubMed1997

Similarity of bacteriorhodopsin structural changes triggered by chromophore removal and light-driven proton transport.

Bacteriorhodopsin (bR) is the light-driven proton pump found in the purple membrane of Halobacterium salinarium. A series of conformational changes occur during the bR photocycle which involve alterations in buried-helical structure as well as in the protonation state of Asp residues which are part of the proton transport pathway. Here we report evidence that similar conformational changes occur upon removal of the retinylidene chromophore of bacteriorhodopsin to form the apoprotein bacterioopsin (bO). This suggests a simple ligand-binding model of proton transport in bacteriorhodopsin which may have relevance to other transport and signal transducing membrane proteins including the visual photoreceptor rhodopsin.

Bacteriorhodopsins↗

PubMed1998

Age-related functional and structural changes in human dermo-epidermal junction components.

Cultured normal human keratinocytes obtained from 14 facial skin biopsies of donors aged 9-79 y were used to study the influence of donor age on the integrin receptors, cell adhesive properties in vitro, and type VII collagen synthesis. Immuno-spectrofluorimetric quantitation of integrins showed a decrease in the beta1- and beta4-subunits in low (0.08 mM) and high (1.8 mM) calcium conditions with aging. Calcium ions decreased the fluorescence intensity by relocating integrins at cell boundaries. Measurements of adhering cells showed that adhesion to bovine serum albumin-, type IV collagen- or laminin 1-coated plastic surfaces initially increased until donor age reached 30 y and then decreased. Specific adhesion to type IV collagen and laminin 1 did not vary with age, but the increase in adhesion to type IV collagen produced by manganese ions increased with age, suggesting an age-dependent feature of beta1 integrin. Synthesis of type VII collagen, increased or not by TGFbeta1 (10 ng per ml), did not vary with the donor age. Global normalized principal component analysis showed that variables related to integrins were strongly correlated, as were those of adhesion. Pre-embedding immunoelectron microscopy of freshly isolated keratinocytes showed that certain hemidesmosomes from aged cells had little or no reaction with anti-beta4-chain antibody. Post-embedding type IV collagen immunostaining and image analysis showed less type IV collagen in adult dermo-epidermal junctions. These findings indicate that there are structural and functional changes in the dermo-epidermal junction components with aging, probably giving a less effective epidermal anchoring system.

Adolescent↗

PubMed1996

Fourier transform IR spectroscopic study of hydration-induced structure changes in the solid state of omega-gliadins.

The hydration of omega-gliadins and party deamidated and esterified omega-gliadins has been studied by Fourier transform IR spectroscopy. The secondary structure of the fully hydrated proteins was a mixture of beta-turns and extended chains, with a small amount of intermolecular beta-sheets. The absorption of the glutamine side chain amide groups contributed considerably to the amide I band with two well-defined peaks at 1658 and 1610 cm-1. the amide I band of the dry native sample could not be resolved into single component bands. There the backbone structure seemed to be distorted by extensive hydrogen bonding involving glutamine side chains. With increasing water content, these hydrogen bonds were broken successively by water molecules, resulting in an increase in extended, hydrated structures, which gave rise to the formation of intermolecular beta-sheet structures. Above 35% (w/w) water the beta-sheet content fell sharply and was replaced by extensively hydrated extended structures. An amide I band similar to dissolved poly-L-proline proved that parts of the polymer were in a solution-like state. The replacement of many glutamine side chains in the esterified protein produced more resolved secondary structures even in the dry sample. The beta-sheet content of the dry sample was higher than in the native omega-gliadins, but hydration generally caused very similar changes. At all hydration levels the spectra indicated a more ordered structure than in the native sample. Overall, the modification caused changes that go beyond the simple presence or absence of glutamine bands.

Gliadin↗

PubMed1985

Functional and structural changes of the human proximal small intestine after cytotoxic therapy.

The effects of cytotoxic therapy on the structure and function of the proximal jejunum were studied in six patients receiving intravenous cyclophosphamide (300 mg/m2), methotrexate (40 mg/m2), and 5-fluorouracil (600 mg/m2) as adjuvant therapy for breast cancer. Using a steady state, triple lumen tube perfusion system the absorption of water and electrolytes was measured before and 48 h after administration of the cytotoxic agents. Jejunal biopsies were obtained at each perfusion. Median (range) water absorption fell from 126 (40-142) to 84 (46-142) ml/h/30 cm, with parallel changes for electrolytes; none of the changes was significant. Brush border disaccharidases did not change at 48 h after chemotherapy, while mature enterocytes appeared normal by both light and electron microscopy. Crypt cells and immature enterocytes, however, showed focal vacuolation by light microscopy, corresponding to the occurrence of large residual bodies (secondary lysosomes) containing partially degraded fragments of damaged crypt cells. The confinement of ultrastructural changes to the immature cell population may explain the failure of this study to show a consistent change in the absorptive function of the jejunum 48 h after chemotherapy.

Adult↗

PubMed1992

Immunological analysis of proteoglycan structural changes in the early stage of experimental osteoarthritic canine cartilage lesions.

Specific modifications of the proteoglycan (PG) structure of osteoarthritic (OA) dog cartilage in relation to endogenous metalloprotease activity were examined using murine anti-proteoglycan monoclonal antibodies (MoAbs). OA lesions were induced over a period of 8 weeks in crossbred dogs (Pond-Nuki model). The articular cartilage was removed and homogenized in a Tris buffer, pH 7.5, and then divided into four groups: direct PG extraction, no addition, presence of 1 mM p-aminophenyl mercuric acetate (APMA), and presence of 1 mM APMA and 10 mM o-phenanthroline, incubated for 42 h at 37 degrees C followed by PG extraction. MoAbs reactive with PG protein and carbohydrate epitopes included 1C6, 3B3, 5D4, D1B2, and m4D6. The results showed marked alterations induced by APMA activation of the endogenous metalloproteases. PG changes were apparent at at least three sites: one was either in the hyaluronic acid-binding region or between the hyaluronic-binding region and the G2 globular domain, another was between the keratan-sulfate-rich domain and the chondroitin sulfate-attachment domain, and a third was in the chondroitin sulfate-attachment domain. Constitutive metalloprotease activity resulted in less marked PG alterations with preservation of functional PG aggregation to hyaluronan.

Animals↗

PubMed2004

Cryoelectron microscopy analysis of the structural changes associated with human rhinovirus type 14 uncoating.

Release of the human rhinovirus (HRV) genome into the cytoplasm of the cell involves a concerted structural modification of the viral capsid. The intracellular adhesion molecule 1 (ICAM-1) cellular receptor of the major-group HRVs and the low-density lipoprotein (LDL) receptor of the minor-group HRVs have different nonoverlapping binding sites. While ICAM-1 binding catalyzes uncoating, LDL receptor binding does not. Uncoating of minor-group HRVs is initiated by the low pH of late endosomes. We have studied the conformational changes concomitant with uncoating in the major-group HRV14 and compared them with previous results for the minor-group HRV2. The structure of empty HRV14 was determined by cryoelectron microscopy, and the atomic structure of native HRV14 was used to examine the conformational changes of the capsid and its constituent viral proteins. For both HRV2 and HRV14, the transformation from full to empty capsid involves an overall 4% expansion and an iris type of movement of viral protein VP1 to open up a 10-A-diameter channel on the fivefold axis to allow exit of the RNA genome. The beta-cylinders formed by the N termini of the VP3 molecules inside the capsid on the fivefold axis all open up in HRV2, but we propose that only one opens up in HRV14. The release of VP4 is less efficient in HRV14 than in HRV2, and the N termini of VP1 may exit at different points. The N-terminal loop of VP2 is modified in both viruses, probably to detach the RNA, but it bends only inwards in HRV2.

Capsid↗

PubMed1994

Continuous darkness and continuous light induce structural changes in the rat thymus.

It is known that neuroendocrine responses to environmental stimuli, such as light, can influence immune responses through the pineal gland. It is also known that periods of constant darkness and constant light cause stimulation and inhibition of melatonin secretion from the pineal gland, successively. In this study, we provide experimental evidence that changes in the rhythm of the photoperiod have considerable effects on thymic structure of the rat. Male albino Wistar rats were divided into 3 groups. Group 1 rats were kept in a dark room, group 2 in a room under a bright artificial light and group 3 (control) animals were exposed to a 12:12 h light: dark cycle. All animals were killed after 4 wk. In group 1, thymus weight increased by 315%, the increase in volume affecting the medulla (cortex 190%, medulla 655%). The absolute number of epithelial cells and lymphocytes increased both in the cortex and medulla. Thymic cortical epithelial cells were hypertrophied and contained numerous large clear vesicles. Perivascular spaces were enlarged. In group 2 thymus weight decreased by 53%, the reduction in volume affecting mainly the cortex (cortex 61%, medulla 27%). The absolute numbers of cortical epithelial cells and lymphocytes were decreased, and pyknotic lymphocyte nuclei were frequent both in the cortex and medulla. It is concluded that constant darkness causes hypertrophy and increased cellularity of the thymus, while constant light causes involution of the thymus and death of lymphocytes. These changes possibly reflect the well known immunostimulatory effects of melatonin acting directly or indirectly, on the thymic lymphocytes and epithelial cells.

Animals↗

PubMed2002

Engineered improvements in DNA-binding function of the MATa1 homeodomain reveal structural changes involved in combinatorial control.

We have engineered enhanced DNA-binding function into the a1 homeodomain by making changes in a loop distant from the DNA-binding surface. Comparison of the free and bound a1 structures suggested a mechanism linking van der Waals stacking changes in this loop to the ordering of a final turn in the DNA-binding helix of a1. Inspection of the protein sequence revealed striking differences in amino acid identity at positions 24 and 25 compared to related homeodomain proteins. These positions lie in the loop connecting helix-1 and helix-2, which is involved in heterodimerization with the alpha 2 protein. A series of single and double amino acid substitutions (a1-Q24R, a1-S25Y, a1-S25F and a1-Q24R/S25Y) were engineered, expressed and purified for biochemical and biophysical study. Calorimetric measurements and HSQC NMR spectra confirm that the engineered variants are folded and are equally or more stable than the wild-type a1 homeodomain. NMR analysis of a1-Q24R/S25Y demonstrates that the DNA recognition helix (helix-3) is extended by at least one turn as a result of the changes in the loop connecting helix-1 and helix-2. As shown by EMSA, the engineered variants bind DNA with enhanced affinity (16-fold) in the absence of the alpha 2 cofactor and the variant alpha 2/a1 heterodimers bind cognate DNA with specificity and affinity reflective of the enhanced a1 binding affinity. Importantly, in vivo assays demonstrate that the a1-Q24R/S25Y protein binds with fivefold greater affinity than wild-type a1 and is able to partially suppress defects in repression by alpha 2 mutants. As a result of these studies, we show how subtle differences in residues at a surface distant from the functional site code for a conformational switch that allows the a1 homeodomain to become active in DNA binding in association with its cofactor alpha 2.

Amino Acid Sequence↗

PubMed1993

Activity-dependent structural changes during neuronal development.

Activity during the early postnatal period can have a pronounced effect on the structure of neurons in the central nervous system. Recent studies in the cat visual system and in the vertebrate and invertebrate neuromuscular system, have provided new insights into the cellular and molecular features of this process.

Animals↗

PubMed1997

Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino acid sequence adjacent to the principal DNA binding helix.

We present the first structural evidence supporting the hypothesis that the binding specificity of the winged helix DNA binding motif is mediated by residues adjacent to the alpha-helix (H3), the moiety which is primarily involved in the interaction with DNA. Using NMR to determine secondary structural elements of a winged helix family member, Genesis (formerly HFH-2), and comparing these with those found in the X-ray crystal structure of the HNF-3gamma/DNA complex [Clark, K. L., Halay, E. D., Lai, E., & Burley, S. K. (1993) Nature 364, 412-420], we show that the major differences observed occur for H3 and the region immediately prior to this. H3 in Genesis is slightly shorter than in HNF-3gamma and, in addition, we observe an extra small helix (H4) in the region between H2 and H3 which is not found in the HNF-3gamma/DNA complex. This is significant as it has been shown previously [Overdier, D. G., Porcella, A., & Costa R. H. (1994) Mol. Cell. Biol. 14, 2755-2766] that the DNA-binding specificity is influenced by amino acid residues in this region.

Amino Acid Sequence↗

PubMed1973

Morphologica and structural changes during the yeast-to mold conversion of Phialophora dermatitidis.

The details of the morphological and structural events occurring during yeast-to-mold conversion of the human pathogenic fungus Phialophora dermatitidis as seen by phase-contrast microscopy and electron microscopy are described and illustrated. Budding yeasts growing exponentially were observed to have thin walls and a cytoplasm exhibiting the characteristics of rapidly growing cells including numerous mitochondria, abundant ribosomes, few vacuoles, and little accumulation of storage material. In contrast, thick-walled yeasts were characterized by less apparent or significantly fewer mitochondria and ribosomes and the presence of considerable amounts of storage materials. Microscope observations of yeast-to-mold conversion revealed that only thick-walled yeasts having prominent lipid bodies in their cytoplasm converted to hyphal forms. Typically, the thick-walled yeast formed two to a number of moniliform hyphal cells which in turn often produced true hyphae. The results indicated that yeasts of P. dermatitidis must acquire spore-like characteristics by becoming thick-walled and by accumulating considerable endogenous substrate reserves before they convert and produce hyphae.

Cell Wall↗

PubMed1996

Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase.

The availability of several X-ray structures at atomic resolution of tRNA(Asp) from yeast, both in its free state and complexed with its cognate tRNA-synthetase, enables a detailed examination of the conformational changes due to interaction with the enzyme. Although the molecule conserves its general L shape, its conformation undergoes important modifications. They may be described as a bending of the two arms which brings the 3' acceptor end and the anticodon part closer together, completed by a drastic change of the anticodon loop, which puts the anticodon bases in a more exposed position, facilitating their interaction with the synthetase. The packing interactions in the crystals are also discussed. Finally, the results of protection studies by chemical probes in solution are discussed in view of the RNA-protein contacts observed in the crystals.

Aspartate-tRNA Ligase↗

PubMed1982

Sodium butyrate induced structural changes in HeLa cell chromatin.

Postsynthetic modifications of core histones by treatment of HeLa S3 cells with 5mM sodium butyrate lead to alterations in the structure of high molecular weight chromatin. Whole chromatin from butyrate-treated cells, which results in highly acetylated core histones, has an ellipticity [theta]282.5 of 3700 deg cm2 dmol-1 (0.2 mM EDTA, pH 7.4) that is 1200 deg c m2 dmol-1 less than chromatin from untreated HeLa cells, suggesting a more condensed structure. No difference in the circular dichroism spectra was observed in H1-stripped, high molecular weight chromatin obtained from control and butyrate-treated cells at low (0.2 mM EDTA, pH 7.4) ionic strength. Thermal denaturation profiles of high molecular weight chromatin were resolved into three transitions and exhibited a shifting of hyperchromicity from transition I to transitions III, at a higher Tm, with butyrate treatment of HeLa cells, further indicating a more compact structure. Thermal denaturation profiles of H1-stripped chromatin were not affected by butyrate treatment. Ionic strength studies in the range of 0-5 mM NaH2PO4, 0.2 mM EDTA, pH 7.4, of high molecular weight chromatin exhibited a decrease in [theta]282.5 and a shifting of hyperchromicity from transition I to transition III with increasing ionic strength. Control high molecular weight chromatin was more sensitive to changes in ionic strength than its highly acetylated counterpart. These results suggest that acetylation of histones alone does not result in a change in histone-DNA interactions but other changes associated with butyrate treatment most probably cause a more condensed structure, of the fraction studied herein, which is mediated by H1 or other materials removed during stripping in 0.35 M NaCl.

Acetylation↗

PubMed1993

Evidence for structural changes in crossbridges during force generation.

During muscle contraction, it is generally thought that myosin heads undergo large scale conformational changes, such as an oar-like rotation between 90 degrees and 45 degrees while attached to actin. However, evidence for conformational changes of the attached crossbridges associated with force generation has been ambiguous. In this study, we compared the conformations of attached crossbridges in (i) the pre-force generating state, (ii) force generating state, (ii) rigor state. High resolution equatorial X-ray diffraction patterns have been obtained from single chemically skinned rabbit psoas fibers under relaxed, fully Ca(2+)-activated and rigor conditions. The experimental condition was chosen (ionic strength = 50 mM and temperature = 5 degrees C) such that there are large fractions (80-100%) of crossbridges attached in all the three states, and the attached crossbridges in the relaxed muscle represent the pre-force generating state. Upon activation, changes in the two innermost intensities I10 and I11 did not follow the familiar reciprocal changes. Instead, there was almost no change in I11 while I10 decreased by 30%. Similarly, greater changes were found in I10 as the fiber goes into rigor from the activate state. Changes were also found in the higher order reflections suggesting that the structure of the force generating crossbridges is not a mixture of those found in the weakly bound and rigor crossbridges. Therefore, our data provides evidence that the average conformation of the force generating crossbridges is different from the weakly attached and from rigor crossbridges.

Actins↗

PubMed1977

Structural changes accompanying the removal of pyridoxal 5'-phosphate from phosphorylase b.

The changes in physical properties accompanying the removal of pyridoxal 5'-phosphate from glycogen phosphorylase b have been examined. The apoenzyme retains a high degree of structural rigidity, as determined from the time decay of anisotropy. The bulk of the secondary structure remains intact, although a significant change in circular dichroism indicates some degree of alteration. The mobility of a sulfhydryl-linked spin label increases. The restoration of pyridoxal 5'-phosphate reverses this effect, with indication of interaction between subunits. One or more new binding sites for 1-anilinonaphthalene-8-sulfonate appear for the apoenzyme. The kinetics of the recombination of pyridoxal 5'-phosphate with the apoenzyme, as monitored by difference spectra, indicate a high activation energy for the process. The apoenzyme is a reversibly associating system at 20-30 degrees C, pH 7.0.

Animals↗

PubMed2006

Exploring time-dependent structural changes during the cold crystallization process of isotactic polystyrene by infrared spectroscopy and multivariate curve resolution.

The present study attempts an application of Fourier transform infrared (FT-IR) spectroscopy in conjunction with multivariate curve resolution (MCR) techniques to explore the structural evolution of isotactic polystyrene (iPS) during the cold crystallization process. The focus of the present study is placed on the performance of MCR techniques, e.g., orthogonal projection (OP), alternating least squares (ALS), and fixed-size moving window evolving factor analysis (FSMWEFA), and the interpretability of spectral changes in the investigated chemical process. As a result, valuable information and conclusions about the structural evolution of iPS during the crystallization process can be extracted: when the amorphous phase of iPS changes, the ordering of the phenyl rings takes place first, and then the polymer chains adjust their local conformations to form short 3(1) helix structures. Furthermore, according to intensity profiles of the spectral variations, the ordering of the phenyl rings proceeds more intensely than the formation of ordered local chains, and the structural evolution of iPS occurs even during the induction period. The spectral variations resulting from the conformational changes in the 3(1) helical structures depend on the sequence length of the helical chains: the longer the polymer chain is, the smaller the corresponding band variations are. It has been demonstrated that the combination of FTIR spectroscopy and chemometric MCR techniques is very promising for the analysis of the crystallization process of polymers. MCR is a powerful tool for analyzing and visualizing spectral data and integrating them with other information, making spectral intensity variations more amenable to interpretation in order to explore the molecular dynamics of polymers.

Algorithms↗