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PubMed2004

Mass spectrometry on segment-specific hydrogen exchange of dihydrofolate reductase.

To address the effects of local structures on structural fluctuations of Escherichia coli dihydrofolate reductase (DHFR), the backbone-fluctuation map was determined by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) coupled with H/D exchange and pepsin digestion. H/D exchange kinetics was examined at 15 degrees C with 18 identified digestion fragments covering almost the entire amino acid sequence of DHFR. These fragments exhibited significant variations in the first-order rate constant of proton exchange, k(ex) (0.47-0.71 min(-1)), the fraction of deuterium incorporation at the initial stage, D(o) (0.20-0.60), the fraction of deuterium incorporation at infinite time, D(infinity) (0.75-0.97), and the number of protons protected from exchange, P (0.4-4.7), relative to the corresponding values for the whole DHFR molecule (k(ex) = 0.51 min(-1), D(o) = 0.41, D(infinity) = 0.85, and P = 20.7). H/D exchange was very fast in the fragment comprising residues 5-28 (Met20 loop), which participates in substrate uptake, and reasonably fast in disordered and hydrophobic fragments, but slow in beta-strand-rich fragments. These results indicate that the local structures contribute differently to the fluctuation of the DHFR molecule, and that mass spectrometry coupled with H/D exchange and protease digestion is a useful tool for detecting segment-dependent protein fluctuation.

Amino Acid Sequence↗
PubMed2001

Characterization of relaxed photo-excited magnetized states in prussian-blue analogous magnets.

Local structure of a photo- or x-ray-induced ferrimagnet Cs0.8Co1.3 [W(CN)8](3-cyanopyridine)1.9 x 2.1H2O was investigated by means of Co K- and W L-edge XAFS spectroscopy. The Co K-edge XANES spectra provide quantitative information on the ratio of Co(II) and Co(III) by virtue of the factor analysis. It was found that the Co(II) ratios are 81.9% at 300 K and 32.7% at 150 K. When the sample was irradiated by x rays at 30 K, a phase transformation occurred in a similar manner to the visible-light irradiation and a relaxed excited state that exhibits ferrimagnetism was formed. The relaxed excited state gives the Co(II) ratio of 67.0%. The W L(III)-edge EXAFS spectra determine the W-C, W-N and W-Co distances. The results of the distances were obtained as R(W-C)=2.16 A, R(W-N)=3.31 A, R(W-CoII)=5.37 A and R(W-CoIII)=5.19 A, irrespective of the three phases. The local structure of the relaxed excited state was found to be identical with that of the high-temperature (300 K) phase. The phase transformation is concluded to be caused by the charge transfer and the spin flipping from the -W(IV)(S=0)-CN-CoIII (S=0)- configuration to -W(V)(S=1/2)-CN-CoII (S=3/2)-.

Journal Article↗
PubMed2000

Structure, chromosomal localization, and promoter analysis of the human elastin microfibril interfase located proteIN (EMILIN) gene.

Elastin microfibril interfase-located protein (EMILIN) is an extracellular matrix glycoprotein abundantly expressed in elastin-rich tissues such as the blood vessels, skin, heart, and lung. It occurs with elastic fibers at the interface between amorphous elastin and microfibrils. In vitro experiments suggested a role for EMILIN in the process of elastin deposition. This multimodular protein consists of 995 amino acids; the domain organization includes a C1q-like globular domain at the C terminus, a short collagenous stalk, a region containing two leucine zippers, and at least four heptad repeats with a high potential for forming coiled-coil alpha-helices and, at the N terminus, a cysteine-rich sequence characterized by a partial epidermal growth factor-like motif and homologous to a region of multimerin. Here we report the complete characterization of the human and murine EMILIN gene, their chromosomal assignment, and preliminary functional data of the human promoter. A cDNA probe corresponding to the C terminus of EMILIN was used to isolate two genomic clones from a human BAC library. Sequencing of several derived subclones allowed the characterization of the whole gene that was found to be about 8 kilobases in size and to contain 8 exons and 7 introns. The internal exons range in size from 17 base pairs to 1929 base pairs. All internal intron/exon junctions are defined by canonical splice donor and acceptor sites, and the different domains potentially involved in the formation of a coiled-coil structure are clustered in the largest exon. The 3'-end of the EMILIN gene overlaps with the 5'-end of the promoter region of the ketohexokinase gene, whose chromosomal position is between markers D2S305 and D2S165 on chromosome 2. A 1600-base pair-long sequence upstream of the translation starting point was evaluated for its promoter activity; five deletion constructs were assayed after transfection in primary chicken fibroblasts and in a human rhabdomyosarcoma cell line. This analysis indicates the existence of two contiguous regions able to modulate luciferase expression in both cell types used, one with a strong activatory function, ranging from positions -204 to -503, and the other, ranging from positions -504 to -683, with a strong inhibitory function.

5' Untranslated Regions↗
PubMedDate not supplied

Eukaryotic initiation factors eIF-2 and eIF-3: interactions, structure and localization in ribosomal initiation complexes.

More than ten different protein factors are involved in initiation of protein synthesis in eukaryotes. For binding of initiator tRNA and mRNA to the 40S ribosomal subunit, the initiation factors eIF-2 and eIF-3 are particularly important. They consist of several different subunits and form stable complexes with the 40S ribosomal subunit. The location of eIF-2 and eIF-3 in these complexes as well as the interactions of the individual components have been analyzed by biochemical methods and electron microscopy. The results obtained are summarized in this article, and a model is derived describing the spatial arrangement of eIF-2 and eIF-3 together with initiator tRNA and mRNA on the 40S subunit. Conclusions on the location of functionally important sites of eukaryotic small ribosomal subunits are discussed with regard to the respective location of these sites in the prokaryotic counterpart.

Binding Sites↗
PubMed2000

Adsorption and Precipitation of Aqueous Zn(II) on Alumina Powders.

The products of aqueous Zn(II) sorption on high-surface-area alumina powders (Linde-A) have been studied using XAFS spectroscopy as a function of Zn(II) sorption density (Gamma=0.2 to 3.3 µmol/m(2)) at pH values of 7.0 to 8.2. Over equilibration times of 15-111 h, we find that at low sorption densities (Gamma=0.2-1.1 µmol/m(2)) Zn(II) forms predominantly inner-sphere bidentate surface complexes with AlO(6) polyhedra, whereas at higher sorption densities (Gamma=1.5 to 3.5 µmol/m(2)), we find evidence for the formation of a mixed-metal Zn(II)-Al(III) hydroxide coprecipitate with a hydrotalcite-type local structure. These conclusions are based on an analysis of first- and second-neighbor interatomic distances derived from EXAFS spectra collected under ambient conditions on wet samples. At low sorption densities the sorption mechanism involves a transformation from six-coordinated Zn-hexaaquo solution complexes (with an average Zn-O distance of 2.07 Å) to four-coordinated surface complexes (with an average Zn-O distance of 1.97 Å) as described by the reaction identical withAl(OH(a))(OH(b))+Zn (H(2)O)(6)(2+)--> identical withAl(OH(a)') (OH(b)')Zn(OH(c)')(OH(d)'+4H(2)O+zH(+), where identical withAl(OH(a))(OH(b)) represents edge-sharing sites of Al(O,OH,OH(2))(6) octahedra to which Zn(O,OH,OH(2))(4) bonds in a bidentate fashion. The proton release consistent with this reaction (z=a-a'+b-b'+4-c'-d'), and with bond valence analysis falls in the range of 0 to 2 H(+)/Zn(II) when hydrolysis of the adsorbed Zn(II) complex is neglected. This interpretation suggests that proton release is likely a strong function of the coordination chemistry of the surface hydroxyl groups. At higher sorption densities (1.5 to 3.5 µmol/m(2)), a high-amplitude, second-shell feature in the Fourier transform of the EXAFS spectra indicates the formation of a three-dimensional mixed-metal coprecipitate, with a hydrotalcite-like local structure. Nitrate anions presumably satisfy the positive layer charge of the Al(III)-Zn(II) hydroxide layers in which the Zn/Al ratio falls in the range of 1 : 1 to 2 : 1. Our results for the higher Gamma-value sorption samples suggest that Zn-hydrotalcite-like phases may be a significant sink for Zn(II) in natural or catalytic systems containing soluble alumina compounds. Copyright 2000 Academic Press.

Journal Article↗
PubMed1985

Strain differences and laminar localization of structural neurochemical changes in aging rat.

To obtain comparisons of age-related microchemical changes in cerebral cortex of two commonly employed rat strains (Fischer 344 and Sprague-Dawley), neurochemical assays of substances regarded as quantitative indices of structural entities in brain were performed. These included DNA as a marker for cells, lipid sialoganglioside as an index of neuronal membrane mass, and galactocerebroside as an index of myelin. Fischer 344 rats were studied at 3-4 months (young), 14-16 months (middle age) and 25-28 months (old). Sprague-Dawleys were examined at 3-6 months (young), 14-17 months (middle age) and 25-28 months (old). Significant differences in the time courses of changes occurred; Fischer rats increased their brain weight at each aging point, while Sprague-Dawley rats reached stable brain weights by 4 months of age. Neither strain had a significant change in cell packing density of somatosensory cortex as measured by DNA. However, total ganglioside sialic acid declined in both strains, occurring by middle age in the Fischer and not until senescence in the Sprague-Dawley cortex. Cerebroside galactose increased in the Fischer between young and middle age, and was not further elevated in the older group. The Sprague-Dawley had its major increase in this marker between the middle aged and senescent groups. Intralaminar assays of these same markers in young and old Fisher 344 rats again indicated that DNA did not change, and that sialoganglioside was lost from all layers of the cortex in equal amounts. However, the increase in galactocerebroside resulted entirely from increases in the lower lamina of somatosensory cortex (lamina IV and below), suggesting on-going myelination of afferent and efferent axons. The time course of lipid membrane alteration is strain-dependent and selective as to cortical laminar localization. The findings are discussed in reference to human aging change in the same neurochemical indices.

Aging↗
PubMed1997

Recognition of Schistosoma mansoni cathepsins B and L by human IgG1 and IgG4 antibodies.

Human schistosome infections are chronic in nature and elevated IgG4 levels are associated with length of exposure. To examine how structure, localization and dynamics of exposure of a protein to the immune system can affect antibody isotype expression, specific antibody levels against two Schistosoma mansoni recombinant cathepsin molecules were determined in S. mansoni-infected individuals. Cathepsin B (rCatB, secreted in the gut) and cathepsin L (rCatL, localized in the reproductive structures) were used to determine IgG1 reactivity, as a measure of the stimulation of the immune response, and the switch to IgG4 as an indicator of the dynamics and rate of presentation to the immune system. Sera from three groups of S. mansoni-infected patients were used: individuals with life-long exposure in an endemic area in Burundi, a group from a recent endemic focus in Senegal, and of acutely infected European travellers. We report for the first time the ability of rCatL to trigger an immune response and show distinct antibody isotype reactivity between rCatB versus rCatL. Patients harbouring long-term chronic infections had elevated levels of IgG4 to both antigen, whereas individuals infected for less than four years had high IgG4 to rCatB but not to rCatL. Acutely infected travellers developed IgG1 to rCatB only. Our results demonstrate that an immune response is mounted more rapidly against a cathepsin molecule secreted in the gut of the worm than against an internally localized cathepsin.

Adolescent↗
PubMed1997

Mouse CD-RAP/MIA gene: structure, chromosomal localization, and expression in cartilage and chondrosarcoma.

A cDNA encoding a novel protein has been previously isolated from two independent sources: melanoma cell cultures and chondrocytes. The protein from human melanoma cell lines and tumors is called melanoma inhibitory activity (MIA) (Blesch et al. [1994] Cancer Res. 54:5695-5701) and the protein from primary bovine chondrocytes and cartilaginous tissues is called cartilage-derived retinoic acid-sensitive protein (CD-RAP) (Dietz and Sandell [1996] J. Biol. Chem. 271:3311-3316). In order to investigate the gene regulation and function of CD-RAP/MIA, the mouse gene locus was isolated and analyzed. Developmental expression was determined by in situ hybridization to mouse embryos. Expression was limited to cartilaginous tissues and was initiated with the advent of chondrogenesis, remaining abundant throughout development. The mouse gene was isolated and sequenced from a 129Sv library and sequenced directly from an additional strain, B6C3Fe. The mouse CD-RAP/MIA gene is 1.5 kbp and consists of four exons. The promoter sequence of the gene contains many potential regulatory domains including 8 basic helix-loop-helix protein-binding domains and an AT-rich domain, both motifs shown to be present in the cartilage-specific enhancer of the type II procollagen gene. Other potential cis-acting motifs include binding sites for GATA-1, NF-IL6, PEA3, w-elements, NF kappa B, Zeste and Sp1. The gene, called cdrap, was localized to the end of an arm of chromosome 7 at the same site as the transforming growth factor beta 1 (Tgf-beta 1) and the glucose phosphate isomerase 1 (Gpi 1) genes. Potential mouse mutants that mapped to the same region of chromosome 7 were identified. Two of the potential mutants with skeletal phenotypes were sequenced, pudgy (pu) and extra toes with spotting (XsJ); however, no mutations were found in the coding sequence. To determine whether CD-RAP/MIA is associated with tumors of cartilage, mRNAs from a variety of rodent tissues and cell lines were screened. Expression was detected in a rodent tumor, the Swarm rat chondrosarcoma and a chondrosarcoma cell line derived from it, but not in other tissues or tumors of non-cartilage origin. Immunolocalization revealed CD-RAP/MIA protein localized in cartilage only. These results show that the normal expression of CD-RAP/MIA is limited to cartilage; however, pathologically, it is expressed both in melanoma and chondrosarcoma. The restricted expression of CD-RAP/MIA may provide an opportunity to monitor cartilage metabolic activity as well as the tumor activity of melanoma and chondrosarcoma.

Amino Acid Sequence↗
PubMed2000

Changes in HOXB6 homeodomain protein structure and localization during human epidermal development and differentiation.

HOX homeodomain proteins are master developmental regulators, which are now thought to function as transcription factors by forming cooperative DNA binding complexes with PBX or other protein partners. Although PBX proteins exhibit regulated subcellular localization and function in the nucleus in other tissues, little data exists on HOX and PBX protein localization during skin development. We now show that the HOXB6 protein is expressed in the suprabasal layer of the early developing epidermis and throughout the upper layers of late fetal and adult human skin. HOXB6 signal is cytoplasmic throughout fetal epidermal development, but substantially nuclear in normal adult skin. HOXB6 protein is also partially nuclear in hyperproliferative skin conditions, but appears to be cytoplasmic in basal and squamous cell carcinomas. Although all three PBX genes are expressed in fetal epidermis, none of the three PBX proteins exhibit nuclear co-localization with HOXB6 in either fetal or adult epidermis. RNA and protein data suggest that a truncated HOXB6 protein, lacking the homeodomain, is expressed in undifferentiated keratinocytes and that the full-length protein is induced by differentiation. GFP-fusion proteins were used to demonstrate that the full-length HOXB6 protein is localized to the nucleus while the truncated protein is largely cytoplasmic. Taken together, these data suggest that during epidermal development the truncated HOXB6 isoform may function by a mechanism other than as DNA binding protein, and that most of the nuclear, homeodomain-containing HOXB6 protein does not utilize PBX proteins as DNA binding partners in the skin. Published 2000 Wiley-Liss, Inc.

Adult↗
PubMed2004

Local dense structural heterogeneities in liquid water from ambient to 300 MPa pressure: evidence for multiple liquid-liquid transitions.

Difference and double-difference near-infrared DO-D and HO-H stretching overtone (2nuOD and 2nuOH) spectroscopy and a rigorous (physically substantiated) band deconvolution technique were applied to reveal three different kinds of inherent (interstitial) structures of liquid water, which determine its high density (compared to ice lh under ambient conditions), its compressibility (under hydrostatic pressure, up to 300MPa), and its high fragility (manifested under temperature variation). Our data processing allowed the rigorous discrimination of up to six vibrational components. On the basis of an extensive comparative analysis combined with available structural data (X-ray and neutron scattering) and molecular dynamics (MD) simulations for liquid water, as well as with experimental and computed data for small non-tetrahedrally arranged water clusters, the major four components could be ascribed to: i) The basic lh icelike substructure; ii) the temperature-dependent remote interstitial "defects" due to tetrahedral displacements (primarily responsible for transport properties); iii) the interstitial "defects" most probably arranged in quasiplanar noncyclic tetramers (totally absent in the ice structure); and iv) the interstitial "defects" formed with increasing pressure, probably arranged in cubic water octamers and composed of two pairs of noncyclic and cyclic tetramer fragments. The latter structures include, essentially, bent hydrogen bonds stabilized by resonance effects.

Journal Article↗
PubMed1998

Genomic structure, chromosomal localization, and expression of human cathepsin W.

A 12 kb genomic fragment containing the entire open reading frame of the human cathepsin W was isolated and the genomic organization of this papain-like protease gene was determined. The 3.8 kb gene was mapped by fluorescence in situ hybridization to chromosome 11q13.1. The gene contained ten exons with introns ranging from 81 to 1119 bp. Four of the nine introns and a 5' untranslated exon were conserved when compared to related genes such as cathepsins L, K and S, whereas there was no similarity to the genomic organization of cathepsins B or C. In contrast to conserved splice site locations in other cysteine protease family members, the cathepsin W gene contained five unique locations. Furthermore, human cathepsin W cDNA was expressed, and was found to be localized within the rough endoplasmic reticulum in transiently transfected Cos-7 and Hela cells.

Cathepsin W↗