Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “local structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
PubMed2000

Genomic structure, chromosomal localization and expression of the human LIM-homeobox gene LHX5.

The LIM-homeobox gene Lhx5 plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system. Mice lacking Lhx5 function show severely disorganized brain morphology and are impaired in cognition and motor coordination. In this study, we characterized the cDNA and genomic organization of the human LHX5 gene and analyzed its expression and chromosomal location. The human gene was found to contain five exons encoding a protein composed of 402 amino acids that is 98.8% identical to mouse Lhx5. By reverse transcriptase polymerase chain reaction, LHX5 transcripts were detected in fetal brain and in various regions of the adult central nervous system including the spinal cord, the thalamus, and the cerebellum. Fluorescence in situ hybridization mapped the LHX5 gene to chromosome 12, position 12q24.31-24.32. These results provide a framework for future analysis of possible association of human hereditary disorders with mutations in LHX5.

Amino Acid Sequence↗
PubMed2001

Gene structure, chromosomal localization, cDNA cloning and expression of the mouse ATP-gated ionotropic receptor P2X5 subunit.

The P2X receptors are oligomeric ligand-gated ion channels operated by extracellular ATP. Here we report the genomic and cDNA sequence of the mouse P2X(5) subunit, as well as its genomic organization, chromosomal localization and expression in select tissues. The mouse gene spans approximately 13 kb of DNA and contains thirteen exons. The cDNA encodes a 455 amino acid protein with 95% identity to the rat subunit. The P2X(5) subunit gene encodes a 2.6 kb mRNA that was found to in a number of tissues, with highest levels detected in heart and kidney. Results from rapid amplification of cDNA ends (RACE) PCR suggest that there are multiple transcriptional start sites located approximately 30-70 bp upstream from the start codon. The gene was localized to band B5 on Chromosome 11 using fluorescence in-situ hybridization (FISH), a region that has a high degree of synteny with human Chromosome 17. These results provide the initial information useful for further investigation into the functional role(s) of the P2X(5) subunit in physiological processes.

Adenosine Triphosphate↗
PubMed1997

The human mitochondrial elongation factor tu (EF-Tu) gene: cDNA sequence, genomic localization, genomic structure, and identification of a pseudogene.

The human mitochondrial elongation factor Tu (EF-Tu) is nuclear-encoded and functions in the translational apparatus of mitochondria. The complete human EF-Tu cDNA sequence of 1677 base pairs (bp) with a 101 bp 5'-untranslated region, a 1368 bp coding region, and a 207 bp 3'-untranslated region, has been determined and updated. The predicted protein from this cDNA sequence is approximately 49.8 kDa in size and is composed of 455 amino acids (aa) with a putative N-terminal mitochondrial leader sequence of approximately 50 aa residues. The predicted amino acid sequence shows high similarity to other EF-Tu protein sequences from ox, yeast, and bacteria, and also shows limited similarity to human cystolic elongation factor 1 alpha. The complete size of this cDNA (1677 bp) obtained by cloning and sequencing was confirmed by Northern blot analysis, which showed a single transcript (mRNA) of approximately 1.7 kb in human liver. The genomic structure of this EF-Tu gene has been determined for the first time. This gene contains nine introns with a predicted size of approximately 3.6 kilobases (kb) and has been mapped to chromosome 16p11.2. In addition, an intronless pseudogene of approximately 1.7 kb with 92.6% nucleotide sequence similarity to the EF-Tu gene has also been identified and mapped to chromosome 17q11.2.

Amino Acid Sequence↗
PubMed1997

Chromosomal localization, gene structure and transcription pattern of the ORFX gene, a homologue of the MHC-linked RING3 gene.

We have mapped the human ORFX gene to chromosome 9q34 and determined its complete gene structure. Comparison with RING3, the human MHC-linked homologue on 6p21.3, shows the two gene structures to be highly conserved but with an approximate threefold expansion in the ORFX introns. RING3 and ORFX are found to be ubiquitously expressed in human adult and foetal tissues. Evidence suggests that the two genes may have arisen from an ancient duplication in a common ancestral chromosome.

Adult↗
PubMed1995

Determination of local protein structure by spin label difference 2D NMR: the region neighboring Asp61 of subunit c of the F1F0 ATP synthase.

Purified subunit c from the H(+)-transporting F1F0 ATP synthase of Escherichia coli folds as an antiparallel pair of extended helices in a solution of chloroform-methanol-water. A similar hairpin-like folding is predicted for the native protein in the multisubunit transmembrane Fo sector of the ATP synthase. A single Cys variant (A67C) of subunit c was created and modified with a maleimido-PROXYL [[3-(maleimidomethyl)-2,2,5,5-tetramethyl-1-pyrrolidinyl]oxy] spin label. Pairs of 1H 2D correlation and NOE spectra were collected with the nitroxide oxidized (paramagnetic) and reduced (diamagnetic). The pairs of spectra were subtracted, yielding difference spectra containing only cross-peaks from 1H within 15 A of the spin label. These greatly simplified spectra were easily analyzed to provide complete assignments for residues 10-25 and 52-79 of the protein, 150 NOE distance restraints, and 27 hydrogen-bonding restraints. The chemical shifts and NOE patterns observed in the derivatized mutant were virtually identical to those which were resolved in the unmodified wild-type protein, strongly suggesting that the spin label was not perturbing the protein structure. The restaints enabled us to calculate a detailed structure for this region of subunit c. The structure consisted of two gently curved helices, crossing at a slight (30 degrees) angle. The C-terminal helix was disrupted from Val60 to Ala62 near the essential Pro64. Asp61, the residue thought to undergo protonation--deprotonation with each H+ transported across the membrane, was in ver der Waals contact with Ala24. The proximity of these residues had been predicted from mutant analyses, where H+ translocation was retained on moving the Asp from position 61 to 24.

Escherichia coli↗
PubMed2002

Catalytic function and local proton structure at the type 2 copper of nitrite reductase: the correlation of enzymatic pH dependence, conserved residues, and proton hyperfine structure.

Electron nuclear double resonance (ENDOR) of protons at Type 2 and Type 1 cupric active sites correlates with the enzymatic pH dependence, the mutation of nearby conserved, nonligating residues, and electron transfer in heterologously expressed Rhodobacter sphaeroides nitrite reductase. Wild-type enzyme showed a pH 6 activity maximum but no kinetic deuterium isotope effect, suggesting protons are not transferred in the rate-limiting step of nitrite reduction. However, protonatable Asp129 and His287, both located near the Type 2 center, modulated enzyme activity. ENDOR of the wild-type Type 2 center at pH 6.0 revealed an exchangeable proton with large hyperfine coupling. Dipolar distance estimates indicated that this proton was 2.50-2.75 or 2.25-2.45 A from Type 2 copper in the presence or absence of nitrite, respectively. This proton may provide a properly oriented hydrogen bond to enhance water formation upon nitrite reduction. This proton was eliminated at pH 5.0 and showed a diminished coupling at pH 7.5. Mutations of Asp129 and His287 reduced enzyme activity and altered the exchangeable proton hyperfine spectra. Mutation of Asp129 prevented a pH-dependent change at the Type 1 Cys167 ligand as observed by Cys C(beta) proton ENDOR, implying there is a Type 2 and pH-dependent alteration of the Type 1 center. Mutation of the Type 1 center ligand Met182 to Thr and mutation of Asp129 increased the activation energy for nitrite reduction. Involvement of both the Type 1 center and Asp129 in modulating activation energy shows that electron transfer from the Type 1 center to a nitrite-ligated Type 2 center is rate-limiting for nitrite reduction. Mutation of Ile289 to Ala and Val caused minor perturbation to enzyme activity, but as detected by ENDOR, allowed formate binding. Thus, bulky Ile289 may exclude non-nitrite ligands from the Type 2 active site.

Amino Acid Substitution↗
PubMed1997

Effects of serpin binding on the target proteinase: global stabilization, localized increased structural flexibility, and conserved hydrogen bonding at the active site.

The binding of human alpha1-proteinase inhibitor to rat trypsin was shown by NMR spectroscopy to raise the pKa' of His57 in the active site but not to disrupt the hydrogen bond between His57 and Asp102. Similar NMR results were observed for the Asp189 to serine mutant of rat trypsin, which is much more stable than wild-type trypsin against autoproteolysis as the result of mutation of the residue at the base of the specificity pocket. This mutant was used in further studies aimed at determining the extent of the conformational transition in trypsin that accompanies serpin binding and leads to disruption of the catalytic activity of the proteinase such that the inhibitor complex is trapped at the acyl enzyme intermediate stage. The stability of rat trypsin toward thermal denaturation was found to be lower in the free enzyme than in the complex with alpha1-proteinase inhibitor. This suggests that the complex contains extensive protein-protein interactions that stabilize overall folding. On the other hand, previous investigations have shown that the proteinase in serpin-proteinase complexes becomes more susceptible to limited proteolysis, suggesting that the conformational change that accompanies binding leads to the exposure of susceptible loops in the enzyme. The existence of this type of conformational change upon complex formation has been confirmed here by investigation of the rate of cleavage of disulfide linkages by added dithiothreitol. This study revealed that, despite the increased stability of trypsin in the complex, one or more of its disulfide bridges becomes much more easily reduced. We suggest that the process of complex formation with alpha1-proteinase inhibitor converts trypsin D189S into an inactive, loose structure, which serves as a "conformational trap" of the enzyme that prevents catalytic deacylation. It is also proposed that plastic region(s) of the activation domain of trypsin may play a crucial role in this inhibitor-induced structural rearrangement.

Anilino Naphthalenesulfonates↗
PubMed2003

Effect of local molecular structure on the chain-length dependence of the electronic properties of thiophene-based pi-conjugated systems.

Three series of thiophene-based pi-conjugated oligomers built with different combinations of thiophene cycles and double bonds have been synthesized and characterized. The analysis of the chain length dependence of the electronic, electrochemical, and vibrational properties of the three series of oligomers has been carried out using cyclic voltammetry, UV-vis, IR, and Raman spectroscopies. These various investigations provide consistent results showing that incorporation of ethylenic linkages in an oligothiophene structure leads to a faster decrease of the HOMO-LUMO gap with chain extension due to the combined effects of enhanced planarity and lower overall aromatic character of the system. Although the incorporation of two consecutive double bonds in the system leads to a stabilization of the dicationic state, this structural modification does not produce the expected further decrease of the HOMO-LUMO gap at large chain extension. This phenomenon is discussed on the basis of an interplay between aromaticity and bond length alternation.

Journal Article↗
PubMed2005

Weak correlations between local density and dynamics near the glass transition.

We perform experiments on two different dense colloidal suspensions with confocal microscopy to probe the relationship between local structure and dynamics near the glass transition. We calculate the Voronoi volume for our particles and show that this quantity is not a universal probe of glassy structure for all colloidal suspensions. We correlate the Voronoi volume to displacement and find that these quantities are only weakly correlated. We observe qualitatively similar results in a simulation of a polymer melt. These results suggest that the Voronoi volume does not predict dynamical behavior in experimental colloidal suspensions; a purely structural approach based on local single particle volume likely cannot describe the colloidal glass transition.

Journal Article↗
PubMed1994

Toward a general theory of stereopsis: binocular matching, occluding contours, and fusion.

Models of stereopsis have focused on developing strategies for identifying common features in the 2 half-images so that disparity may be computed. This emphasis ignores the unpairable features that arise at occluding contours (half-occlusions). Most models treat half-occlusions as noise or outliers that are interpreted after disparity processing is completed. A series of experiments reveal that occlusion relationships are sensed during the earliest stages of binocular processing. The authors hypothesize the existence of receptive field structures that sense the local structure of stereoscopic occlusion relationships to account for these findings. Finally, a simple theoretical framework is presented in which fusion, stereopsis, and occlusion are unified. This theory explains the co-occurrence of stereopsis and diplopia and how half-occlusions escape the suppression characteristic of binocular rivalry.

Contrast Sensitivity↗
PubMed1999

Acceleration of the folding of acylphosphatase by stabilization of local secondary structure.

The addition of trifluoroethanol or hexafluoroisopropanol converts the apparent two-state folding of acylphosphatase, a small alpha/beta protein, into a multistate mechanism where secondary structure accumulates significantly in the denatured state before folding to the native state. This results in a marked acceleration of folding as revealed by following the intrinsic fluorescence and circular dichroism changes upon folding. The folding rate is at a maximum when the secondary-structure content of the denatured state corresponds to that of the native state, while further stabilization of secondary structure decreases the folding rate. These findings indicate that stabilization of intermediate structure can either enhance or retard folding depending on its nature and content of native-like interactions.

Acid Anhydride Hydrolases↗
PubMed1984

Localization and structure of endonuclease cleavage sites involved in the processing of the rat 32S precursor to ribosomal RNA.

The initial endonuclease cleavage site in 32 S pre-rRNA (precursor to rRNA) is located within the rate rDNA sequence by S1-nuclease protection mapping of purified nucleolar 28 S rRNA and 12 S pre-rRNA. The heterogeneous 5'- and 3'-termini of these rRNA abut and map within two CTC motifs in tSi2 (internal transcribed spacer 2) located at 50-65 and 4-20 base-pairs upstream from the homogeneous 5'-end of the 28 S rRNA gene. These results show that multiple endonuclease cleavages occur at CUC sites in tSi2 to generate 28 S rRNA and 12 S pre-rRNA with heterogeneous 5'- and 3'-termini, respectively. These molecules have to be processed further to yield mature 28 S and 5.8 S rRNA. Thermal-denaturation studies revealed that the base-pairing association in the 12 S pre-rRNA:28 S rRNA complex is markedly stronger than that in the 5.8 S:28 S rRNA complex. The sequence of about one-quarter (1322 base-pairs) of the 5'-part of the rat 28 S rDNA was determined. A computer search reveals the possibility that the cleavage sites in the CUC motifs are single-stranded, flanked by strongly base-paired GC tracts, involving tSi2 and 28 S rRNA sequences. The subsequent nuclease cleavages, generating the termini of mature rRNA, seem to be directed by secondary-structure interactions between 5.8 S and 28 S rRNA segments in pre-rRNA. An analysis for base-pairing among evolutionarily conserved sequences in 32 S pre-rRNA suggests that the cleavages yielding mature 5.8 S and 28 S rRNA are directed by base-pairing between (i) the 3'-terminus of 5.8 S rRNA and the 5'-terminus of 28 S rRNA and (ii) the 5'-terminus of 5.8 S rRNA and internal sequences in domain I of 28 S rRNA. A general model for primary- and secondary-structure interactions in pre-rRNA processing is proposed, and its implications for ribosome biogenesis in eukaryotes are briefly discussed.

Animals↗
PubMed1998

Human mitochondrial phosphoenolpyruvate carboxykinase 2 gene. Structure, chromosomal localization and tissue-specific expression.

The mitochodrial (mt) phosphoenolpyruvate carboxykinase 2 (PCK2) gene was isolated by screening a human genomic library with a rat cytosolic (cy) PCK1 cDNA probe comprising sequences from exons 2-9 and by PCR amplification of human genomic DNA spanning consecutive exons with known primer pairs from mtPCK2 cDNA containing sequences from two putative neighbouring exons. The mtPCK2 gene spans approx. 10 kb and consists of ten exons and nine introns. All exon-intron junction sequences match the classical GT/AG rule. Northern blot analysis of poly(A)+ and total RNA from various tissues revealed one mRNA species of approx. 2.4 kb. The gene is expressed in a variety of human tissues, mainly in liver, kidney, pancreas, intestine and fibroblasts. In contrast with the cytosolic isoenzyme, the mitochondrial form might not have a purely gluconeogenic function. The mtPCK2 gene maps to chromosome 14q11.2-q12, in contrast with the cyPCK1 gene located on 20q13.2-q13.31.

Animals↗
PubMed1999

Expression pattern, subcellular localization and structure--function relationship of rat Tpx-1, a spermatogenic cell adhesion molecule responsible for association with Sertoli cells.

The gene for a testicular cell adhesion protein called Tpx-1, which mediates the binding of spermatogenic cells to Sertoli cells of the rat in primary culture, was previously cloned. Here the characterization of Tpx-1 is reported. Tpx-1 messenger ribonucleic acid (mRNA) became detectable in pachytene spermatocytes and continued to be present throughout development into elongated spermatids, while the amount of Tpx-1 protein seemed to increase some time after the increment of mRNA. Tpx-1 protein was also present, although less abundantly, in spermatozoa prepared from the epididymis. Tpx-1 contains a cluster of hydrophobic amino acid residues near the amino terminus and a cysteine-rich region in the carboxyl-terminal half. Tpx-1 fused with green fluorescence protein was secreted into the medium when expressed in a cultured cell line, depending on the presence of the amino-terminal hydrophobic region. Moreover, Tpx-1 was present in the medium of testicular cell primary culture. Structure-function analysis revealed that the amino-terminal 101 amino acid residues were sufficient for cell adhesion activity, whereas the carboxyl-terminal cysteine-rich region was dispensable. In conclusion, Tpx-1 is produced and secreted from spermatogenic cells at various differentiation stages, and mediates the interaction of those cells with Sertoli cells.

Animals↗
PubMed2002

Synovial chondromatosis of the metacarpophalangeal joint.

We describe a case of synovial chondromatosis in a metacarpophalangeal joint with invasion of local structures. The degree of local tissue involvement was not demonstrated on the preoperative MRI scans. This case highlights that synovial chondromatosis can be invasive and that even the best preoperative imaging may not demonstrate this.

Adult↗
PubMed2004

A combined molecular dynamics+quantum mechanics method for investigation of dynamic effects on local surface structures.

A combined molecular dynamics (MD)+quantum mechanics (QM) method for studying processes on ionic surfaces is presented. Through the combination of classical MD and ab initio embedded-cluster calculations, this method allows the modeling of surface processes involving both the structural and dynamic features of the substrate, even for large-scale systems. The embedding approach used to link the information from the MD simulation to the cluster calculation is presented, and rigorous tests have been carried out to ensure the feasibility of the method. The electrostatic potential and electron density resulting from our embedded-cluster model have been compared with periodic slab results, and confirm the satisfying quality of our embedding scheme as well as the importance of applying embedding in our combined MD+QM approach. We show that a highly accurate representation of the Madelung potential becomes a prerequisite when the embedded-cluster approach is applied to temperature-distorted surface snapshots from the MD simulation.

Journal Article↗