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 271 records · Page 15Linked to original sources
PubMed1989

Microtubule-associated protein 1B: molecular structure, localization, and phosphorylation-dependent expression in developing neurons.

Two monoclonal antibodies, 5E6 and 1B6, were raised against microtubule-associated protein 1B (MAP1B), a major component of the neuronal cytoskeleton. 5E6 recognized the entire MAP1B population, while 1B6 detected only phosphorylated forms. Affinity-purified MAP1B appeared as a long, filamentous molecule (186 +/- 38 nm) with a small spherical portion at one end, forming long cross-bridges between microtubules in vitro. These results, together with in vivo data from immunogold methods, demonstrate that MAP1B is a component of cross-bridges between microtubules in neurons. By immunohistochemical analysis, phosphorylated forms were shown to exist mainly in axons, whereas unphosphorylated forms were limited to cell bodies and dendrites. Phosphorylated MAP1B was quite abundant in developing axons, suggesting its essential role in axonal elongation.

Animals↗
PubMed1977

Ribosome structure: localization of N6,N6-dimethyladenosine by electron microscopy of a ribosome-antibody complex.

Antibodies to the minor nucleoside N6,N6-dimethyladenosine have been used to map a unique location of the nucleoside in the small subunit of the Escherichia coli ribosome. Antibodies were induced in rabbits by a nucleoside-bovine albumin conjugate and shown to be highly specific for the dimethyladenosine hapten. The antibodies were shown to interact with 30S ribosomal subunits from strain PR7, but not with subunits from its mutant strain TPR201, which is resistant to kasugamycin and lacks the two successive residues of dimethyladenosine normally found near the 3'-end of E. coli 16S ribosomal RNA. Electron micrographs of strain PR7 subunits, crosslinked by single IgG molecules, show a single binding site on the surface of the ribosome. This binding site is consistent with observations relating the 3'-end of the ribosomal RNA, binding of initiation factor IF-3 and messenger RNA, and mapping of specific ribosomal proteins.

Adenosine↗
PubMed1990

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

We present a prototype of a new approach to the folding problem of polypeptide chains. This approach is based on the analysis of known protein structures. It derives the energy potentials for the atomic interactions of all amino acid residue pairs as a function of the distance between the involved atoms. These potentials are then used to calculate the energies of all conformations that exist in the data base with respect to a given sequence. Then, by using only the most stable conformations, clusters of the most probable conformations for the given sequence are obtained. To discuss the results properly we introduce a new classification of segments based on their conformational stability. Special care is taken to allow for sparse data sets. The use of the method is demonstrated in the discussion of the identical oligopeptide sequences found in different conformations in unrelated proteins. VNTFV, for example, adopts a beta-strand in ribonuclease but it is found in an alpha-helical conformation in erythrocruorin. In the case of VNTFV the ensemble obtained consists of a single cluster of beta-strand conformations, indicating that this may be the preferred conformation for the pentapeptide. When the flanking residues are included in the calculation the hepapeptide P-VNTFV-H (ribonuclease) again yields an ensemble of beta-strands. However, in the ensemble of D-VNTFV-A (erythrocruorin) the major cluster is of alpha-helical type. In the present study we concentrate on the local aspects of protein conformations. However, the theory presented is quite general and not restricted to oligopeptides. We indicate extensions of the approach to the calculation of global conformations of proteins as well as conceivable applications to a number of molecular systems.

Amino Acid Sequence↗
PubMed1987

Local structure in a tryptic fragment of performic acid oxidized ribonuclease A corresponding to a proposed polypeptide chain-folding initiation site detected by tyrosine fluorescence lifetime and proton magnetic resonance measurements.

The effects of proline and X-Pro peptide bond conformations on the fluorescence properties of tyrosine in peptides corresponding to parts of a proposed chain-folding initiation site in bovine pancreatic ribonuclease A are examined by time-resolved and steady-state fluorescence spectroscopy. In peptides with Tyr-Pro sequences, the conformational constraints of proline on a preceding residue result in significant fluorescence quenching for both trans and cis peptide bond conformations. Small peptides containing Pro-Tyr sequences, on the other hand, do not exhibit fluorescence quenching compared to Ac-Tyr-NHMe. Studies of fluorescence decay in the tryptic fragment of performic acid oxidized ribonuclease corresponding to residues 105-124 (i.e., O-T-16) demonstrate the presence of at least two environments of the single tyrosine chromophore (in the sequence Asn113-Pro114-Tyr115). In these two (ensemble-averaged) environments, tyrosine has shorter and longer lifetimes, respectively, than in Ac-Tyr-NHMe. The fluorescence heterogeneity in O-T-16 does not correlate with X-Pro cis/trans conformational heterogeneity that can be detected by nuclear magnetic resonance (NMR) spectroscopy. Instead, the fluorescence heterogeneity in O-T-16 arises from the presence of multiple conformations with the same X-Pro peptide bond conformations which interconvert rapidly on the 1H NMR time scale (tau much less than 1 ms) but are distinguishable on the fluorescence lifetime time scale (tau greater than or equal to 1 ns). From comparisons with the tyrosine fluorescence decay of smaller synthetic peptides, it is concluded that the long-lifetime tyrosine fluorescence component of O-T-16 arises from interactions involving residues outside the Asn113-Pro114-Tyr115-Val116-Pro117 sequence, which either stabilize particular local conformations in the vicinity of Tyr115 or act directly to protect Tyr115 from efficient fluorescence quenching. The short-lifetime component of O-T-16 is also observed for the pentapeptide Ac-Asn-Pro-Tyr-Val-Pro-NHMe. The data provide evidence for a nonrandom polypeptide conformation of O-T-16 under conditions of solvent pH and temperature at which the complete disulfide-intact ribonuclease molecule is fully folded. Implications of this work for the interpretation of fluorescence-detected unfolding experiments are discussed.

Amino Acid Sequence↗
PubMed2001

Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium.

The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-binding domain and an immunoglobulin-like domain followed by a cell-wall anchorage signal, typical of cell-surface proteins from Gram-positive bacteria. Binding of saccharides was analyzed by differential scanning calorimetry, allowing to distinguish unequivocally the catalytic domain from the galactose-binding domain and to study binding specificities. The results suggest that ArChb could play a role in bacterium attachment to natural hosts. Kinetic parameters of ArChb demonstrate perfect adaptation to catalysis at low temperatures, as shown by a low activation energy associated with unusually low K(m) and high k(cat) values. Thermodependence of these parameters indicates that discrete amino acid substitutions in the catalytic center have optimized the thermodynamic properties of weak interactions involved in substrate binding at low temperatures. Microcalorimetry also reveals that heat-lability, a general trait of psychrophilic enzymes, only affects the active site domain of ArChb.

Acetylglucosaminidase↗
PubMed1986

Influence of local structure on the location of antigenic determinants in tobacco mosaic virus protein.

Early work on protein antigenicity led to the common belief that proteins possess a finite number of antigenic determinants located in accessible regions of the molecule's surface. This view is now changing. As a result of extensive studies, seven continuous epitopes have been located on tobacco mosaic virus (TMV) protein by measuring the antigenic activity of short peptides with anti-protein antibodies. The structure of the viral protein has been refined in Cambridge, enabling the Strasbourg workers to correlate the position of these epitopes with regions of high segmental mobility in the protein. Surface accessibility is not a sufficient condition for antigenicity, because six short peptides corresponding to accessible regions of the protein possess no antigenic activity. Recent work in Strasbourg shows that when longer peptides of TMV protein are used, more antigenic determinants are found and these lie in more structured regions of the protein (e.g. helices). In these cases the longer peptide may be folding up in solution to mimic part of the native structure.

Antigens, Viral↗
PubMed2003

Fine structural localization of connexin-36 immunoreactivity in mouse cerebral cortex and thalamus.

The mounting physiological evidence for low-resistance electrical coupling between thalamic and cortical neurons contrasts with a lack of morphological data on gap junctions in thalamus and cortex. Connexin-36 is a neuronally specific protein associated with low-resistance gap junctions in the central nervous system. Connexin-36 localization was studied in the mouse somatosensory cortex and thalamus by using immunocytochemistry and immunoelectron microscopy. Expression of connexin-36 immunoreactivity is widespread in the forebrain and significantly enhanced in the barrel cortex and thalamic reticular nucleus during the second postnatal week, but it extends to other thalamic nuclei as well. At the electron microscopic level, pre- and postembedding immunogold labeling revealed that 70-76% of connexin-36-immunolabeled particles were localized at focal sites on apposed plasma membranes of cortical and thalamic dendrites; approximately 5% of the particles were associated with parasynaptic membranes; but on no occasion could overt, morphologically identifiable gap junctions be demonstrated in association with connexin-36 immunoreactivity. The widespread distribution of focal concentrations of connexin-36 subunits could provide a basis for the electrical coupling that exists between cortical and reticular thalamic neurons, but morphologically definable gap junctions may be too small to be adequately visualized by conventional immunoelectron microscopy.

Animals↗
PubMed2004

Local structure of amorphous ice as revealed by O K-edge EXAFS.

The oxygen K-edge extended X-ray absorption fine structure (EXAFS) spectrum of an ice film prepared by deposition of water vapor on a substrate at 100 K was measured in the surface-sensitive Auger yield mode. Five distinct peaks are revealed in the Fourier transform spectrum of the EXAFS data. The peaks are attributed to O-H bonds (with overlapping contributions from intramolecular covalent and intermolecular hydrogen bonds) as well as to intermolecular O...O scattering paths in the distance range of 1-7 A. The pattern of the longer O...O distances resembles that of a high-pressure crystalline modification of ice (ice II).

Journal Article↗