Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Freeze-dried and shadowed Escherichia coli 50 S ribosomal subunits have been examined by electron microscopy and a model of the subunit has been constructed. High resolution shadow casting has enabled us to determine independently the absolute hand of the subunit and to reveal some new structural features.
J Mol Biol 1983 Dec 25
PMID:Structure of the Escherichia coli 50 S ribosomal subunit. 636 11

The morphology of the high molecular weight complex of aminoacyl-tRNA synthetases purified from rabbit reticulocytes has been investigated by electron microscopy. To stabilize it against dissociation, the complex was also studied after chemical crosslinking. Freeze fracture, drying shadowing and negative staining were used. The reticulocyte complex appears as a moderately elongated object with no simple compact shape. Upon rapid drying, the native complex dissociates and shows the presence of approximately 8 globular components, the individual size of which is 80-100 A. The surface of the cross-linked complex shows several distinct globules which appear to extend out of a central core. The irregularly shaped crosslinked complex has a maximal dimension of 350 +/- 50 A. The morphology of the synthetase complex is discussed with respect to some of the properties of this type of multienzymatic system.
Mol Biol Rep 1984 Jul
PMID:Electron microscopy study of the aminoacyl-tRNA synthetase multienzymatic complex purified from rabbit reticulocytes. 647 57

The correlation between structures of chemicals and their inducibility for megamitochondrial formation was investigated. Since the chemical structure universal to the inducers of megamitochondria previously reported (cuprizone and isonicotinic acid derivatives) is the carbazoyl group (-CONHNH2), semicarbazide (NH2NHCONH2) was tested first. Then, hydrazine (NH2NH2) was tested, replacing the carbazoyl group of semicarbazide by an amino group (-NH2). The present study demonstrates that (1) megamitochondria were induced in mouse and rat hepatocytes by feeding the animals with a diet containing semicarbazide or hydrazine, suggesting that the carbazoyl group was not essential for megamitochondrial formation; (2) hydrazine-induced megamitochondrial formation was a reversible process. Coupling efficiencies and activities of ATPase and cytochrome oxidase of megamitochondria induced by hydrazine were slightly decreased, while the activity of monoamine oxidase was moderately decreased. Freeze-fracture electron microscopy revealed particle-free regions in the outer membranes of megamitochondria fixed with glutaraldehyde at 22 degrees C; the regions disappeared at 25 degrees C, indicating that the temperature of the liquid crystalline to gel state lipid phase transition in the megamitochondrial outer membrane was elevated. It is speculated that chemical structure of inducer of megamitochondria could be simplified to NH2-G (G, substituting group).
Exp Mol Pathol 1983 Oct
PMID:Induction of megamitochondria in the mouse and rat livers by hydrazine. 661 23

Freeze fracture and deep-etching of quick-frozen insect flight muscles provides unusually clear views of thick filament projections in rigor and relaxed states. In rigor, these projections form crossbridges that are deployed helically. The tracks of these helices are left-handed, repeat every approximately 38 nm, tilt at approximately 42 degrees to the muscle axis, and, when viewed on edge, produce the unique "double chevron" pattern of crossbridges that characterizes this muscle type in thin sections (Reedy, 1968). These helical parameters substantiate Reedy's earlier deduction that rigor crossbridges form two-start helices in this muscle. On the other hand, deep-etchings of insect flight muscles relaxed with Mg-ATP before freezing do not fit with earlier results. Contrary to earlier thin section views and the expectations of X-ray diffraction, thick filaments in such relaxed muscles display no hint of a 14.5 nm axial periodicity; instead, their projections appear to be very disordered. This suggests that when crossbridges are detached, they are free to "wobble" by at least +/- 7 nm in the axial direction and thus obscure their points of origin from the thick filaments. With the images of detached crossbridges in mind, closer inspection of rigor thick filaments yields no indication of any "extra" projections between the helically deployed ones, i.e. there is no indication of any detached crossbridges in rigor muscles. Thus in this type of muscle, at least, the establishment of a rigor pattern may not involve a "selection" of suitably located myosin heads from a larger population, as is generally thought, but may instead involve a systematic redistribution of the whole population of heads until all of them became crossbridges.
J Mol Biol 1983 Sep 05
PMID:Structure of the myosin crossbridge lattice in insect flight muscle. 662 Mar 79

A new method of preparing biological samples for electron microscopy has been used to re-examine the structure of actin filaments, actin filaments decorated by myosin subfragment-1 (S1), and insect flight muscles. Samples were quick-frozen by contact with a block of copper cooled to approximately 4 K; then were freeze-fractured, deep-etched, rotary-replicated with platinum, and viewed in a transmission electron microscope. By this approach, actin filaments display prominent transverse bands whose repeat (approximately 5.5 nm) and pitch (approximately 15 to 20 degrees) fit with the expected left-handed "genetic" helix. Freeze-etched actin filaments do not, however, display the usual two-start helix as prominently as is seen after negative staining, and they also appear substantially thicker than after negative staining (9 to 10 nm versus 8 nm). The latter two-start helix appears very clearly after S1 decoration. Nevertheless, freeze-etched acto-S1 does not display the "arrowheads" that are seen after negative staining. Instead it displays the outer envelope of the helically deployed S1, and as would be expected from current models derived from optical reconstruction of negatively stained samples, this surface view looks only slightly polarized. Finally, the quick-freeze, deep-etch approach provides particularly distinct images of the crossbridges in insect flight muscles. These are plentiful and regularly arranged in rigor muscles, but rare in muscles relaxed with ATP before freezing. In rigor muscles fixed with aldehydes, these crossbridges assume a broad distribution of inclination, ranging from 45 degrees to 90 degrees with a mean of approximately 80 degrees, which is less tilt than has been seen before in thin-sectioned muscles. However, when aldehyde fixation is followed by exposure to tannic acid with or without uranyl acetate block-staining, crossbridges assume a more acute angle with respect to the fiber axis, centering around 45 degrees. This is associated with a commensurate reduction in interfilament spacing within the muscle fibers, such that tilted crossbridges are not any longer than untilted ones (both measuring approximately 15 nm). At the opposite extreme, crossbridges often become stretched in unfixed muscles, owing to an unnatural increase in interfilament spacing that occurs during sample preparation; in such regions, crossbridges display narrow "stalks", which invariably emerge from the thick filaments at close to 90 degrees. We conclude that crossbridge shape and orientation is strongly affected by different methods of sample preparation, and this will make it difficult to visualize natural crossbridge movements by electron microscopy.
J Mol Biol 1983 Sep 05
PMID:Actin-myosin interactions visualized by the quick-freeze, deep-etch replica technique. 662 Mar 83

The crystal structure of the double-helical B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved and refined independently in three forms: (1) the parent sequence at room temperature; (2) the same sequence at 16 K; and (3) the 9-bromo variant C-G-C-G-A-A-T-TBrC-G-C-G at 7 degrees C in 60% (v/v) 2-methyl-2,4-pentanediol. The latter two structures show extensive hydration along the phosphate backbone, a feature that was invisible in the native structure because of high temperature factors (indicating thermal or static disorder) of the backbone atoms. Sixty-five solvent peaks are associated with the phosphate backbone, or an average of three per phosphate group. Nineteen other molecules form a first shell of hydration to base edge N and O atoms within the major groove, and 36 more are found in upper hydration layers. The latter tend to occur in strings or clusters spanning the major groove from one phosphate group to another. A single spermine molecule also spans the major groove. In the minor groove, the zig-zag spine of hydration that we believe to be principally responsible for stabilizing the B form of DNA is found in all three structures. Upper level hydration in the minor groove is relatively sparse, and consists mainly of strings of water molecules extending across the groove, with few contacts to the spine below. Sugar O-1' atoms are closely associated with water molecules, but these are chiefly molecules in the spine, so the association may reflect the geometry of the minor groove rather than any intrinsic attraction of O-1' atoms for hydration. The phosphate O-3' and O-5' atoms within the backbone chain are least hydrated of all, although no physical or steric impediment seems to exist that would deny access to these oxygen atoms by water molecules.
J Mol Biol 1983 Jan 05
PMID:Ordered water structure around a B-DNA dodecamer. A quantitative study. 683 28

Salivarian trypanosomes have the ability to evade the immune response of their hosts by the sequential expression of different cell surface glycoproteins. Among the isolated specific antigens from cloned variants of Trypanosoma equiperdum, a structural study was undertaken on two immunologically cross-reacting variant surface glycoproteins, and results concerning the basic antigenic type are reported. The glycoprotein was cleaved by cyanogen bromide, and amino acids of several purified fractions obtained by gel filtration chromatography of this cleavage mixture were sequenced by automated Edman degradation. Sequencing in particular allowed the identification of the N-terminal portion of the molecule (residues 1-74). Sugar compositions of the fractions have demonstrated the presence of at least two carbohydrate moieties in the glycoprotein. Using a subsequent enzymatic subcleavage we were able to locate the first glycosylation site in position 57. An important observation was that the first oligosaccharide identified was rich in mannose and devoid of galactose.
Mol Biochem Parasitol 1983 May
PMID:Partial determination of the primary structure of a variant surface glycoprotein from Trypanosoma equiperdum. Composition and location of a carbohydrate moiety. 687 78

When confronted with the task of finding homology to large numbers of sequences, database searching tools such as Blast and Fasta generate prohibitively large amounts of information. An automatic way of making most of the decisions a trained sequence analyst would make was developed by means of a rule-based expert system combined with an algorithm to avoid non-informative biased residue composition matches. The results found relevant by the system are presented in a very concise and clear way, so that the homology can be assessed with minimum effort. The expert system, HSPcrunch, was implemented to process the output to the programs in the BLAST suite. HSPcrunch embodies rules on detecting distant similarities when pairs of weak matches are consistent with a larger gapped alignment, i.e. when Blast has broken a longer gapped alignment up into smaller ungapped ones. This way, more distant similarities can be detected with no or little side-effects of more spurious matches. The rules for how small the gaps must be to be considered significant have been derived empirically. Currently a set of rules are used that operate on two different scoring levels, one for very weak matches that have very small gaps and one for medium weak matches that have slightly larger gaps. This set of rules proved to be robust for most cases and gives high fidelity separation between real homologies and spurious matches. One of the most important rules for reducing the amount of output is to limit the number of overlapping matches to the same region of the query sequence.(ABSTRACT TRUNCATED AT 250 WORDS)
Proc Int Conf Intell Syst Mol Biol 1994
PMID:An expert system for processing sequence homology data. 758 13

We present in this paper an algorithm for the multiple comparison of a set of protein sequences. Our approach is that of peptide matching and consists in looking for all the words that occur approximatively in at least q of the sequences in the set, where q is a parameter. Words are compared by using a reference object called a model, that is itself a word over the alphabet of the amino acids, and the comparison between a model and a word is based on w-length words instead of single symbols. This idea is similar to the one used in the Blast program in the case of pairwise comparisons. Two w-length words are considered to be related if an alignment without gaps of the two using a similarity matrix has a score greater than a certain threshold value t. In our case, we say that a k-length word u is an occurrence of a model m of the same length if every w-length subword of u is related to the corresponding subword of m in the sense given above. If a model m has occurrences in at least q of the sequences of the set, m is said to occur in the set. In percentage terms, the value of q may correspond to something as small as 5% of the sequences (search for recurrent words in a set of non homologous proteins) or as high as 70-100% (establishment of a list of all similar words as a first step in a multiple alignment program). The algorithm presented here is an efficient and exact way of looking for all the models, of a fixed length k or of the greatest possible length kmax, that occur in a set of sequences. It can work with any kind of scoring matrix and an extension of the algorithm allows for the introduction of gaps between a model and its occurrences.
Proc Int Conf Intell Syst Mol Biol 1995
PMID:A distance-based block searching algorithm. 758 55

A method of image classification based on multivariate statistics has been developed and applied to freeze-etch images of outer dynein arms (ODAs) from cockerel sperm flagella. Demembranated flagella were cryofixed in three different nucleotide states: rigor (i.e. no added ATP); relaxed (i.e. 1 mM ATP plus vanadate); and active (i.e. 1 mM ATP). Freeze-etch replica fragments from them were coded to conceal their identities and sampled for flagella. From these a total of 6048 individual ODA images were successfully windowed and aligned, covering an angular range of 66 degrees. Each nucleotide condition produced a statistically significant ODA morphology. The relaxed and active morphologies differed only in the angulation of their heads, with the relaxed ODA favouring a more tilted position. The rigor morphology was more distinct and showed a conformational change involving a 12 nm distal shift relative to the A-tubule and highly variable heads and B-links, suggesting an ability to develop tension. Outer arms were classified by discriminant analysis as being either rigor-like, relaxed-like or active-like, and 80% of all ODAs were correctly classified. The misclassification of the remaining 20% indicated morphological heterogeneity in some of the groups. From the rigor group, 8.8% of the ODAs were misclassified as relaxed-like or active-like (i.e. non-rigor-like). It is speculated that this is a consequence of mechanochemical interactions between the B-tubules and the rigor ODAs and/or contaminating ATP remaining after demembranation. Active flagella were found to show all three morphologies, with 5.4% in the rigor conformation and 18.6% in the relaxed conformation. The finding of rigor-like and relaxed-like ODAs in flagella exposed to ATP is discussed in relation to the cross-bridge cycle.
J Mol Biol 1995 Jun 30
PMID:Rigor and relaxed outer dynein arms in replicas of cryofixed motile flagella. 760 96


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>