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D Moras

Publications and source records attributed to D Moras.

198 records · Page 11Linked to original sources
PubMed1983

Loop stereochemistry and dynamics in transfer RNA.

The stereochemistry and the dynamics of two loops of yeast tRNA-asp, the thymine loop and the anticodon loop, are compared in the hope of a better understanding of the relationships between loop sequence and loop topology. Both loops are seven residues long and both present sharp turns after the second residue, U33 and psi 55, stabilized by hydrogen bonds between N3-H of the pyrimidine and the phosphates of C36 and A58 and stacking interactions of the pyrimidine ring with the phosphates of U35 and A57, respectively. In the thymine loop, the two purines following C56, A57 and A58, open up to leave space for the intercalation of the first invariant guanine residue of the D-loop, while the two pyrimidine bases, which follow A58, turn away from the stacking pattern of the thymine arm and stack instead with the last base pair of the dihydrouridine arm A15-U48. In the anticodon loop, however, the bases G34 to C38 form an helical stack in continuity with the anticodon stem on the 3'-end. At the same time C36 forms Watson-Crick hydrogen bonds with G34 of a twofold symmetrically related molecule. The anticodon-anticodon base pairing interactions between symmetrically-related molecules are stabilized by stacking with the modified base G37 on both sides of the triplet. Some comparisons are made with the structure of yeast tRNA-phe and some implications about the structure of mitochondrial tRNAs are discussed.

Anticodon↗
PubMed1982

Formation of a catalytically active complex between tRNAAsp and aspartyl-tRNA synthetase from yeast in high concentrations of ammonium sulphate.

The interactions of yeast tRNAAsp with cognate aspartyl-tRNA synthetase have been studied in high concentrations of either sodium chloride or ammonium sulphate by fluorescence titration and small-angle neutron scattering. In solutions containing more than 1M NaCl no complex is formed and enzymatic activity is abolished. In strong contrast, however, the physical measurements showed the formation of a two-to-one tRNA-enzyme complex, with high affinity, in 1.6 M (NH4)2SO4. Aminoacylation assays under the same salt conditions showed the enzymatic fixation of aspartic acid to tRNAAsp to occur at an appreciable rate. The present study emphasizes that the effects of salts on protein-nucleic acid interactions do not depend only on ionic strength but also on the nature of the salt. This study has allowed a rational approach to the crystallisation of a functional tRNAAsp-aspartyl-tRNA synthetase complex (Giegé, Lorber, Ebel, Thierry and Moras (1980) C.R. Acad. Sci. Paris, série D, 291, 393-396).

Amino Acyl-tRNA Synthetases↗
PubMed1980

Crystal structure of yeast tRNAAsp.

Two independent, three-dimensional structures of yeast tRNAAsp, mainly differing by the conformation of the D loop, have been obtained from a multiple isomorphous replacement (MIR) X-ray analysis at 3.5-A resolution. The folding of the ribose-phosphate backbone is similar to that found for tRNAPhe; major differences concern the relative positioning of the acceptor and anticodon stems, and the conformation of the loops in the two molecules. Crystal packing involves self-complementary GUC anticodon interactions.

Aspartic Acid↗
PubMed1977

A neutron investigation of yeast valyl-tRNA synthetase interaction with tRNAs.

A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) are added to valyl-tRNA synthetase, a complex consisting of two enzyme molecules and one tRNA molecule is first formed. It is subsequently dissociated to a one to one complex when more tRNA is present in the solution. The association curve shows a maximum for a molecular ratio, enzyme over tRNA, equal to 2.

Amino Acyl-tRNA Synthetases↗
PubMed1975

Sequence variability and structure of D-glyceraldehyde-3-phosphate dehydrogenase.

The amino acid sequences of pig muscle and of yeast glyceraldehyde-3-phosphate dehydrogenase are compared with the three-dimensional structure of the lobster muscle enzyme. Residues in sheet and helical regions, on the exterior and interior, in subunit and domain interfaces, as well as residues in the active site have been examined for evolutionary conservation. The residues in the first (NAD binding) domain (1-147) are less conserved than residues in the second (catalytic) domain (148-334) probably because there are fewer internal residues and fewer residues involved in interactions between subunits. Residues in subunit interface are conserved to a significantly greater extent than others, and those involved in catalysis are conserved most of all. Patterns of residues in helices and sheets follow those found for other proteins.

Amino Acid Sequence↗
PubMed1975

Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.

An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is known to be exact in the human holoenzyme. The map showed possible asymmetry between the subunits in which the active centers are closely related across the R axis (that is, between the red and green or between the yellow and blue subunits). A difference map between the electron density of citrate and sulfate-soaked crystals gave further evidence for possible asymmetry. The major differences of electron density between R axis-related subunits appear around the active center and suggest the following interpretations. 1. The conformation of the adenine about the glycosidic bond is the more frequently observed anti with a C-2' endo conformation for the ribose ring in the red and yellow subunits, but is probably syn with a C-3' endo conformation in the green and blue subunits.2. The adenine ribose has its 3'-hydroxyl group hydrogen-bonded to a main chain carbonyl group in the red and yellow subunits but not in the green and blue subunits, as a consequence of the differing ribose conformations. 3. Cysteine-149 is more closely associated with histidine-176 in the green and blue subunits, and appears nearer the nicotinamide in the red and yellow subunits.

Amino Acid Sequence↗
PubMed1973

D-glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance.

A 3.0-A resolution electron density map of lobster glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) was computed. The essentially single isomorphous replacement map was very substantially improved by averaging subunits. NAD binds in an open conformation at sites close to subunit interfaces. The coenzyme binding portion of the enzyme has almost the same fold as the corresponding portion of lactate dehydrogenase (EC 1.1.1.27). The presence of this structure in the five enzymes, analyzed so far, that use nucleotide coenzymes might indicate a fundamental primordial structural element.

Animals↗
PubMedDate not supplied

Solvent distribution in crystals of B- and Z-oligomers.

Two crystal structures of deoxyoligomers were refined to high resolution using the programs NUCLIN and NUCLSQ developed for refining the structure of yeast aspartic acid tRNA. The B form oligomer is the dodecamer d(5'OH-C-G-C-G-A-A-T-T-C-G-C-G-3'OH) solved by Dickerson and coworkers in 1981; the data used for the refinement are those deposited in the Brookhaven Data Bank. The crystal structure of the Z form hexamer d(5'OH-5BrC-G-5BrC-G-5BrC-G-3'OH) was resolved in Strasbourg. During the refinement each compound exhibits a different behaviour. Over sixty water molecules were located for each oligomer. The distribution of water molecules is typical of each helical form. Probably due to disorder, the hydration of the B form is not extensive. The minor groove of the B form presents the "spine of hydration" much discussed by Dickerson and coworkers. The Z form hexamer presents its most extended hydration network in the deep cavernous groove corresponding to the minor groove. Intermolecular contacts occur in both oligomers in the minor groove: in the B form through twisted guanine-guanine hydrogen bonding, and in the Z form through base-base stacking and the water network. The role and importance of solvent structure for DNA structure is discussed in the light of the results presented.

Crystallization↗
PubMedDate not supplied

Correlation between segmental mobility and the location of antigenic determinants in proteins.

Most continuous antigenic determinants of tobacco mosaic virus protein (TMVP), myoglobin and lysozyme correspond to those surface regions in the protein structure, as determined by X-ray crystallography, which possess a run of high-temperature factors along the polypeptide backbone, that is, a high segmental mobility. The mobility of an antigenic determinant may make it easier to adjust to a pre-existing antibody site not fashioned to fit the exact geometry of a protein. The correlation found between temperature factors and antigenicity is better than that between hydrophilicity and antigenicity.

Antigens, Viral↗