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C Massire

Publications and source records attributed to C Massire.

7 recordsLinked to original sources
PubMed2001

Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature.

Bacterial tmRNA mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. Its action results in the addition of a small number of C-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. Previous work has identified pseudoknots and stem-loops that are widely conserved in divergent bacteria. In the present work an alignment of tmRNA gene sequences within 13 beta-proteobacteria reveals an additional sub-structure specific for this bacterial group. This sub-structure is in pseudoknot Pk2, and consists of one to two additional stem-loop(s) capped by stable GNRA tetraloop(s). Three-dimensional models of tmRNA pseudoknot 2 (Pk2) containing various topological versions of the additional sub-structure suggest that the sub-structures likely point away from the core of the RNA, containing both the tRNA and the mRNA domains. A putative tertiary interaction has also been identified.

Base Sequence↗
PubMed1999

Structural basis for the specificity of the initiation of HIV-1 reverse transcription.

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV-1 RNA and tRNA3Lys, but remains poorly understood at the three-dimensional level. We used chemical probing to gain insight into the three-dimensional structure of the viral RNA-tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA-tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3' end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.

Base Sequence↗
PubMed1998

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis.

The secondary structure of bacterial RNase P RNA, a ribozyme responsible for the maturation of the 5' end of tRNAs, is well established on the basis of sequence comparison analysis. RNase P RNA secondary structures fall into two types, A and B, which share a common core formed by the assembly of two main folding domains, but differ in their peripheral elements.A revised alignment of 137 available sequences reveals new covariations allowing for the refinement of both types of secondary structures. Phylogenetic evidence is thus provided for the extension of stems P11, P14, P19, P10.1 and P15.1 through further canonical base-pairs or GAellipsisGA mismatches. These refinements led in turn to a new organization of the catalytic core, with coaxial stackings of helices P2 and P19 as well as P1 and P4. New inter-domain tertiary interactions involve loop L9 and helix P1 and loop L8 with helix P4. These features were incorporated into atomic-scale 3D models of RNase P RNA for representatives of each structural type, namely Escherichia coli and Bacillus subtilis. In each model, the juxtaposition of the core helices creates a cradle onto which the pre-tRNA substrate binds with most evolutionarily conserved residues converging towards the cleavage site. The inner cores of both types are stabilized similarly, albeit by different peripheral elements, emphasizing the modular and hierarchical organisation of the architecture of RNase P RNAs. Similarities are thus apparent between the type A modules, P16/P17/P6 and P13/P14, and their type B analogs, P5.1/P15.1 and P10. 1/P10.1a, respectively. Other noteworthy features of these models include compactness and good agreement with published crosslinking data.

Bacteria↗
PubMed1994

DRAWNA: a program for drawing schematic views of nucleic acids.

A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X11/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.

Computer Graphics↗
PubMedDate not supplied

MANIP: an interactive tool for modelling RNA.

Large RNA structures can be viewed as assemblies of smaller units or modules that are usually clearly identified (helices, hairpin loops, other recurrent motifs, etc.). We have developed a program, MANIP, which allows the rapid assembly of separate motifs (each with a specified sequence) into a complex three-dimensional architecture. The already determined modules are present in a database from which they can be extracted with the appropriate sequence. Their assembly is performed in real time on the computer screen with buttons and dials that command rotation and translation of any chosen fragment with respect to the chosen pivot, or that generate all possible variations of any torsion angle within a specified segment either in the 5' or in the 3' direction. The possible in-built manipulations follow the general stereochemical rules of RNA structure. MANIP automatically recognizes and displays the allowed and nonallowed hydrogen bonds between the residues. The program is interfaced with a rapid and automatic online refinement tool of partial or full assemblies, NUCLIN-NUCLSQ. The refinement protocol incorporates canonical as well as noncanonical base pairing constraints together with restraints imposed by covalent geometry, stereochemistry, and van der Waals contacts. The computer package runs on UNIX Silicon Graphics workstations and is written in C with OpenGL and X11/Motif libraries.

Algorithms↗