Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA

Abstract

SynopsisChemical reactivities of the functional groups of yeast phenylalanine transfer RNA are compared with surface accessibilities of the groups calculated with various probe radii representing effective radii of the chemical reagents used. We observe 97% agreement with the hypothesis that the chemically modified bases are those with the greatest surface accessibility. This overall strong correlation supports the conclusion that base exposure is an important determinant of chemical modification in this polynucleotide.

The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure

“…Three-dimensional model of the loop E of spinach chloroplast 5S rRNA generated from the 3D structure of E. coli by isosteric replacements of G102/U74 by A/C, G100/G76 by A/A, and G98/A78 by A/A+ FIGURE 12. Most commonly occurring variations of an "internal loop" within bacterial 16S rRNA (residues 581-583 and 758-760 in the E. coli 16S rRNA sequence)+ The most abundant (59+8% of all bacterial sequences) corresponds exactly to submotif 2 of loop E (boxed)+ Submotif 1, although less abundant (6+4%) is also present (boxed)+ were essentially correct+ Loop E is highly structured, with extensive base pairing within the loop, and magnesium ions play a key role in that structuring (Romby et al+, 1988;Westhof et al+, 1989;Brunel et al+, 1991)+ However, it is now apparent that the key role played by water and ions in protecting positions not involved in direct RNA-RNA H-bonds and particularly the direct involvement of water molecules in completing the H-bonding in some pairings render the process of deriving a given base pairing scheme from chemical probing data extremely difficult, except for trans-Hoogsteen A/U and sheared A/G pairs, which possess clear signatures in chemical probing+ Thus, the cautious view reached after the present analysis is rather different from that attained after the extensive comparisons between chemical and enzymatic probing and crystallographic structures of tRNAs made several years ago (Holbrook & Kim, 1983;Romby et al+, 1985)+ In tRNAs, also, the phosphate protections were rather well reproduced by the calculations based on the structures (Romby et al+, 1985)+ Interestingly, the most frequent non-Watson-Crick pair in tRNAs is the trans-Hoogsteen A/U pair, for which we see a clearcut chemical probing signature+ 2+ To evaluate the range of possible isosteric substitutions existing in a conserved molecule such as 5S rRNA, it is necessary to separate conservative sequence changes at the single base pair level from concerted changes involving several base pairs+ The large majority of conservative substitutions appear to be capable of forming isosteric replacements requiring little or no geometrical readjustment relative to the crystal structure+ In most cases, identical hydration patterns can also be proposed for these substitutions, emphasizing the integral part of water molecules in RNA structures+ 3+ The G100/G76 and G102/U74 bifurcated pairings are essentially identical in geometry+ The overlapping covariations observed in the database, particularly the occurrence of A/A at both positions, provides evidence that these may substitute for each other in other occurrences of the loop E motif+ 4+ Loop E comprises semi-independent submotifs+ This is supported by the observation that in most loop E's having concerted changes, these are localized to one or the other of submotifs 1 and 2+ The U. urealyticum and the Bacillus globigii sequences demonstrate that deletion of one base may transform a submotif of a bacterial loop E into the related eucaryal loop E motif+ 5+ Analysis in the light of phylogenetic data of the structures of noncanonical pairings of "internal loops" (such as loop E) allows one to generate a dictionary of isosteric substitutions for noncanonical pairings+ These in turn can be applied to postulate 3D structures for other internal loops that show overlapping patterns of sequence variation+ This analysis supports the suggestion that at least one internal loop in 16S and another in SRP RNA (4+5 S RNA in bacteria) share a common structure with submotifs 1 and 2 of loop E of bacterial 5S rRNA+…”

Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena.

“…We have now extended the structure model to three dimensions by application of RNA-structure rules derived from a consideration of tRNA structure. Additional constraints were imposed by the results of comparative sequence analysis and chemical-modification studies; the latter proved to give information quantitatively consistent with the known structure of tRNA (28).…”

Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model

“…At the end of the modeling, as well as during construction of sub-structures, accessible surfaces of the probed atoms were calculated (28) and compared to the experimental data. The radius of the solvent sphere rolling onto the van der Waals surface was adapted to the chemical probe (between 1.4 and 2.8 A) (29). The methodology is detailed in (15).…”