Ribosome, protein conformation role

C. The Unrecognized Role of the Ribosome in the Energetics of Protein Conformations... 

It is likely that protein binding and other macromolecular interactions also play a role in stabilizing the rRNA structures. A recent analysis12 reveals that the binding of specific ribosomal protein to rRNA in vitro results in changes within the rRNA modification patterns. Because the experiments detailed herein examine a population of rRNA within the cell, and thus may be analyzing a variety of RNA conformations, it is remarkable that very consistent results are observed. However, the consequence of polysome assembly and translation on the structure of the rRNA and how these structures might be distinct are not addressed in this analysis. In vitro DMS modification of soybean RNA has revealed some differences in base reactivity relative to that observed on RNA modified in vivo as described herein.36 ... 

Riboflavin phosphate and FAD may be either covalently or noncovalenfly bound at the catalytic sites of enzymes. Even in those enzymes in which the binding is not covalent, the flavin is tightly bound in many cases, the flavin has a role in maintaining or determining the conformation of the enzyme protein. In some cases, the flavin is incorporated into the nascent polypeptide chain, while it is stUl attached to the ribosome. However, in others a flavin-free apoenzyme is synthesized and accumulates in riboflavin deficiency (Section 7.5.2). 

The other two domains of the tripartite EF-Tu are distinctive they mediate interactions with aminoacyl-tRNA and the ribosome. In all these related enzymes, the change in conformation between the GTP and the GDP forms leads to a change in interaction partners. A further similarity is the requirement that an additional protein catalyze the exchange of GTP for GDP an activated receptor plays the role of EF-Ts for a heterotrimeric G protein, as does Sos for Ras. 

The pseudouridines within the H69 loop are synthesized by the RulD protein, one of the few modification enzymes in E. coli that is required for normal growth, that is, the mutant is severely impaired. Consistent with the findings of Noller and coworkers, and the modification results of Maivali and Remme, biochemical evidence supports a role for pseudouridine modification where a specific -dependent structure of H69 is necessary for subunit association. Our current understanding of the ribosome structure is insufficient to ascertain whether the ips are directly involved in subunit interactions, or whether modification causes a conformation change involving other conserved bases in the H69 loop. Since "0 modification of H69 is absolutely conserved and necessary for proper function, an understanding of the influence of modification on structure would be informative. 

DNA structures in a conformation-specific rather than sequence-specific manner (Copenhaver etal., 1994). For this reason, it has been proposed that UBF plays an architectural role at the ribosomal DNA promoter. In agreement with this model, electron microscopic imaging analysis indicated that DNA is wrapped around a UBF dimer in a structure reminiscent of the nucleosome (Bazettjones et al., 1994). Therefore, UBF may function as a scaffold protein, which, by establishing the proper DNA-protein structure, facilitates the formation of the transcription initiation complex at the ribosomal DNA promoter. This model also predicts that the UCE and core elements will cooperate with each other in the recruitment of UBF. Indeed, changes in the spacing between the UCE and core have profound consequences on the ability of UBF to stimulate RNA Pol I transcription. 

The ribosome is a complex structure in which several components are involved. It is known that Mg " " plays an important role in determining this structure moreover, experiments on RNA-proteins interactions have suggested that these two species of molecules can exert a strong mutual influence on their respective conformation(1). 

We have found that in intraribosomal RNA the base-stacking interactions are less than in the free RNA, and that the presence of Mg" alone, does not allow RNA in solution to assume the same conformation as it has in the ribosome, and that proteins play an important role in determining this conformation. 

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