Internal loops structural stabilization

Although the role of RNA internal loops in the formation of RNA tertiary structure is only beginning to be understood, the crystal structure of the P4-P6 domain of the group I intron provides us with an instance of an internal loop which causes an approximately 180° bend between the two long helices which make up the three-dimensional structure and another internal loop which clamps down the two extended helices parallel to each other by forming a tertiary interaction with a tetraloop at the end of the other helbc (5)(7). The role of internal loops in stabilization of intermolecular RNA-RNA complexes has also been studied in several systems as discussed below. 

Regulation of transcription by iron. A cell s ability to acquire and store iron is a carefully controlled process. Iron obtained from the diet is absorbed in the intestine and released into the circulation, where it is bound by transferrin, the iron transport protein in plasma. When a cell requires iron, the plasma iron-transferrin complex binds to the transferrin receptor in the cell membrane and is internalized into the cell. Once the iron is freed from transferrin, it then binds to ferritin, which is the cellular storage protein for iron. Ferritin has the capacity to store up to 4,000 molecules of iron per ferritin molecule. Both transcriptional and translational controls work to maintain intracellular levels of iron (see Figs. 16.23 and 16.24). When iron levels are low, the iron response element binding protein (IRE-BP) binds to specific looped structures on both the ferritin and transferrin receptor mRNAs. This binding event stabilizes the transferrin receptor mRNA so that it can be translated and the number of transferrin receptors in the cell membrane increased. Consequently, cells will take up more iron, even when plasma transferrin/iron levels are low. The binding of IRE-BP to the ferritin mRNA, however, blocks translation of the mRNA. With low levels of intracellular iron, there is little iron to store and less need for intracellular ferritin. Thus, the IRE-BP can stabilize one mRNA, and block translation from a different mRNA. 

Figure 8. Water structure stabilizing (a) U-C and (b) U-G base pairs found in internal loops. Waters are denoted by blackened circles with hydrogen bonds indicated by grey lines. Atom type is shown in key.

Assignments of Exchangeable Protons ID NMR spectra of the 28mer collected at 9 1 H20 D20 at 10°C and 15°C also showed a significant structural stabilization of the internal loop in the presence of Mg + (5 mM) evident from the sharpening of several internal loop NH resonances. 

Summary. In this chapter the control problem of output tracking with disturbance rejection of chemical reactors operating under forced oscillations subjected to load disturbances and parameter uncertainty is addressed. An error feedback nonlinear control law which relies on the existence of an internal model of the exosystem that generates all the possible steady state inputs for all the admissible values of the system parameters is proposed, to guarantee that the output tracking error is maintained within predefined bounds and ensures at the same time the stability of the closed-loop system. Key theoretical concepts and results are first reviewed with particular emphasis on the development of continuous and discrete control structures for the proposed robust regulator. The role of disturbances and model uncertainty is also discussed. Several numerical examples are presented to illustrate the results. 

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