Secondary structure interactions

A single molecule of RNA often contains segments of sequence that are complementary to each other. These complementary sequences can base-pair and form helical regions of secondary structure. Interactions between the secondary structures give RNA a significant folded, three-dimensional structure. 

Although the native-like secondary structure interactions are weak in the absence of tertiary interactions, residual native structure does exist in some small peptide fragments and can help guide the protein on its way to folding. 

The nucleation-condensation mechanism can be accommodated in modified framework and hydrophobic-collapse models the framework model must be modified so that formation of secondary structure is linked to the formation of tertiary interactions and the hydrophobic collapse model must have the formation of tertiary interactions linked to the formation of secondary structure. Another variation of concerted structure formation is the hydrophobic zipper. 68 Whatever the distinctions of names, stable tertiary and secondary structural interactions must form concurrently. 

As we have seen in the previous Section 19.6, secondary-structure hydrogen-bonding geometry in the a-helices, / -pleated sheets and / -turns is constrained by the requirements of polypeptide chain folding. When the hydrogen bonds which are not involved in secondary-structure interactions are examined, their geometry is in better agreement to that observed in the small molecule crystal structures discussed in Part IB, Chapter 7. In most cases, therefore, the discussion can be limited to situations where deviations occur [596]. 

In the same vein, otic could pose several other questions pertaining to uncertainty propagatiOTi, system identification, vibratiOTi energy flow modeling, and treatment of multiphysics problems (such as fluid-structure interactions, soil-structure interactions, primary-secondary structure interactions, etc.). The discussion in the following sections will focus on a few of these issues. 

Nothing is known from experimental studies about the formation of supersecondary structures, i.e., about the mechanisms by which segments of secondary structure interact. Characteristics and tentative rules concerning supersecondary structure formation were deduced from the examination of three-dimensional structures. 

Figure 6.2 The molten globule state is an important intermediate in the folding pathway when a polypeptide chain converts from an unfolded to a folded state. The molten globule has most of the secondary structure of the native state but it is less compact and the proper packing interactions in the interior of the protein have not been formed.

Role of the Amino Acid Sequence in Protein Structure Secondary Structure in Protein.s Protein Folding and Tertiary Structure Subunit Interaction.s and Quaternary Structure... 

Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions (marginal figure). The different species of rRNA are generally referred to according to their sedimentation coefficients (see the Appendix to Chapter 5), which are a rough measure of their relative size (Table 11.2 and Figure 11.25). 

FIGURE 12.39 The proposed secondary structure for E. coli 16S rRNA, based on comparative sequence analysis in which the folding pattern is assumed to be conserved across different species. The molecule can be subdivided into four domains—I, II, III, and IV—on the basis of contiguous stretches of the chain that are closed by long-range base-pairing interactions. I, the 5 -domain, includes nucleotides 27 through 556. II, the central domain, runs from nucleotide 564 to 912. Two domains comprise the 3 -end of the molecule. Ill, the major one, comprises nucleotides 923 to 1391. IV, the 3 -terminal domain, covers residues 1392 to 1541. 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

The cathodically protected primary structures may be the hulls of ships, jetties, pipes, etc. immersed in water, or pipes, cables, tanks, etc. buried in the soil. The nearby unprotected secondary structures subjected to interaction may be the hulls of adjacent ships, unbonded parts of a ship s hull such as the propeller blades, or pipes and cables laid close to the primary structure or to the cathodic-protection anode system or groundbed. 

The severity of corrosion interaction will depend on the density of the stray current discharged at any point on the secondary structure. This may be assessed by measuring the changes in structure/soil potential due to the application of the protection current. Potential tests should be concentrated on the portions of pipe or cable which are close to the structure to be cathodic-ally protected, where the potential change is likely to be more positive. 

Interaction Testing routine investigation carried out when installing cathodic protection schemes on pipelines. The accepted criterion in the UK is that when the secondary structure potential has been moved more than 0-02 V in a positive direction, steps must be taken to eliminate the interaction. 

Primary Structure a buried or immersed structure cathodically protected by a system that rpay constitute a source of corrosion interaction with another (secondary) structure. 

Remedial Bond a bond established between a primary and secondary structure in order to eliminate or reduce corrosion interaction. 

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