Primary and Secondary Structure

Bacterial ribosomes contain three RNA molecules the 5 S, 16 S, and 23 S RNAs. The nucleotide sequence of the 5 S RNA with 120 nucleo- 

The knowledge of the primary structure was the basis for the construction of models of the secondary structure of the RNA molecules. Different approaches have been used in several laboratories to get experimental support for developing secondary structure models for example, chemic modification of the RNA, treatment with single- or double-strand-specihc nucleases, intramolecular RNA cross-linking, isolation and sequence analysis of double-stranded RNA, and, last but not least, comparison of ribosomal RNA sequences from different organisms (reviewed by Brimacombe et al., 1983). 

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The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

The shape of a large protein is influenced by many factors including of course Its primary and secondary structure The disulfide bond shown m Figure 27 18 links Cys 138 of carboxypeptidase A to Cys 161 and contributes to the tertiary structure Car boxypeptidase A contains a Zn " ion which is essential to the catalytic activity of the enzyme and its presence influences the tertiary structure The Zn ion lies near the cen ter of the enzyme where it is coordinated to the imidazole nitrogens of two histidine residues (His 69 His 196) and to the carboxylate side chain of Glu 72... 

Primary and Secondary Structure. The DNA double helix was first identified by Watson and Crick in 1953 (4). Not only was the Watson-Crick model consistent with the known physical and chemical properties of DNA, but it also suggested how genetic information could be organized and rephcated, thus providing a foundation for modem molecular biology. 

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

During 1944 at U.S. Air Force, Wright-Patterson AFB, Dayton, OH the first successful all plastic airplane (primary and secondary structures) was designed, fabricated, and flight tested (Fig. 4-11). It used... 

Olafson RW, WD McCubbin, CM Kay (1988) Primary- and secondary-structural analysis of a unique prokaryotic metallothionein from a Synechococcus sp. cyanobacterium. Biochem J 251 691-699. 

Traditionally, G-proteins have been classified in terms of the effector coupling of the a subunit. In spite of the facts that (1) this predates information on primary and secondary structure from cloning work, and (2) the fly subunits are also involved in effector coupling, this classification is still quite useful. 

Nucleic acid structures and sequences primary and secondary structure of DNA fragments, translocation of genes between two chromosomes, detection of nucleic acid hybridization, formation of hairpin structures (see Box 9.4), interaction with drugs, DNA triple helix, DNA-protein interaction, automated DNA sequencing, etc. 

Sequencing.—With the elucidation of the primary and secondary structure of the replicase gene, the complete 3569-nucleotide-long sequence of the RNA of bacteriophage MS2 is now known.153 This is the first organism for which theentire nucleic acid structure has been elucidated, and Fiers and his group richly deserve their bouquet. 

Plant defensins are cystine-rich, cationic peptides ranging in size from 45 to 54 amino acids, of which eight are cysteine. They were first discovered in wheat and barley ° and were proposed to form a novel subclass of thionins, the 7-thionins. As it became clear that they closely resemble mammalian and insect defensins in primary and secondary structure, the term plant defensins was introduced to describe these peptides. It is generally assumed that all plants express plant defensins " and that they are expressed in a wide range of plant tissue, that is, leaves, floral tissue,tubers,bark, root, pods, and seeds,with seeds in particular being from where most plant defensins have been isolated. ... 

Huet JC et al (1995) The relationships between the toxicity and the primary and secondary structures of elicitin-hke protein elicitors secreted by the phytopathogenic fungus Pythium vexans. Mol Plant Microbe Interact 8 302... 

Chain folding depends on the primary and secondary structures of materials. Thus, the particular atomic composition of a chain dictates, under equilibrium conditions, its tertiary and quaternary structures. 

While we characterize nonstructural proteins as being globular in shape, these shapes vary considerably according to their use. Again, this overall shape is governed by a combination of factors including primary and secondary structures. 

The primary and secondary structures greatly influence possible processing scenarios. Here, the secondary structure is generally the same as the physical structure and the primary structure is generally the same as the chemical structure. The end properties and uses are governed by intrinsic properties that in turn are related to the primary and secondary structures—the chemical and physical structures. 

DIMS9052 and DIMS9054 have similar primary and secondary structures, but nevertheless differ in their ability to form specific tertiary structures of parallel G4-tetramers (Fig. 3). This can be correlated to the difference in their IFN stimulatory capacity (Table 2) as well as in their ability to reduce the rate of disease progression in the EAE in vivo rat model (Fig. 4). 

Biochemists use the terms primary and secondary structure to designate configurations and conformations of proteins, respectively. 

Holt, C., Sawyer, L. (1993). Caseins as rheomorphic proteins interpretation of the primary and secondary structures of the otsi-, p- and K-caseins. Journal of the Chemical Society, Faraday Transactions, 89, 2683-2692. 

The application of the primary databases and structural analytical tools will be introduced using a protein from a future experiment. In Experiment 4, you will extract, purify, and characterize a-lactalbumin from bovine milk. To prepare for this activity, here you will learn about the structure of a related protein, a-lactalbumin from humans. We will search databases to find and view its primary and secondary structure and also determine if there are other proteins with a similar amino acid sequence and structure. After completion of these exercises, you will be able to apply these computer tools to proteins of your own choice. 

Fisher, D. Z., Chaudhary, N., and Blobel, G. (1986). cDNA sequencing of nuclear lamins A and C reveals primary and secondary structural homology to intermediate filament proteins. Proc. Natl. Acad. Sci. USA 83, 6450-6454. 

McKeon, F. D., Kirschner, M. W., and Caput, D. (1986). Homologies in both primary and secondary structure between nuclear envelope and intermediate filament proteins. Nature (London) 319, 463-468. 

Formaldehyde introduces both intramolecular and intermolecular crosslinks between proteins involving hydroxymethylene bridges, which change the three-dimensional structure of proteins. Such changes involve the tertiary and quaternary structures of proteins, whereas the primary and secondary structures are little affected. It has been shown that the secondary structure of purified protein molecules remains mostly unaltered during fixation with formaldehyde (Mason and O Leary, 1991). Even when the quaternary structure is changed by formaldehyde fixation, the secondary structure can remain intact. 

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