Tertiary structures classification

Initial classification of some cytokines was also undertaken on the basis of the specific biological activity by which the cytokine was first discovered (e.g. TNF exhibited cytotoxic effects on some cancer cell lines CSFs promoted the growth in vitro of various leukocytes in clumps or colonies). This, too, proved an unsatisfactory classification mechanism, as it was subsequently shown that most cytokines display a range of biological activities (e.g. the major biological function of TNF is believed to be as a regulator of both the immune and inflammatory response). More recently, primary sequence analysis of cytokines coupled to determination of secondary and tertiary structure reveal that most cytokines can be grouped into one of six families (Table 8.2). 

There is still much to be learned about the structure and mechanism of action of this class of enzymes. Their mode of attack in terms of gross effects on substrates is now fairly well understood, especially in the cellulases, and this has resulted in a clearer classification of the purified components of the cellulase system. In order to explain the catalytic effects at a molecular level, it will be necessary first to obtain more information on the primary and, eventually, tertiary structures of the enzymes. The molecular mechanism, defined as a description of the number and structures of intermediates lying on the reaction path (6), then can be fully identified and from this the origin of the observed catalytic rate enhancements can be sought. 

The overall three-dimensional structure of a protein is called the tertiary structure. The tertiary structure represents the spatial packing of secondary structures (Ofran and Rost, 2005). As for secondary structures, there are several different classes of tertiary structures. More advanced classification schemes take into account common topologies, motifs, or folds (Wishart, 2005). Common tertiary folds include the a/p-barrel, the four-helix bundle, and the Greek key (we will discuss protein folding further in Chapter 14). Any change to any part of the structure of a protein will have an impact on its biological activity (Thomas, 2003). 

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

It has been observed that the use of protein tertiary structural class improved the accuracy for a 2-state secondary structure prediction (Kneller et al., 1990). A modular network architecture was proposed using separate networks (i.e., a- or P-type network) for classification of different secondary structures (Sasagawa Tajima, 1993). Recently, Chandonia Karplus (1995) trained a pair of neural networks to predict the protein secondary structure and the structural class respectively. Using predicted class information, the secondary structure prediction network realized a small increase in accuracy. 

While the methods for characterizing celluloses on the basis of their accessibility have been useful, they do not provide a basis for understanding the level of structure at which the response of a particular cellulose is determined. This follows from the ratlier simple categorization of the substrate cellulose into ordered and disordered fractions corresponding to the fractions that are thought to be crystalline and those that are not. This classification does not allow discrimination between effects that have their origin at the level of secondary structure and those that arise from the nature of the tertiary structure. Thus, in terms of chemical reactions, this approach does not facilitate separation of steric effects that follow from the conformation of the molecule as it is approached by a reacting species, from the effects of accessibility, which is inherently a consequence of the tertiary structure. 

Benzenedicarboyxylic acid Termination step, 154—156 Terpenes, 1025—1034, 1044 biosynthesis of, 1028—1034 classification, 1026 and isoprene rule, 1028 c<-Terpineol, 1031 Tertiary carbon, 65 Tertiary structure, 1086—1089 Tesla, Nikola, 491 Tesla... 

PP-fold family, a member of the gastroen-teropancreatic peptide families according to the classification proposed by Reh-feld. This family comprises pancreatic polypeptide (PP), peptide YY, and neuropeptide Y. The overall similarity in the primary structure varies between 45% and 70%. This similarity is connected to an almost identical and stable tertiary structure characterized by the PP-fold motif consisting of a polyproline-like helix (residues... 

The classification into primary, secondary, tertiary, and quaternary structures is not rigorous from a chemical or a physical viewpoint. For example, covalent bonds are classified under the primary as well as the tertiary structures and conformations under the secondary as well as under the tertiary structures. 

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