Loop variable

The ASCII input file includes elements of a scripting language. Thus, the input can contain variables, loops, and procedures. This is one of the aspects of the program that makes it possible to do very complex calculations. The documentation describes the input options, but does not discuss when and why they should be used. The user must have a solid understanding of ah initio theory in order to correctly utilize many of the functions in this program. It is very powerful, but not for beginners. 

Fig. 4. Schematic of the protein threading problem, where I L represent particular core segments and (-) corresponds to variable loop segments ...

Homologous proteins have conserved structural cores and variable loop regions... 

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

FIGURE 12.34 A general diagram for the structure of tRNA. The positions of invariant bases as well as bases that seldom vary are shown in color. The numbering system is based on yeast tRNA R = purine Y= pyrimidine. Dotted lines denote sites in the D loop and variable loop regions where varying numbers of nucleotides are found in different tRNAs. 

Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001 288(l) 51-62. 

Figure 29-7 (A) Generalized cloverleaf diagram of all tRNA sequences except for initiator tRNAs numbered as in yeast tRNAae (Fig. 5-30). Invariant bases A, C, G, T, U, and semivariant bases Y (pyrimidine base), R (purine base), H (hypermodified purine base). The dotted regions (a, P, variable loop) contain different numbers of nucleotides in various tRNA sequences. See Rich.179 (B) L form of the yeast phenyl-alanine-specific tRNAphe. The structure is the same as that in Fig. 5-31 but has recently been redetermined at a resolution of 0.20 nm.175 The new data revealed the presence of ten bound Mg2+ ions (green circles) as well as bound spermine (green).

The product of the selC gene, tRNA =, was identified as a novel tRNA species. Its structure differs from the features of all elongator tRNAs. With 95 nucleotides, it is the longest tRNA known to date. It has a variable loop of 22 nucleotides, an eight-base-pair aminoacyl acceptor stem, and a number of deviations from tRNA consensus structure. tRNA is charged with L-serine by the cellular seryl-tRNA synthetase, which is responsible for aminoacylation of the serine isoacceptor species. Thus, selenocysteine is formed from a serine residue charged to tRNA =. 

Chapman and Liljas, Fig. 21. Structure of HIV gpl20 (Kwong et al., 1998). Strands 1 through 25 are marked, as well as the positions of the variable loops that were deleted from the protein construct used for the structural study. 

Unique architectural features of tRNAs also can serve as identity elements (2). For example, the long variable loop of IRNA " interacts specifically with SerRS. In addition, the tertiary G15 G48 Levitt base pair in E. coli tRNA , and the triplet interaction in tRNA P, is formed between G45, and the G10 U25 parr confers identity. Occasionally, modified nucleotides can act as determinants, as in the case of coli tRNA , tRNA , tRNA T , and yeast tRNA . All of these tRNAs contain modifications in the anticodon loop. 

For Kelch-repeat proteins, the two loops on the bottom of the propeller (the AB and CD loops) are both short and well conserved. Instead, the longer and more variable loops (the BC and DA loops) both extend from the top surface. Thus the longer loops of the Keapi propeller present a more elaborate top surface when its side view is compared with that of Gp (F. IB). 

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