Genetic protein secondary structures

Johnson, W.C. 1990. Protein secondary structure and circular dichroism A practical guide. Proteins Struct., Fund, Genet. 7 205-214. 

Vivarelli et al. (1995) used a hybrid system that combined a local genetic algorithm (LGA) and neural networks for the protein secondary structure prediction. The LGA, a version of the genetic algorithms (GAs), was particularly suitable for parallel computational architectures. Although the LGA was effective in selecting different... 

Rost, B. and Sander, C. (1994) Combining Evolutionary Information and Neural Networks to Predict Protein Secondary Structure, PROTEINS Structure, Function, and Genetics 19 55-72. 

Cuff, J. A., and G. J. Barton. 1999. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. PROTEINS Structure, Function and Genetics 34 508-19. 

The small size of the biarsenical-tetracysteine tag has made it useful in biological studies requiring a genetically encoded fluorescent tag and GFP is not tolerated or has deleterious effects because of its size. FlAsH binding occurs rapidly, does not require any protein secondary structure to generate fluorescence (unlike GFP and its variants that can take minutes to days to become fully fluorescent) and should therefore be a more faithful reporter of the initiation of protein synthesis. The following examples include studies in viruses, bacteria, yeast, and mammalian cells and also indicate the broad applicability of the biarsenical-tetracysteine system. 

B. Rost and C. Sander, Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct. Fund Genet. 20, 216-226 (1994). 

The relationship between nucleotide frequencies and protein secondary structures is associated not only with the physico-chemical properties of these structures, but also with the organisation of the genetic code. In fact, this organisation seems to have evolved so as to preserve the secondary structures of proteins by preventing deleterious amino acid substitutions that could modify the physico-chemical properties required for an optimal structure Chiusano et al., 2000). 

Cuff J A and G J Barton 1999. Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction. Proteins Structure, Function and Genetics 34 508-519... 

The use of sequence information to frame structural, functional, and evolutionary hypotheses represents a major challenge for the postgeno-mic era. Central to an understanding of the evolution of sequence families is the concept of the domain a structurally conserved, genetically mobile unit. When viewed at the three-dimensional level of protein structure, a domain is a compact arrangement of secondary structures connected by linker polypeptides. It usually folds independently and possesses a relatively hydrophobic core (Janin and Chothia, 1985). The importance of domains is that they cannot be divided into smaller units— they represent a fundamental building block that can be used to understand the evolution of proteins. 

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Vivardli, F Giusti, G., Villani, M Campanini, R., Fariselli, P., Compiani, M. Casadio, R. (1995). LG ANN a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins. ComputAppl Biosci 11,253-60. 

To explore the feasibility of such an approach for the design of active catalysts, we have systematically replaced the secondary structural elements in the homodimeric helical bundle chorismate mutase (Fig. 3.18) with binary-patterned units of random sequence. Genetic selection was then used to assess the catalytic capabilities of the proteins in the resulting libraries, providing quantitative information about the robustness of this particular protein scaffold and insight into the subtle interactions needed to form a functional active site [119]. 

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