Amino acid sequence overview

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Table 10.1 Overview of some polypeptide growth factors. Many can be grouped into families on the basis of amino acid sequence homology, or the cell types affected. Most growth factors are produced by more than one cell type and display endocrine, paracrine or autocrine effects on target cells by interacting with specific cell surface receptors...

Neorecormon is one such product. Produced in an engineered CHO cell line constitutively expressing the EPO gene, the product displays an amino acid sequence identical to the native human molecule. An overview of its manufacturing process is presented in Figure 6.7. The final freeze-dried product contains urea, sodium chloride, polysorbate, phosphate buffer and several amino acids as excipients. It displays a shelf-life of 3 years when stored at 2-8 °C. A pre-filled syrine form of the product (in solution) is also available, which is assigned a 2 year shelf-life at 2-8 °C. 

An overview of protein synthesis is shown in Fig. S.A12. The linear sequence in mRNA that is translated to protein contains four bases, adenine, uracil, guanine and cytosine. The four letters A,U,G and C constitute the mRNA alphabet . This basic alphabet is used in triplets of bases called codons. The codons on mRNA pair up with anticodon or complementary triplets on the tRNA, thus matching the mRNA code to an amino-acid sequence. 

This extracellular enzyme is a relatively small (269 amino acids) single polypeptide chain and one-domain protein. The gene coding for it has been cloned and a cDNA-derived amino acid sequence is available (Boel et al., 1988). RmL crystallizes readily from high concentrations of phosphate buffers and yields orthorhombic crystals (see Table I) of high quality, diffracting to beyond 1.9 A. A detailed description of the RmL structure appears elsewhere (Z. S. Derewenda et al., 1992) an overview is presented here. 

Chapter 19 provides an overview of protein synthesis. The chapter begins with a discussion of the genetic code, the mechanism by which nucleic acid base sequences specify the amino acid sequences of polypeptides. This is followed by discussions of protein synthesis as it occurs in both prokaryotes and eukary-KEY CONCEPTS 1 9.1 otes and a description of the mechanisms that convert polypeptides into their... 

A field of research, on which solid-state NMR spectroscopy had a tremendous impact during the past decade, is the structural study of amyloid fibrils. Solid-state NMR spectroscopy can provide information on several aspects of the cross-p core structure of amyloid fibrils such as the localization of p-strands within the amino acid sequence and their relative arrangement within protofilaments and at the protofilament interface. Even high-resolution structures for the fibril core have been determined. An overview over emerging central motifs for amyloid structure is given in Fig. 4. 

It is clear that in this brief overview of molecular biology, we have not covered a number of important areas that have an important impact on the study of metalloproteins. These include molecular cloning and recombinant DNA technology, which allow proteins to be over-expressed and individual amino acids to be mutated to any other of the 19 protein amino acids genome and proteome analysis that enables the sequences of all the genes of the entire organisms to be determined, and the quantification, localization, interactions and, where possible, activities and identification of all of the proteins in an organism,... 

Due to the problems in identification of cellular substrates of protein kinases, as described in Chapter 7, it has been a difficult and lengthy process to determine the functionally relevant substrates. Pig. 13.11 gives an overview of the ceU-cycle-specific activation of CDKs and some important substrates. Comparatively sparse information is available on the Gj and S phase substrates of the CDKs. In contrast, many proteins have been described that undergo specific phosphorylation in G2/M phase. The sequence (K/R)-S/T-P-X-K (X any amino acid) has been identified as a consensus sequence for phosphorylation by CDKs. 

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