Proteins alpha amino acid sequencing

Example Molecular dynamics simulations of selected portions of proteins can demonstrate the motion of an amino acid sequence while fixing the terminal residues. These simulations can probe the motion of an alpha helix, keeping the ends restrained, as occurs n atiirally m transmembrane proteins. You can also investigate the conformations of loops with fixed endpoints. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

Figure 4.2 This three-dimensional image of a protein shows the many twists and folds in its structure. The coils, called alpha helices, and the ribbons, called beta pleated sheets, are generally determined by the amino acid sequence of the protein and how the amino acids in different parts form weak bonds with each other. The shape of a protein is often critical for its function.

This protein has a molecular mass of 41-43 kDa and in rats has an amino acid sequence that is 60% of the human protein. Antiserum to human alpha,-AGP cannot be used for rats and mice because there are at least two forms of the protein. Alpha,-AGP is synthesized primarily in the liver and the half-life is approximately 24 h. This protein transports hormones and cationic xenobiotics and may also act in nonspecific immunosuppression. 

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