Amino acid sequences primary structure determined

Proteins contain many single bonds capable of free rotation. Theoretically, therefore, proteins can assume an infinite number of possible conformations but under normal biological conditions, they assume only one or a very small number of most stable conformations. Proteins depend upon these stable conformations for their specific biological functions. A functional protein is said to be in its native form, usually the most stable one. The three-dimensional conformation of a polypeptide chain is ultimately determined by its amino acid sequence (primary structure). Changes in that sequence, as they arise from mutations in DNA, may yield conformationally altered (and often less stable, less active, or inactive) proteins. Since the biological function of a protein depends on a... 

The complete amino acid sequences (primary structure) of hemoglobins can, in principle, be determined by methods currently available. Although detailed studies of the primary structure of human and horse hemoglobins are in progress in several laboratories, the methods are so laborious that complete sequences have not yet been established. Important questions in the realm of genetics and evolution require the immediate examination of the structure, primary and other, of... 

It is important to appreciate that nmr cannot be used to determine the amino acid sequence (primary structure) of a protein. However, provided that the amino acid sequence is known, 2D nmr techniques can be used to deduce the secondary and tertiary structure of a protein (i.e. the way in which the polypeptide chain is coiled to give a-helical, -stranded or random coil regions and the way in which these re-... 

Another feature of peptide structure must be considered. The overall structure of a long polypeptide is determined by its amino acid sequence (primary structure) and whether it forms an a-helix or a P-pleated sheet (secondary structure). It is also possible to fold or coil the peptide chain into a complex, globular structure that is known as its tertiary structure. This is illustrated by the ribbon diagram for ribonuclease A, 131. The peptide chain folds and coils into a very complex structure in 131. This is the tertiary structure of the peptide. 

Somatostatin is a tetradecapeptide of the hypothalamus that inhibits the release of pituitary growth hormone. Its amino acid sequence has been determined by a combination of Edman degradations and enzymic hydrolysis experiments. On the basis of the following data, deduce the primary structure of somatostatin ... 

Currently, there exists an enormous and growing deficit between the number of polypeptides whose amino acid sequence has been determined and the numbers of polypeptides whose three-dimensional structure has been resolved. Given the complexities of resolving three-dimensional structure experimentally, it is not surprising that scientists are continually attempting to develop methods by which they could predict higher order structure from amino acid sequence data. Although modestly successful secondary structure predictive approaches have been developed, no method by which tertiary structure may be predicted from primary data has thus far been developed. 

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... 

The structure that the protein molecule assumes depends on both the surrounding environment (buffer solution, storage containers, etc.), and the primary amino-acid sequence. In addition there are intrinsic properties embedded in the primary amino-acid sequence that may determine... 

The application of the primary databases and structural analytical tools will be introduced using a protein from a future experiment. In Experiment 4, you will extract, purify, and characterize a-lactalbumin from bovine milk. To prepare for this activity, here you will learn about the structure of a related protein, a-lactalbumin from humans. We will search databases to find and view its primary and secondary structure and also determine if there are other proteins with a similar amino acid sequence and structure. After completion of these exercises, you will be able to apply these computer tools to proteins of your own choice. 

Enzymes are made from just 20 a-amino acid building blocks (structures and abbreviations are shown in Table 5.1). Each amino acid has a unique side chain, or residue, which can be polar, aliphatic, aromatic, acidic, or basic. The amide bonds (peptide bonds) make up the enzyme s backbone, and the residues determine the ultimate structure and catalytic activity of the enzyme. When the sequence of amino acids (the primary structure) for an enzyme is assembled in vivo, it folds... 

The amino acid sequence can be determined in a number of ways. The sequence can be established directly by combining a number of different techniques. The sequence of the protein can also be determined from the sequence of the gene that codes for it, and the primary, secondary, tertiary, and quaternary structures can be determined crystallographi-cally, which gives a complete model of the protein. 

The primary structure of a protein is the sequence of amino acids in its chain(s). Primary structure, which determines the other three kinds of structure, is maintained by the covalent peptide bonds between individual amino acids. The primary structure of egg-white lysozyme—a protein that helps fight infection—is shown in Figure 21.10 . The figure illustrates the amino acid sequence, the N-terminal and C-terminal ends, and the presence of disulfide linkages, covalent cross-links between cysteine amino acids in the polymer. We discuss disulfide linkages in more detail later in the section on tertiary structure. Researchers determined the first amino acid sequences for proteins in the 1950s. Today, the amino acid sequences for thousands of proteins are known. 

Peptides are formed by the condensation of carboxyl and amino groups in amino acids. Their primary structure is the sequence of amino acids. Secondary structure is determined by the required planarity of the amide group and interactions between side chains. a-Helices and p-pleated sheets are common motifs. Tertiary structure is the full three-dimensional structure of the peptide. 

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Different techniques give different and complementary information about protein structure. The primary structure is obtained by biochemical methods, either by direct determination of the amino acid sequence from the protein or indirectly, but more rapidly, from the nucleotide sequence of the... 

There are several levels of peptide structure. The primary structure is the amino acid sequence plus any disulfide links. With the 20 anino acids of Table 27.1 as building blocks, 20 dipeptides, 20 tripeptides, 20" tetrapeptides, and so on, are possible. Given a peptide of unknown structure, how do we determine its anino acid sequence ... 

The Primary Structure of a Protein Determining the Amino Acid Sequence... 

Amino Acid Sequence Determines Primary Structure... 

Proteins start out life as a bunch of amino acids linked together in a head-to-tail fashion—the primary sequence. The one-dimensional information contained in the primary amino acid sequence of cellular proteins is enough to guide a protein into its three-dimensional structure, to determine its specificity for interaction with other molecules, to determine its ability to function as an enzyme, and to set its stability and lifetime. 

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