Amino acid sequence primary structure and

Figure 25-15 Lysozyme from hen egg-white showing the amino-acid sequence (primary structure) and the four intrachain disulfide bridges. [Adapted from D. C. Phillips, Sc/. Amer. 5, 215 (1966).]...

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. 

Within both of the light and heavy chains are regions of amino acid sequences (primary structures) which are constant, that is, they are the same for each type of antibody molecule we will consider. There are five types of antibodies and five sets of constant amino acid sequences for the heavy chains. The light chains have a... 

The enormous structural diversity of proteins begins with different amino acid sequences (primary structure) of polypeptide chains that fold into complex 3D structures. The final folded arrangement of the polypeptide chain is referred to as its conformation (secondary and tertiary structures). It appears that the information for folding to the native conformation is present in the amino acid sequences (Anfinsen, 1973) however, a special class of proteins known as chaperons is required to facilitate in vivo folding of a protein to form its native conformation (Martin and Hartl, 1997). 

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... 

Next, we describe the H NMR spectra of the two forms of Bomhyx mori fibroins, silk I and silk II (/3-sheet) forms, as shown in Fig. 31 (B) and (C). It should be noted that the amino-acid sequence (primary structure) of these two samples is completely identical, but their main-chain conformations are different. As expected, these two conformations are quite different to each other in terms of H CRAMPS NMR spectra. The H" signals of Bomhyx mori-I (silk-I) and Bomhyx mori-ll (silk-II) showed a singlet (h = 3.9) and doublet (S = 5.0 and 3.9), respectively. In addition, the chemical shift of the H protons... 

If the only structural characteristics of proteins were their amino acid sequences (primary structures), all protein molecules would consist of long chains arranged in random fashion. However, protein chains fold and become aligned in such a way that certain orderly patterns result. These orderly patterns, referred to as secondary structures, result from hydrogen bonding and include the a-helix (alpha-helix) and the P-pleated (beta-pleated) sheet. 

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-... 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

The similarity of the primary structure of different sea snake venoms has already been discussed. Postsynaptic neurotoxins from Elapidae venom have been extensively studied. Elapidae include well-known snakes such as cobra, krait, mambas, coral snakes, and all Australian snakes. Like sea snake toxins, Elapidae toxins can also be grouped into short-chain (Type I) and long-chain (Type II) toxins. Moreover, two types of neurotoxins are also similar to cardiotoxins, especially in the positions of disulfide bonds. However, amino acid sequences between cardiotoxins and sea snake and Elapidae neurotoxins are quite different. In comparing the sequence of sea snake and Elapidae neurotoxins, there is a considerable conservation in amino acid sequence, but the difference is greater than among the various sea snake toxins. 

Fig. 2 Illustration of protein structure levels. Shown are primary structure (amino acid sequence), secondary structure (local order of protein chain, a-helix shown as an example), tertiary structure (assembly of secondary structure elements), and quaternary structure (relationship of different protein chain in multisubunit protein). (From Ref. 66.)...

Empirical statistical methods, which are based upon data generated from studying proteins of known three-dimensional structure and correlation of such proteins primary amino acid sequences with structural features. 

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... 

PS II [134], Primary structure information is available for linker polypeptides of Synechococcus 6301 [77] and M. laminosus [105]. The complete amino acid sequences of the and the have been established and large N-terminal... 

Four levels of structure are frequently cited in discussions of protein architecture. So far, we have considered three of them. Primary structure is the amino acid sequence. Secondary structure refers to the spatial arrangement of amino acid residues that are nearby in the sequence. Some of these arrangements are of a regular kind, giving rise to a periodic structure. The a liel ix and (3 strand are elements of secondary structure. Tertiary structure refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds. We now turn to proteins containing more than one polypeptide chain. Such proteins exhibit a fourth level of structural organization. Each polypeptide chain in such a protein is called a subunit. 

Protein molecules are described in terms of their primary, secondary, and tertiary structures. The primary structure of a protein is the linear sequence of its amino acids. The primary structure for BPTI is... 

The primary structure of a protein is its amino acid sequence. Secondary structure is the shape defined by hydrogen bonds joining the CO and NH groups of the amino acid backbone. Tertiary and quaternary structures are the three-dimensional folded arrangements of proteins that are stabilized by hydrogen bonds and other intermolecular forces. 

In order to characterize and confirm the analytic structure in the case of r-DNA technology-derived proteins or peptides, amino acid sequencing is the method of choice. Both the overall amino acid composition as well as N- and or C-terminal amino acid sequencing are useful and well-established tools in protein chemistry. Amino-terminal analysis reveals information about the primary structure, homogeneity and occurrence of cleavages in the polypeptide. The... 

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