Amino acid residues definition

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

The aldehyde oxidoreductase from Desulfovibrio gigas shows 52% sequence identity with xanthine oxidase (199, 212) and is, so far, the single representative of the xanthine oxidase family. The 3D structure of MOP was analyzed at 1.8 A resolution in several states oxidized, reduced, desulfo and sulfo forms, and alcohol-bound (200), which has allowed more precise definition of the metal coordination site and contributed to the understanding of its role in catalysis. The overall structure, composed of a single polypeptide of 907 amino acid residues, is organized into four domains two N-terminus smaller domains, which bind the two types of [2Fe-2S] centers and two much larger domains, which harbor the molybdopterin cofactor, deeply buried in the molecule (Fig. 10). The pterin cofactor is present as a cytosine dinucleotide (MCD) and is 15 A away from the molecular surface,... 

By means of a procedure described above, Hanson and Fittkau (HI) isolated seventeen different peptides from normal urine. One of them, not belonging to the main peptide fraction, consisted of glutamic acid, and phenylalanine with alanine as the third not definitely established component. The remaining peptides contained five to ten different amino acid residues and some unidentified ninhydrin-positive constituents. Four amino acids, i.e., glutamic acid, aspartic acid, glycine, and alanine, were found in the majority of the peptides analyzed. Twelve peptides contained lysine and eight valine. Less frequently encountered were serine, threonine, tyrosine, leucine, phenylalanine, proline, hydroxyproline, and a-aminobutyric acid (found only in two cases). The amino acid composi-... 

The sizes of the prion domains vary from 70 amino acid residues (HET-s) to 250 amino acid residues (Rnqlp) (Fig. 1), but their borders are not precisely defined by functional criteria since these domains may be subjected to sizeable truncations while retaining their prionogenic properties (Edskes and Wickner, 2002 Ross et al., 2005). Nor are they precisely defined by the extent of N/Q-rich tracts since not all prion domains have them and the preponderance of these residues can vary within a given prion domain. Since the functional domains tend to have globular folds (Section II.B), an operational definition of a prion domain may be that it terminates with the last (or first) residue that is not part of the functional domain, although this definition is applicable only when that fold is known. 

A protein, of course, is a polypeptide chain made up of amino acid residues linked together in a definite sequence. Amino acids are handed (except for glycine, in which the normally asymmetric o-carbon has two hydrogens), and naturally occurring proteins contain only L-amino acids. That handedness has far-reaching effects on protein structure, as we shall see, and it is very useful to be able to distin-... 

Proteinases (Prt), again by definition, are responsible for the cleavage of peptide bonds, usually with a preference for particular types of side chain on the amino acid residues on one or the other or both sides of the scissile bond (Equation (7)). 

There are two definitions of protein hydrophobicity average hydrophobicity and surface hydrophobicity. The average hydrophobicity was defined by Bigelow (1967) as the total hydrophobicity of all amino acid residues comprising a protein divided by the number of amino acids in the protein. There is no standard definition of surface (or effective) hydrophobicity except the concept that there must be hydrophobic regions on the molecular surface that play an effective role in protein function. Readers who are interested in a more detailed discussion are referred to Nakai and Li-Chan (1988). 

Oxidation of two out of 13 tryptophan residues in a cellulase from Penicillium notatum resulted in a complete loss of enzymic activity (59). There was an interaction between cellobiose and tryptophan residues in the enzyme. Participation of histidine residues is also suspected in the catalytic mechanism since diazonium-l-H-tetrazole inactivated the enzyme. A xylanase from Trametes hirsuta was inactivated by N-bromosuc-cinimide and partially inactivated by N-acetylimidazole (60), indicating the possible involvement of tryptophan and tyrosine residues in the active site. As with many chemical modification experiments, it is not possible to state definitively that certain residues are involved in the active site since inactivation might be caused by conformational changes in the enzyme molecule produced by the change in properties of residues distant from the active site. However, from a summary of the available evidence it appears that, for many / -(l- 4) glycoside hydrolases, acidic and aromatic amino acid residues are involved in the catalytic site, probably at the active and binding sites, respectively. 

Proteins consist of a primary structure of amino acid residues connected in a definite sequence by peptide linkages to form polypeptide chains ... 

Protein chains generally contain hydrophobic, hydrophilic and/or charged amino acid residues, which can be regarded as amphiphilic copolymers in a broad definition. The coordinate and cooperative interactions, such as... 

At this temperature, the entropy change for dissolution of liquid hydrocarbons in water is zero. However, the entropy of protein denaturation is far from zero at this temperature but amounts to 17.6 J - K l per mole of amino acid residues (Privalov, 1979), a value that corresponds to an 8-fold increase of the number of possible configurations and is close to the value expected for the helix-coil transition of polypeptides (Schellman, 1955). This difference shows that an oil drop is an inadequate model for a globular protein. A more suitable model resembles that of a small crystal with a quite definite positive melting entropy (see also Bellow, 1977, 1978). 

It is possible to alter amino-acid residues to see if this perturbs the EPR signal, e.g. by iodination of tyrosine residues [142]. Recently site-directed mutagenesis has been used extensively for this purpose. Whilst this can yield definitive negative results it is unlikely to lead to clear positive identification of a... 

The amino acid residue that bridges the two-metal sites is shown in italic boldface. When the symbol H2O is given this may represent from one to three metal-bound water molecules. R is the distance between the metal atoms. When Trp is listed as a ligand, the a-amino and a amide carbonyl are the ligands. See footnote of Table 1 for the definitions of other terms. 

The position of several amino acid residues at certain definite sites of the chain suggests that these residues play a specific role in the formation of the secondary and tertiary structure (Watson and Kendrew, 1961). Thus, e.g., phenylalanines in positions 43 and 46 (a-chain) and histidine in position 87 (a-chain) obviously participate in the stabilization of the heme. The hydrogen bond linking tyrosine in position 42 and aspartic acid in position 94 stabilizes two sections of the o-helix. At those sites where the chains... 

If the hemoglobin chains are compared with respect to simple amino acid interchanges (within the definition given in the preceding section) the number of matching amino acid residues is increased to 92, i.e., 65%... 

Jones manually derived positions of amino acid residues in the apoenzyme structure and some ternary complexes published before 1977. Figure 21 shows a comparison between the present results with the earlier definition. The boundary region of model (co13) has also been assigned in the Figure. Ser-48, Phe-93 and lle-318 are in the same location while Leu-57 is in layers 3, 4 and 5 in our X-ray derived model. Using the present method positions of residues were positioned more accurately. 

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