Amino acid side chains definition

Metalloclusters consist of at least two metal ions associated with inorganic and/or otherwise nonprotein ligands. Bimetallic centers in which the metal ion ligands are composed of H20/0H ligands in addition to amino acid side chains are excluded from the definition of a metallocluster. Several metalloclusters have been characterized structurally in metalloproteins. 

XV), but this evidence is probably not definitive since a similar discrepancy exists for other proteins as well. Although the interactions of L-amino acid side chains with a right-handed helix will be different from those with a left-handed helix, rotatory dispersion is primarily a function of the helical skeleton rather than side-chain interactions and cannot at present distinguish among helices of different sense mixed with disordered regions. 

The side chain dihedral angle Xi is important for high-resolution definition of protein structures as it determines the angle at which each amino acid side chain branches out from the protein backbone. Moreover, in combination with certain types of NOEs, it can allow stereospecific assignment of prochiral /3-methylene protons, which improves the precision of NMR structures by obviating the need to include pseudoatom distance corrections.140-142... 

The results of X-ray crystallography show, in addition to the binding site for aromatic amino acid side chains of substrate molecules, a definite arrangement of the amino acid side chains that are responsible for the catalytic activity of the enzyme. The residues involved in this arrangement are serine 195 and histidine 57. 

Certain classes of enzymes require small, auxiliary, nonprotein molecules called cofactors, coenzymes, and prosthetic groups. Definitions for these three terms are somewhat arbitrary and, in fact, the term cofactor will be used in the following chapters to represent broadly the identity and functional roles of cocatalysts. The roles of cofactors are structural, functional, or both. They provide the enzyme with the chemical or photochemical capabilities lacking in the normal amino acid side chains. An enzyme devoid of a cofactor is called an apoenzyme. Apoenzymes are catalytically inactive. The active complex of the protein and the cofactor is termed a holoenzyme. The cocatalysts can be defined on the basis of the catalytic functions that are mediated (76). 

More localized variations can be detected by immunochemical studies when the antibodies are purified to monospecificity. To obtain information regarding very localized parts of the polypeptide chain during the folding (or the unfolding) process, the most suitable methods are certainly those which allow one to determine the accessibility of amino acid side chains to chemical reagents in the precise position of the sequence, or the accessibility of definite peptide bonds to specific proteases. Nuclear magnetic resonance allows one to follow the behavior of individual protons when correct assignment is possible and thus provides the same type of local... 

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. 

Different side chains have been found to have weak but definite preferences either for or against being in a helices. Thus Ala (A), Glu (E), Leu (L), and Met (M) are good a-helix formers, while Pro (P), Gly (G), Tyr (Y), and Ser (S) are very poor. Such preferences were central to all early attempts to predict secondary structure from amino acid sequence, but they are not strong enough to give accurate predictions. 

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

For the purpose of this chapter, all amino acids containing side chains that differ from the L-a-amino acids will be designated as either unusual or nonprotein amino acids. This is due to the observation that these unusual amino acids are generally not found to be the constituents of proteins. The scope of this chapter is limited to nonprotein L-a-amino acids. The definition of nonprotein amino acid is not absolute and, therefore, the... 

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)). 

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