Amino acids general features

The decarboxylation of amino acids generally involves pyridoxal 5 -phosphate (PLP) as a cofactor (101-104) (Editor s note For additional features of PLP-dependent decarboxylation, see Chapter 7 by Kluger.). The general reaction is shown in Eq. (17),... 

Amino acid sequence comparisons have permitted some generalizations to be made about the residues likely to be important for catalysis of glycosyl transfer by certain classes of protein. However, it is not yet possible to correlate conserved primary amino acid sequence features of a glycosyltransferase with the nature of the sugar it transfers or the type of linkage it forms. 

By examining some of the over one thousand tumor-causing point mutations of p53 in the light of its structure, we can identify features of p53 that are necessary for tumor suppression. The amino acids most frequently changed in cancer cells are at or near the protein-DNA interface residues that are infrequently mutated, if at all, are in general far from the DNA-binding site. 

Post-column reaction is a common feature of many special types of analyses, the most well-known being the amino acid analyzer that uses ninhydrin with a post-column reactor to detect the separated amino acids. In general, derivatization and post-column reactor systems are techniques of last resort. In some applications they are unavoidable, but if possible, every effort should made to find a suitable detector for the actual sample materials before resorting to derivatization procedures. 

Some other types of macrocycle compounds have been synthesized using adamantane and its derivatives. Recently, a new class of cyclobisamides has been synthesized using adamantane derivatives, which shows the general profiles of amino acid (serine or cystine)-ether composites. They were shown to be efficient ion transporters (especially for Na+ ions) in the model membranes [159]. Another interesting family of compounds to which adamantane derivatives have been introduced in order to obtain cyclic frameworks is crown ethers [160]. The outstanding feature of these adamantane-bearing crown ethers (which are also called diamond crowns ) is that ot-amino acids can be incorporated into the adamantano-crown backbone [160]. This family of... 

A general feature of optimum sample preparation is that maximum recovery of the analyte is observed. Consider a graph of recovery vs. variation in one experimental condition. Figure 5 shows such a graph, with temperature as the experimental variable. The curve exhibits a maximum and a decline on either side of the maximum. The assay will be most reproducible at the point of zero slope, i.e., at the maximum recovery, because small variations in conditions will not affect the result. In hydrolysis of a protein to its constituent amino acids, for example, it will be found that at very high temperatures or long hydrolysis times, degradation of the product amino acids occurs, while at low temperatures or short hydrolysis times, the protein... 

An affinity label is a molecule that contains a functionality that is chemically reactive and will therefore form a covalent bond with other molecules containing a complementary functionality. Generally, affinity labels contain electrophilic functionalities that form covalent bonds with protein nucleophiles, leading to protein alkylation or protein acylation. In some cases affinity labels interact selectively with specific amino acid side chains, and this feature of the molecule can make them useful reagents for defining the importance of certain amino acid types in enzyme function. For example, iodoacetate and A-ethyl maleimide are two compounds that selectively modify the sulfur atom of cysteine side chains. These compounds can therefore be used to test the functional importance of cysteine residues for an enzyme s activity. This topic is covered in more detail below in Section 8.4. 

In view of the large variations in phi/psi preferences for the different amino acids observed in folded protein (see Fig. 5), it follows that the task of encoding the general features of long-range structure does not... 

Fig. 1. Cross-/] structure of amyloid fibrils. (A) Cartoon representation of a cross-/] X-ray diffraction pattern. The defining features are a meridional reflection at 4.7 A and an equatorial reflection on the order of 10 A. The 4.7-A reflection is generally much brighter and sharper than the reflection at 10 A. (B) The cross-/] core structure of amyloid fibrils. Parallel /(-sheets are depicted, but the structure could equivalendy be composed of antiparallel /(-sheets or a mix of parallel and antiparallel. The 4.7-A spacing of /(-strands within each /(-sheet is parallel to the long fibril axis. The depicted 10-A sheet-to-sheet spacing actually ranges from about 5 to 14 A (Fandrich and Dobson, 2002), depending on the size and packing of amino acid side chains. Amyloid fibrils have diameters on the order of 100 A.

Virtually all biological reactions are stereospecific. This generalization applies not only to the enzyme-catalyzed reactions of intermediary metabolism, but also to the processes of nucleic acid synthesis and to the process of translation, in which the amino acids are linked in specific sequence to form the peptide chains of the enzymes. This review will be restricted mainly to some of the more elementary aspects of the stereospecificity of enzyme reactions, particularly to those features of chirality which have been worked out with the help of isotopes. 

The binding affinity of carbohydrate-mimetic peptides can be quite high, often higher than the natural carbohydrate ligand. Carbohydrate-mimetic peptides do not share any general chemical features, and all amino acid residues are represented there is no evidence for an unusual importance of aromatic residues in mimicry. In several cases, o-amino acids have been incorporated, and unusual amino acids (derived from nonribosomal peptide synthesis) have been found in naturally occurring carbohydrate-mimetic peptides. 

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