Amino acid functional groups

Coenzymes complement the catalytic action of the amino-acid functional groups. They are bound to apoenzymes (apoproteins) either covalently or non-covalently. It is interesting to note that non-covalently-bound coenzymes are polyanions at neutral pH as exemplified by the structures of glutathione (GSH) [17] and thiamine pyrophosphate [18]. Shinkai and Kunitake (1976b, 1977a) demonstrated the efficient binding of glutathione and coenzyme A (a polyphosphate) to cationic micelles and cationic polysoaps. Thus, the combina- ... 

Coenzymes facilitate chemical reactions through a range of different reaction mechanisms, some of which will be discussed in detail in this review. However, in all cases structural features of the coenzyme allow particular reactions to proceed along a mechanistic pathway in which reaction intermediates are more thermodynamically and kinetically accessible. When incorporated into apoen-zyme active sites, the coenzyme reactivity is influenced by a well-defined array of amino acid functional groups. For a given coenzyme, the particular array of amino acids presented by the different apoenzymes can drastically alter the degree of rate acceleration and product turnover and can specify the nature of the reaction catalyzed. 

In this section, the structure, function, and reactivity of amino acids, peptides, and proteins will be discussed with the goal of providing a foundation of successful deriva-tization. The interplay of amino acid functional groups and the three-dimensional folding of polypeptide chains will be seen as forming the basis for protein activity. Understanding how the attachment of foreign molecules can affect this tenuous relationship, and thus alter protein function, ultimately will create a rational approach to protein chemistry and modification. 

The pi of a protein depends of the sum total of the pK values of its constituent amino acid side chains. Although the pfC values of each amino acid functional group are known (Table 4.2), if these were incorporated into a protein,... 

Amino acid Functional group Cleaving agent Type of cleavage Yield Reference... 

To the investigator studying chemical modification of proteins, derivatives like those listed above are of interest for two primary reasons (1) some derivatives are sites of modification and (2) complete modification of a particular class of amino acid functional groups with a reagent may not be possible because of the presence of these derivatives. For any protein being investigated by chemical modification and containing these types of derivatives, any results and conclusions must account for the effects of these derivatives. 

A mechanism-based inhibitor may be defined as a chemically unreactive compound that is treated by the target enzyme as a substrate, but instead of forming the usual product, it is converted into a highly reactive species via the normal catalytic mechanism. Prior to release from the active site, the reactive intermediate may alkylate amino acid functional groups, forming a new covalent bond and inactivating the enzyme (90). Irreversible, mechanism-based inactivation is typified by first-order, time-dependent loss of enzyme activity saturation kinetics inactivation protection by substrates and reversible inhibitors failure to recover activity following dialysis and usually a chemical stoichiometry of one covalent adduct formed per enzyme active site. 

FIGURE 6-9 Amino acids in general acid-base catalysis. Many organic reactions are promoted by proton donors (general acids) or proton acceptors (general bases). The active sites of some enzymes contain amino acid functional groups, such as those shown here, that can participate in the catalytic process as proton donors or proton acceptors. 

It is most desirable that a given amino acid should form a single-derivative peak after treatment with a single derivatization agent. Unfortunately, that is not the case for many important determinations. Thus, for example, permethylation [481] and the formation of W-dimethylaminomethylene alkyl esters [482] appeared limited to only some amino acids. Persilylation of all amino acid functional groups with potent silyl donors [483] comes perhaps closest to definition of a universal reaction , but even here some problems are encountered (a) derivatization can be time-consuming (b) multiple derivatives are occasionally formed even under precautions (c) Si-N bonds are moisture-sensitive and (d) truly quantitative derivatization is difficult to achieve for all protein amino acids. 

Draw the structure of an amino acid and indicate the following features, which are common to all amino acids functional groups, side chains, ionicforms, and isomeric forms. 

TABLE 11.9 Commonly used chemical modifications of amino acid functional groups... 

Peslyakas, I.H.I. Synthesis of dissymmetric sorbents with neutral and hydroxyl-containing amino acid functional groups and their apphcation in hgand exchange chromatography , Ph. D. Thesis, Vilnyus, 1972. 

Bode et al. devised a unique chemoselective amide ligation by the decarboxylative condensations of a-ketoacids and A -alkylhydroxylamines (KAHA ligation) (Scheme 12) [64, 150-154]. This process requires neither coupling reagents nor catalysts, produces only water and carbon dioxide as by-products, and tolerates unprotected amino acid functional groups. It is also completely orthogonal to NCL and theoretically can be utilized at any junction. However, the limited access to A-alkylhydroxylamines and a-ketoacids restricts broader application of this chemistry. 

The essential part of SPPS is the protection of amino acid functional groups, which should not participate in peptide bond formation. To prevent undesired reactions with those functionalities, the so-called protection groups are required. There are two types of protection groups used in SPPS. The first protects the functional groups of amino acid side chains and should remain stable during the peptide synthesis process but be easily removed after the synthesis is complete. The second is a protection group of the alpha amino group in amino acids. This... 

Affinity labeling experiments with bromoacetyl compounds are biased by two important limitations, which often make them inferior to comparable photoaffinity labels. The number of properly oriented amino acid functional groups that can undergo a nucleophilic displacement reaction in the active site of a protein is limited to histidine, lysine, tyrosine, cysteine, and glutamic acid. Reactions are strongly influenced by the intrinsic piC of the respective amino acid residue and by the pH of the incubation mixture. It should be noted that bromoacetyl compounds can also react with RNA . The other limitation is that the time point for the affinity labeling reaction to occur cannot be freely chosen. One can only incubate the reactants and let them react for a given time. Reactions are usually quite slow and take considerable time for completion, which can vary between 1 and 20 hr. - ... 

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