Amino acid functional groups chemical modifications

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. 

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

It is not only the activity that can be altered by incorporation of noncoded amino acids. Introduction of structures possessing certain chemical functions leads to the possibility of highly regioselective modification of enzymes. For example, selective enzymatic modification of cystein residues with compounds containing azide groups has led to the preparation of enzymes that could be selectively immobilized using click chemistry methods [99]. 

GC-C-IRMS instrumentation enables the compound-specific isotope analysis of individual organic compounds, for example, n-alkanes, fatty acids, sterols and amino acids, extracted and purified from bulk organic materials. The principle caveat of compound-specific work is the requirement for chemical modification, or derivatisation, of compounds containing polar functional groups primarily to enhance their volatility prior to introduction to the GC-C-IRMS instrument. Figure 14.7 summarises the most commonly employed procedures for derivatisation of polar, nonvolatile compounds for compound-specific stable isotope analysis using GC-C-IRMS. 

The chemical modification studies have thus not yet led to a much more conclusive picture of the active site than that outlined in Fig. 12, and the identification of amino acid side chains involved in catalysis or substrate binding may have to await the completion of the crystal structure determination. The reporter properties of the Co(II) enzyme clearly show, however, that an open coordination position is of decisive functional importance, that the metal ion is intimately associated with the basic group participating in the reaction, and that the metal ion is probably also involved in the binding of one of the substrates, HCO3. 

Natural product molecules are biosynthesized by a sequence of reactions which, with very few exceptions, are catalysed by enzymes. Enzymes are protein molecules which facilitate chemical modification of substrates by virtue of their specific binding properties conferred by the particular combination of functional groups in the constituent amino acids. In many cases, a suitable cofactor, e.g. NAD+, PLP, HSCoA (see below), as well as the substrate, may also be bound to participate in the transformation. Although enzymes catalyse some fairly elaborate and sometimes unexpected changes, it is generally possible to account for the reactions using sound chemical principles and mechanisms. As we explore the pathways to a wide variety of natural products, the reactions will generally be... 

Enzymes are proteins that act as biological catalysts. They facilitate chemical modification of substrate molecules by virtue of their specific binding properties, which arise from particular combinations of functional groups in the constituent amino acids at the so-called active site. In many cases, an essential cofactor, e.g. NAD+, PLP, or TPP, may also be bound to participate in the transformation. The involvement of enzymes in biochemical reactions has been a major theme throughout this book. The ability of enzymes to carry out quite complex chemical reactions, rapidly, at room temperature, and under essentially neutral conditions is viewed with envy by synthetic chemists, who are making rapid progress in harnessing this ability for their own uses. Several enzymes are currently of importance commercially, or for medical use, and... 

There are numerous ways to determine experimentally pK values of chemical compounds (205). Classical methods are potentiometric titration and ultraviolet (UV) spectroscopy, among others. These techniques have been widely applied for nucleobases and also for metal-nucleobase complexes. For the extremes such as negative pK values (pK < —2) of singly or multiply protonated nucleobases, or very high pK values (pK >15) for deprotonation of exocyclic amino groups of nucleobases (C, G, A), modifications have to be employed. These include the consideration of the Hammett acidity function in superacidic solvents or solvent mixtures (206), as well as extrapolative techniques according to Bunnett-Olsen and Marziano-Cimino-Passerini to be applied in polar, aprotic solvents (45, 207). 

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