The Configuration of Amino Acids

Unfortunately, the 3-phenyl-2-thiohydantoins formed in the Edman stepwise degradation suffer racemisation (Davies and Mohammed, 1984) so that the method cannot be used to determine the configuration of amino acids in a peptide. This is not usually a serious limitation, but enantiomerisation is a perpetual hazard in peptide synthesis (Chapter 7). It is therefore desirable to determine if enantiomerisation has occurred at any residue. Such information could be important, for example, in dating bone proteins obtained in archaeological excavations. Examination of the chiral purity of the amino acids in a total acid hydrolysate is not satisfactory. 

The chemistry of Rh(DIPAMP) and mechanism has been reviewed [9,14-16,19]. Marginally higher catalyst efficiencies are observed with higher alcohols compared with methanol, whereas the presence of water can result in the reduction of slurries. Filtration of the product can improve the %ee while the catalyst and D,L-product remain in the mother liquor. The catalyst stereoselectivities decreases as hydrogen pressure increases. [Rh(COD)(R,A-DIPAMP)] + BF4 (13) affords the -configuration of amino acids upon reduction of the cnamide substrate. Reduction of enamides in the presence of base eliminates the pressure variances on the stereoselectivities, but the rate of reaction under these conditions is slow [15]. 

ORD spectra and the configuration of amino acids indicated by an extremum around 530 nm. The only exception was the copper complex of L-(—)-proline, the entire curve of which is shifted hyposochromically. 

The alternative R,S convention is also used to specify the configurations of amino acids. According to this convention, L-alanine is designated (S)-alanine. Although the D,L method of designating the stereochemistry of amino add chiral centers is awkward, the historical use of this system is so deeply rooted in the scientific literature that it is still most commonly used when referring to amino adds as well as carbohydrates. We will therefore use the d,l convention throughout the remainder of this chapter. 

The configuration of amino acids relative to that of D-glyceraldehyde has also been established. The work of Freudenberg and Kuhn which is based on a careful and circumscribed application.of the principle of optical superposition is reviewed and it is su ested that it is not by itself conclusive. A more decisive proof for the n configuration of amino acids is obtained from the X-ray structure of glucosamine and enzymic specificity. The configuration of secondary asymmetric centers in certain amino-acids is considered and it is concluded that the carboxyl and hydroxyl groups in hydroxy-proline are in trans position to each other. 

Isolated from the same strain of Bacillus marinus it is likely that the configurations of amino acids in marihysin A and maribasins A-B are identical. 

The configuration of the amine was retained, except in the case of amino acid derivatives, which racemized at the stage of the pyridinium salt product. Control experiments showed that, while the starting amino acid was configurationally stable under the reaction conditions, the pyridinium salt readily underwent deuterium exchange at the rz-position in D2O. In another early example, optically active amino alcohol 73 and amino acetate 74 provided chiral 1,4-dihydronicotinamide precursors 75 and 76, respectively, upon reaction with Zincke salt 8 (Scheme 8.4.24). The 1,4-dihydro forms of 75 and 76 were used in studies on the asymmetric reduction of rz,>S-unsaturated iminium salts. 

The number and the type of amino acids and their sequence determine the surface charge of the protein, its molecular configuration and its unique chemical and physical properties. The function of a protein is dependent on its three-dimensional structure. A number of agents can dismpt this structure thus denaturing it, for example changes in pH, temperature, salt concentration, and the presence of reducing substances. 

The absolute configurations of amino acids 198a (the racemic counterpart was designated 186c) and 198i on the basis of X-ray crystal structure analysis data of the a-azido esters 197a-Me and 197i-Bn were (R) and (S,S,S), respectively. 

The term primary structure is used to describe the sequence of amino acid units (configuration) in a polypeptide chain. Structure 10.5 is an example of a primary structure. 

Helices can be described by the number of amino acid residues in a complete turn. In order to fit into a good helix, the amino acids must have the same configuration. For proteins, that configuration is described as an L-configuration, with the helix being a right-handed helix, referred to as an alpha-helix. 

As noted above, with the exception of alanine, the addition of amino acids to form polypeptides allows for a large number of stereochemical isomers to be formed, even considering that all are of the L form. But nature does not allow for this diversity and rather selects only one configuration for a sequence to occur in its synthesis of structure-specific proteins such as those employed as enzymes. Even those employed for other activities such as muscle have a specific geochemistry. In fact, the cell produces only geometry-specific polypeptides. 

The foundation for the configuration of these amino acids will be obtained if a-amino-y8-chloropropionic acid can be converted into aspartic acid, the configuration of which is known from its relationship to malic acid, (d-aspartic acid is converted into d-malic acid by nitrous acid.) The configuration of malic acid can be referred to that of tartaric acid and thence to d-glucose. 

Differences of <5 = 0.32-0.40 in the, 9F chemical shift for epimeric A -acylated Mosher derivatives of aliphatic a-amino acids, in particular alanine, as well as its amides and peptide derivatives, are sufficiently large to serve as a racemisation test23. However, high-field spectrometers are recommended to provide improved sensitivity (<0.5%). Table 19, representing analysis data taken at 376.5 MHz, can be found in Section 3.2.2.9. Analysis of absolute configuration of amino acids and amines can be more accurate using a modified Mosher method24. 

Related to this is the use of amino acid derived reagents for resolution of racemic carbonyl compounds and determination of absolute configurations by X-ray analysis at the imine stage. This is exemplified by the L-valinol derived imine of tricarboxyl (l-formyl-2-methoxyphenyl) chromium (see p 417)88. 

It has been reported that a variety of single-chain amphiphiies spontaneously produce stable, membrane-forming aggregates when dispersed in water 258 260). Dialky 1-amphiphile l-III (l or d means l- or D-configuration of amino acid unit in compound III, respectively), which was prepared by condensation of didodecyl L-glutamate and p-(4-bromobutoxy)benzoic acid and the subsequent quarterization with tri-methylamine, produces bilayer vesicles in water as probed by electron microscopy 251 >. 

A novel technique for dating archaeological samples called amino acid racemiza-tion (AAR) is based on the stereochemistry of amino acids. Over time, the configuration at the a-carbon atom of a protein s amino acids is lost in a reaction that follows first-order kinetics. When the a carbon is the only chirality center, this process corresponds to racemization. For an amino acid with two chirality centers, changing the configuration of the a carbon from L to D gives a diastereomer. In the case of isoleucine, for example, the diastereomer is an amino acid not normally present in proteins, called alloisoleucine. 

Figure 1.4 The D/L configurations of amino acids. Note that the carboxylic acid group must be drawn at the top and the R group at the bottom of the Fischer projection. Stereogenetic centres in the R group do not affect the D/L assignment...

Thus, we have developed a method for the detection of the absolute configuration of amino acids with low enantioenrichment. We thought that the absolute configuration of amino acids can be determined by detecting the absolute configuration of the produced pyrimidyl alkanol with high enantiomeric excess by asymmetric autocatalysis using amino acids as chiral initiators (Scheme 18). 

Highly sensitive chiral discrimination of amino acids with low ee was described. Amino acids with low ee act as a chiral initiator of asymmetric autocatalysis. In the presence of amino acids with low ee, pyrimidine-5-carbaldehyde was treated with z-P Zn to produce chiral pyrimidyl alkanol with the absolute configuration correlated with that of the amino acid by the consecutive asymmetric autocatalysis with amplification of ee. In addition, direct examination of extraterrestrial chirality was performed using meteorites by applying the asymmetric autocatalysis as the chiral sensor. The results indicated the presence of some chiral factor in the meteorites other than known organic compounds such as amino acids. 

Whether the enantiomeric preference, such as found in the L-configuration of amino acids or the D-configuration of sugars, comes from a deterministic or a random process... 

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