Amino acid protein structure

T. Kohno, D. Kohda, M. Haruki, S. Yokoyama, and T. Miyazawa, Non-protein amino acid furanomycin, unlike isoleucine in chemical structure, is changed to isoleucine tRNA by isoleucyl-tRNA synthetase and incorporated into protein. J. Biol. 

Several factors indicate that the amino acids detected in all of these carbonaceous chondrites are indigenous and that they must have originated abiotically. First, the presence of protein and non-protein amino acids, with approximately equal quantities of D and L enantiomers points to a nonbiological origin and precludes terrestrial contamination. In addition, the non-extractable fraction of the Murchison is significantly heavier in 13C than terrestrial samples. Finally, the relative abundances of some compounds detected resemble those of products formed in prebiotic synthesis experiments. The aliphatic hydrocarbons are randomly distributed in chain length, and the C2, C3, and C4 amino acids have the highest concentrations (i.e., the most easily synthesized amino acids with the least number of possible structures are most abundant) [4]. 

Figure 3.1 Principal protein amino acid side-chain metal-ion binding modes (the metal ion represented as a dark filled circle) and (right) the structure of the Ca2+-binding y-carboxyglutamate found in proteins of the blood-clotting cascade.

Most HPLC instruments monitor sample elution via ultraviolet (UV) light absorption, so the technique is most useful for molecules that absorb UV. Pure amino acids generally do not absorb UV therefore, they normally must be chemically derivatized (structurally altered) before HPLC analysis is possible. The need to derivatize increases the complexity of the methods. Examples of derivatizing agents include o-phthaldehyde, dansyl chloride, and phenylisothiocyanate. Peptides, proteins, amino acids cleaved from polypeptide chains, nucleotides, and nucleic acid fragments all absorb UV, so derivatization is not required for these molecules. 

The calorific capacity of amino acids is comparable to that of carbohydrates so despite their prime importance in maintaining structural integrity of cells as proteins, amino acids may be used as fuels especially during times when carbohydrate metabolism is compromised, for example, starvation or prolonged vigorous exercise. Muscle and liver are particularly important in the metabolism of amino acids as both have transaminase enzymes (see Figures 6.2 and 6.3 and Section 6.4.2) which convert the carbon skeletons of several different amino acids into intermediates of glycolysis (e.g. pyruvate) or the TCA cycle (e.g. oxaloacetate). Not all amino acids are catabolized to the same extent... 

Fig. 6. Chemical structures of some protein amino acids found in soils...

Figure 4.1 Correlation of predicted and observed retention times in reversed-phase chromatography. The predicted retention times for 58 peptides of 2 to 16 residues in length were obtained by summation of retention coefficients for each residue in the peptide. Retention coefficients were determined from the retention of model synthetic peptides with the structure Ac-Gly-XX-(Leu)3-(Lys)2-amide, where X was substituted by the 20 protein amino acids. (Reproduced from D. Guo, C.T. Mant, A.K. Taneja, and R.S. Hodges, J. Chromatogr., 359 519 [1986]. With permission from Elsevier Science.)...

In this section, you learned how to recognize addition and condensation polymerization reactions. You examined the structures and functions of several important biological molecules, such as proteins, amino acids, carbohydrates, DNA, and lipids. In the next section, you will examine the risks and benefits of manufacturing and using organic compounds. 

In addition to this, it has been reported that nonprotein amino acids could be formed by structural modifications to protein amino acids (methylation, hydroxylation, and halogenation) through modified L-a-amino acid biosynthetic pathways and through novel biosynthetic routes. Some examples of the nonprotein amino acids derived through these biosynthetic pathways are given below (Figure 3). A detailed discussion of known biosyntheses for certain nonprotein amino acids will be discussed later in this chapter. 

The primary structure of proteins is not the whole story. To really understand how proteins work, we have got to understand them as three-dimensional objects. So on to higher dimensions in the next chapter. But first, a few paragraphs about another role for the protein amino acids biosynthesis. 

About 300 different non-protein amino acids occur in plants. They may be incorporated into proteins in place of the correct amino acids. If they are incorporated into enzymes, they can prevent them from functioning. This often leads to death of the animal. For example, azetidine 2-carhoxylic acid in lily-of-the-valley, Comallaria majalis, and several legumes interferes with synthesis or utilization of structurally similar proline (Fig. 11.9). 

L-Canavanine, another non-protein amino acid, occurs in high concentrations in the tropical vine Dioclea megacarpa (sea purse, a legume) and is very toxic to mice. Its structure is NH2C(NH2)=N0(CH2)2CH(NH2)C02H. This is very similar to arginine, with which it interferes. 

AMINO ACIDS, PEPTIDES AND PROTEINS Table 13.1 Amino acids structures and standard abbreviations... 

This has obvious advantages over the process seen for glutamate synthesis via the reductive amination of 2-oxoglutarate, in that it no longer requires the intervention of free ammonia. We thus have the situation that some organisms are able to carry out the fixation of ammonia via reductive amination, whereas others manipulate via transamination the amino acid structures obtained from protein in the diet. 

Selected entries from Methods in Enzymology [vol, page(s)] Acquisition of frequency-discriminated spectrum, 239, 162-166, 170 sensitivity, 239, 169-173 constant-time, 239, 23-26 doublequantum filtered, 239, 236 gradient pulse experiments, 239, 185-189 protein structural information, 239, 377-379 pulse sequence and coherence transfer pathway, 239, 148-149 paramagnetic metalloprotein, 239, 494-497 data recording, SWAT method, 239, 166-169, 172 line shapes, effects of gradient pulses, 239, 162-166 identification of protein amino acid resonances, 232, 100 cyclosporin A, 239, 240-241. 

Deciphering amino acid structure and how these protein building blocks form... 

Polymastiamide A (579), an antimicrobial steroid with an unusual side chain modification involving an amide bond to a non-protein amino acid, was isolated from the Norwegian marine sponge Polymastia boletiformis. The structure of polymastiamide A (579) was elucidated by analysis of spectroscopic data and chemical interconversions [470]. Polymastiamides B-F (580-584), additional amino acid conjugates of steroids, were later isolated from the same sponge [471],... 

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