Amino acids in peptides and proteins

A great many protective groups have been developed for the amino group, including carbamates (>NC02R), used for the protection of amino acids in peptide and protein syntheses, and amides (>NCOR), used more vv idely in syntheses of alkaloids and for the protection of the nitrogen bases adenine, cytosine, and guanine in nucleotide syntheses. 

Coupling constants are routinely used to determine the side-chain conformation of amino acids in peptides and proteins. Whereas proteins nowadays are almost exclusively studied as C- and N-labeled isotopomers, peptides usually have these isotopes in natural abundance, i.e. the magnetically active heteronuclei are highly diluted. Most amino acids contain a methylene group at the ji-position for which the X angle is determined by the conformation of the Ca—Cp bond. Two vicinal Jhh coupling constants can be measured Ha to and H to Usually... 

Racemization of the native L-amino acid in peptides and proteins to the D-enantiomer generally results... 

Peptide chains have a direction and therefore two different ends. The amino terminus (N terminus) of a peptide has a free ammonium group, while the carboxy terminus (C terminus) is formed by the carboxylate group of the last amino acid. In peptides and proteins, the amino acid components are usually linked in linear fashion. To express the sequence of a peptide, it is therefore suf cient to combine the three-letter or single-letter abbreviations for the amino acid residues (see p. 60). This sequence always starts at the N terminus. For... 

The formation of methyl- (MTH) or phenylthiohydantoin (PTH) amino acids is a valuable technique for sequencing of amino acids in peptides and proteins by the Edman degradation procedure [1], HPLC is very useful for the separation of MTH- or PTH-amino acids as adsorption [2,3], reversed-phase [4] and ion-exchange [S] chromatography. 

Spatola, A. F. (1983) Peptide backbone modifications in chemistry and biochemistry of amino acids, in Peptides and Proteins (Weinstein, B ed.), Marcel Dekker, New York, pp. 267-357. 

Amino acid residue (Section 28.5) The individual amino acids in peptides and proteins. 

The identification of N-terminal amino acids in peptides and proteins is of considerable practical importance because it constitutes an essential step in the process of sequential analysis of peptide structures. 

Carboxypeptidase A catalyzes the hydrolysis of the C-terminal amino acids in peptides and proteins it shows a preference for aromatic and branched aliphatic side chains at the C-terminal end. The enzyme also acts as an esterase. The X-ray structure of the native form of carboxypeptidase A, was solved by Rees and Lipscomb to 1.5 A... 

The isoelectric point for histidine is the pH value halfway between the pK values for the two nitrogen-containing groups. The p.Aa and pi values of amino acids in peptides and proteins differ somewhat from those of free amino acids, principally because most of the a-amino and a-carboxyl groups are not ionized but are covalently joined in peptide bonds. 

The genetics part the program was guided by Sydney Brenner, who subsequently won the 2002 Nobel Prize in physiology and medicine. Brenner showed that each three-nucleotide sequence of nucleotides in DNA encoded an amino acid. The nucleotide bases in DNA program the sequence of amino acids in peptides and proteins. 

Peptide bond, amide bond, the covalent bond between the carboxy group of one amino acid and the amino group of the following amino acid in peptides and proteins. The free rotation about the C-N... 

The label-free voltammetry of DNA and proteins has been known for a long time bnt has recently started to blossom as an exciting field which new researchers are tempted to pursne with high motivation. With the endless possible combinations of amino acids in peptides and proteins, as well as the nucleobases in DNA and RNA, an immense variety of voltammetric signals can be obtained as a resnlt of aptamer-protein interactions. Since the method does not require any... 

The identification of N-terminal amino acids in peptides and proteins is of considerable practical importance because it constitutes an essential step in the process of sequential analysis of peptide structures. Many N-amino acid derivatives have been proposed for this purpose and the ones most commonly studied by TLC are 2,4-dinitrophenyl (DNP)-and 5-dimethylaminonaphthalene-l-sulfonyl (dansyl, Dns)-amino acids, and 3-phenyl-2-thiohydantoins (PTH-amino acids). Recently, 4-(dimethylamino)azobenzaie-4/-isothio-cyanate (DABITC) and phenyl-isothiocyanate (PITC) have also been investigated as derivatizing agents of amino acids. 

Aside from the peptide bond, the only other type of covalent bond between amino acids in peptides and proteins is the disulfide bond. It links two cysteine units. Recall that thiols are easily oxidized to disulfides (eq. 7.49). Two cysteine units can be linked by a disulfide bond. 

In HPLC-PDA studies, Grego et al. first reported on the use of derivative spectroscopy for the analysis of aromatic amino acids in peptides and proteins [23], extending the static studies of Balestrieri et al. [21] to separations-based analyses of mixtures. First, derivative spectra for a set of model peptides and... 

PDA deteetion is now a mature technique, with nearly 20 years of practical application in the laboratory. The analysis and quantitation of aromatic amino acids in peptides and proteins are probably one the most widely reported uses of PDA for these molecules. Conformational and stability analyses of proteins are another significant application. Also useful, although less frequently appearing in the literature, is PDA deteetion of a variety of naturally occurring chromophores and detection of chemical modifications such as oxidation that result in spectral changes. In all likelihood, chromophore analysis is more widespread than the literature indicates and is just routinely applied with little fanfare. 

An important application of phenyl isothiocyanates is the analysis of end amino acids in peptides and proteins. This is represented by equations (35) to (39), and involves derivatives of the end amino acids such as thiazolines (45), phenylthioureas (46), and phenylthiohy-dantoins (47)2 -3 ... 

Two cysteines in a protein can be oxidized to a disulfide, creating a bond known as a disulfide bridge. Disulfide bridges are the only covalent bonds that are found between nonadjacent amino acids in peptides and proteins. They contribute to the overall shape of a protein by linking cysteines found in different parts of the peptide backbone, as shown in Figure 22.7. 

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