Amino acids groupings

The dinitrophenyl group has been used to protect the imidazole — NH group in histidines (45% yield)" by reaction with 2,4-dinitrofluorobenzene and potassium carbonate. Imidazole —NH groups, but not a-amino acid groups, are quantitatively regenerated by reaction with 2-mercaptoethanol (22°, pH 8, 1 h)." The 2,4-... 

Peptide bond resonance has several important consequences. First, it restricts free rotation around the peptide bond and leaves the peptide backbone with only two degrees of freedom per amino acid group rotation around... 

Scheme 1.—Reaction Scheme for the Total, Reductive [ C]Methylation of the 6-Amino Group of Lysine, and the 2-Amino Group of an N-terminal Amino Acid Group.

Pd"(mida)] chelate (mida2 = methyliminodiacetate) is used to approximate the distorted tetragonal Cun-IMAC sites in order to identify which amino acid groups or their side-chain donors of SPHHGG and HHHHHH become attached to the metal site.214... 

Table 1.1 pKa of lonizable Amino Acids Group location... 

Isocyanide polymers functionalized with amino acid groups, typically di-or tripeptides containing histidine or serine, give enantioselective deacylation and rate enhancements. Their activity is increased by addition of cationic surfactants (Visser et al., 1985). 

Intramolecular redox reactions for bichromophoric compounds containing nitro and amino (or amino acid) groups have also been examined. For example4, irreversible... 

More specific evidence came from affinity labeling with molecules which could react with specific amino acid group sat or adjacent to the substrate site. These labels were substrate analogues and competitive inhibitors. Substituted aryl alkyl ketones were used. TV-p-toluene-sulphonyl-L-phenylalanine chloromethyl ketone (TPCK) blocked the activity of chymotrypsin. Subsequent sequence analysis identified histidine 57 as its site of binding (see Hess, 1971, p 213, The Enzymes, 3rd ed.). Trypsin, with its preference for basic rather than aromatic residues adjacent to the peptide bond, was not blocked by TPCK but was susceptible to iV-p-toluenesulphonyl-L-lysine chloromethyl ketone (TLCK) (Keil, ibid, p249). 

Another application of bioinformatics is the use of pharmacogenomics. There are some diseases, such as sickle cell anemia (Exhibit 2.3), in which the difference of one amino acid group can have drastic consequences. These differences in nucleotides are termed single nucleotide polymorphisms (SNPs). SNPs, whether due to genetic origins or environmental factors, translate to individual differences. By understanding these SNPs using bioinformatics, more individualized medicines with better efficacy and less adverse effects can be prescribed. 

The shape and biological function of a protein depends on its sequence of amino acids. A typical protein, such as insulin, contains at least 50 amino acid groups. Depending on the sequence of these amino acids, an infinite number of different proteins are possible. Each species of animal has its own distinct proteins. The DNA in your body contains the blueprints for making specific proteins for your body s structure and function. 

The hydrogen ion concentration has an effect on enzyme activity because many of the amino acid groups in an enzyme bear ionisable groups. Changes in pH will alter the degree of ionisation of some of these groups and so affect the ionisation of the enzyme molecule as a whole, modifying enzyme activity in at least three ways ... 

There are several such toxic agents that cause considerable medical, public and political concern. Two examples are discussed here the heavy metal ions (e.g. lead, mercury, copper, cadmium) and the fluorophosphonates. Heavy metal ions readily form complexes with organic compounds which are lipid soluble so that they readily enter cells, where the ions bind to amino acid groups in the active site of enzymes. These two types of inhibitors are discussed in Boxes 3.5 and 3.6. There is also concern that some chemicals in the environment, (e.g. those found in industrial effluents, rubbish tips and agricultural sprays), although present at very low levels, can react with enhanced reactivity groups in enzymes. Consequently, only minute amounts concentrations are effective inhibitors and therefore can be toxic. It is suggested that they are responsible for some non-specific or even specific diseases (e.g. breast tumours). 

When a protein contains more than about 200 amino acid groups, it often assumes two or more somewhat spherical tertiary structural units. These units are often referred to as domains. Thus, hemoglobin is a combination of four myoglobin units with each of the four units influenced by the other three, and where each unit contains a site to interact with oxygen. 

With the exception of alanine, all of the naturally occurring amino acids contain a chiral carbon adjacent to the amino acid grouping. All of these amino acids are of the 1 or L form, meaning they rotate light in a negative direction. The rules governing the specification of the absolute configuration are such that you can get both S and R forms of the amino acids. Thus L-phenylalanine is an S enantiomer while L-cysteine is an R enantiomer. 

The 1,3,2-oxaazasilacyclopentane ring can be used to protect the amino acid grouping (Equation (13)) <9ITL475>. 

Since the discovery that glycolate was an alternate substrate for pyruvate kinase ( ), several other o-hydroxy acids have also been found to be substrates for this enzyme ( ). This class of alternate substrates provides a new approach the problem of substrate specificity for pyruvate kinase. 3-Nitrolactate is one such alternate substrate. Interestingly, the phosphorylated product of this reaction inactivates the enzyme (86). However, 3-nitrolac-tate does not behave as a straightforward affinity label since covalent modification occurs nonspecifically. It is hoped that this new Information may lead to the design of an affinity label of this enzyme, further serving to pinpoint amino acid groups at the active site. 

Fig. 7 Sequence alignment of GPR motifs. Consensus amino acids are red chemically similar amino acids are blue. Consensus I refers to the conserved sequence defined with die family of AGS3-related proteins. Consensus II refers to the conserved sequence defined widi all known GPR proteins. Consensus II amino acid groupings are. =any, +=positive (HKR), —negative (DE), h=hydrophobic (ACFILMVWY), u=tiny (AGS), p=polar (CDEHKNQRST), and l=aliphatic (ILV). (C.e. C. elegans, D.m. D. melanogaster, A.t.. A. thaliand) The core GPR motif is as defined in Peterson et al. 2002. This figure is ad ted from die thesis of Dr. Yuri Peterson.

TABLE 14-4 by Site of Entry Glucogenic Amino Acids, Grouped... 

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