Amino acid residues substitution

Electrospray mass spectrometry (see Chapter 7) is becoming the method of choice for the complete characterization of newly discovered Hb variants.With it, die mass of the variant, whether the variant is an a- or 3-chain variant, the possible location and identity of the amino acid residue substitution, and the quantity of variant present may be derived. 

Grundemar, L., Kahl, U., Langel, U., Callreus, T. Bienen, Beyermann, M. (1996) Ligand binding and functional effects of systematic double D-amino-acid residue substituted neuropeptide Y analogs on Y1 and Y2 receptors Regul. Peptides 62, 131-136. 

Fig. 7.4 Schematic description of the amino acid residue substitutions within the screened calf intestinal alkaline phosphatase (cIAP) variants which are functionally expressed in E. coli. I represents synonymous nucleotide substitution.

The PAM matrices, ° which were developed by Dayhoff et ah, are based on the probability of an amino acid residue mutating to another amino acid residue. The original PAM matrix was derived using a small group of closely related sequences and tracking the amino acid residue substitutions. Each evolutionary PAM matrix is determined by multiplying the original PAM matrix by itself n — 1 times, where n is the number of desired evolutionary... 

Modified toxins could be produced with site-specific mutations to produce toxins with amino acid residue substitutions, additions or deletions. These modified toxins could then be characterized by a variety of techniques including bioassays, binding studies. X-ray crystallography and NMR analyses. Additionally, these studies will lead to a better understanding of the insect sodium channel. In fact, results gathered from X-ray analysis, binding assays and NMR studies may... 

FIGURE 5.19 N-Tertninal analysis using Edman s reagent, phenylisothiocyanate. Phenylisothiocyanate combines with the N-terminus of a peptide under mildly alkaline conditions to form a phenylthiocarbamoyl substitution. Upon treatment with TFA (trifluo-roacetic acid), this cyclizes to release the N-terminal amino acid residue as a thiazolinone derivative, but the other peptide bonds are not hydrolyzed. Organic extraction and treatment with aqueous acid yield the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative. 

The electron transport protein, cytochrome c, found in the mitochondria of all eukaryotic organisms, provides the best-studied example of homology. The polypeptide chain of cytochrome c from most species contains slightly more than 100 amino acids and has a molecular weight of about 12.5 kD. Amino acid sequencing of cytochrome c from more than 40 different species has revealed that there are 28 positions in the polypeptide chain where the same amino acid residues are always found (Figure 5.27). These invariant residues apparently serve roles crucial to the biological function of this protein, and thus substitutions of other amino acids at these positions cannot be tolerated. 

Note The amino acid residues of lysine (K) and arginine (R) which may be responsible for the binding of POs to polysaccharides are in bold. According to Demand et al. (2002), the mutual substitution of these amino acids has no influence on the sorption properties of the ATg08770 PO of Arabidopsis with pectins, and the deletion of the fragment results in the loss of this function. 

A nomenclature was proposed by Seebach for the description of / -amino acids according to their substitution pattern, and for naming the resulting / -peptides [66, 67]. Enantiomerically pure / -amino acid derivatives with substituents in the 2-or 3-position are thus defined as - and / -amino acids, respectively (abbreviated to H-/ -HXaa-OH and H-/ -HXaa-OH). The corresponding /S-peptides built from these monomers will be named ff - and / -peptides. Similarly, /S -peptides consist of / -amino acid residues with substituents in both the 2- and 3-positions. Finally, peptides built from geminally disubsituted amino acids are referred to as and / -peptides (Fig. 2.6). 

This effect is particularly well documented for y - and -amino acid residues [217, 218] which in several natural products (bleomycin A2 [219], calyculins [220]) have been shown to play a substantial role in the pre-organization of the whole molecule into its bioactive conformation. For example, changes in the substitution pattern of the y-amino acid linker in bleomycin A2 result in reduced DNA cleavage efficiency [219]. In the case of y-peptides, changing the relative configuration like or unlike of y " -amino acids has been used as a strategy to generate different local conformations (Fig. 2.34) suitable either for the construction of helices [201] or turns ]202-204]. 

Several results are quite apparent from the data shown in Table II. It is evident from the pentapeptide model compounds that substitution of amino acid residues at positions 4 and 5 does not significantly affect the structure about the N-terminus. This observation corroborated earlier work from agglutination-inhibition assays, which demonstrated that the nature of the amino acid at position 4 of the peptide (or glycopeptide) is not a requirement for specificity. 

Detection of Variants With Altered Functional Properties. When substitutions In either a-or 3-chains Involve amino acid residues that participate In the contact with heme or the contact between chains, changes In functional properties can occur and the determination of the oxygen affinity of the blood sample or of an Isolated hemoglobin variant Is desirable. Oxygen affinity Is affected by temperature, pH, salt concentration, the level of 2,3-dlphosphoglycerate (2,3-DPG), and to a lesser extent by the concentration of the hemoglobin. The concentration of 2,3-DPG In blood changes rather rapidly after collection and a... 

The introduction of redox activity through a Co11 center in place of redox-inactive Zn11 can be revealing. Carboxypeptidase B (another Zn enzyme) and its Co-substituted derivative were oxidized by the active-site-selective m-chloroperbenzoic acid.1209 In the Co-substituted oxidized (Co111) enzyme there was a decrease in both the peptidase and the esterase activities, whereas in the zinc enzyme only the peptidase activity decreased. Oxidation of the native enzyme resulted in modification of a methionine residue instead. These studies indicate that the two metal ions impose different structural and functional properties on the active site, leading to differing reactivities of specific amino acid residues. Replacement of zinc(II) in the methyltransferase enzyme MT2-A by cobalt(II) yields an enzyme with enhanced activity, where spectroscopy also indicates coordination by two thiolates and two histidines, supported by EXAFS analysis of the zinc coordination sphere.1210... 

Fig. 23. Possible helical models for the gramicidin A ion channel. The polypeptides are represented as helical strips, one molecule being stippled for clarity. Numbers refer to the substituted terminal amino acid residues. Model (i), proposed originally by Urry, is the one now generally accepted...

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