Peptides amino acid composition

To study the role of lysine residues in susceptibility to formalin fixation, the amino acid composition of immunoreactive peptides (to various monoclonal antibodies) was studied. Each peptide was evaluated to determine if immu-noreactivity was lost after formalin fixation. Formalin sensitivity was correlated with the peptides amino acid composition. The first step in the method is biopanning from a peptide combinatorial library with a monoclonal antibody. The peptides that bind to the antibody were tested for their sensitivity to formalin fixation. Some peptides remain immunoreactive whereas others do not. The peptides were then sequenced to look for differences between those that were sensitive to formaldehyde versus those that were not. The goal was to find whether there is a particular amino acid that is present in formalin-sensitive epitopes but absent in formalin-resistant epitopes, or vice versa. An advantage of this approach is that it is open-ended, without excluding any amino acids. 

Bitterness of Peptides Amino Acid Composition and Chain Length... 

Ney, K.H. 1971. Bitterness of peptides amino acids composition and chain length In Food Taste Chemistry , Advances in Chemistry Series 115 (J.C. Boudreau ed.), pp. 149-173, American Chemical Society, Washington, DC. 

Source. Reprinted with permission from K.H. Ney, Bitterness of Peptides Amino Acid Composition and Chain Length, in Food Taste Chemistry, J.C. Boudreau, ed., ACS Symp. Ser. 115, 1979, American Chemical Society. 

Ney, K. H. (1979b). Bitterness of peptides Amino acid composition and chain length. ACS Symp. Ser. 115, 149-173. 

Our results confirmed the tendency of Lys-flanked peptides to compensate the positive mismatch between peptide and membrane hydrophobic core by tilting. Some of the peptides, however, prodnce superhelical donble-twisted structure. This only occurs in the membrane in the gel phase, where only a small hydrophobic mismatch exists. The peptide also alters certain properties of the surrounding hpids snch as membrane ordering, the amount of dihedral angles in tram conformation and the nnmber of transitions between tram and gauche conformation. It is likely that these effects shonld provide some preferable stmctnral state of the peptides in a membrane. The lipid stmctural state around the peptide is probably between gel and hqnid-ciystalline state. This effect depends on peptide amino acid composition. Amino acids with large side chains branched at (He, Val) produce hehx, which has more side chains finctuates than that of a poly-Len helix. This holds also for small side chains (Ala). 

Cleave the peptide into smaller fragments, separate these fragments, and deter-mine the amino acid composition of the fragments. 

FIGURE 5.5 (a) The hydroxy amino acids serine and threonine are slowly destroyed during the course of protein hydrolysis for amino acid composition analysis. Extrapolation of the data back to time zero allows an accurate estimation of the amonnt of these amino acids originally present in the protein sample, (b) Peptide bonds involving hydrophobic amino acid residues snch as valine and isolencine resist hydrolysis by HCl. With time, these amino acids are released and their free concentrations approach a limiting value that can be approximated with reliability. 

Implicit in the presumption of folding pathways is the existence of intermediate, partially folded conformational states. The notion of intermediate states on the pathway to a tertiary structure raises the possibility that segments of a protein might independently adopt local and well-defined secondary structures (a-helices and /3-sheets). The tendency of a peptide segment to prefer a particular secondary structure depends in turn on its amino acid composition and sequence. 

When extracting sequence information from mass spectra, not only is the m/z value at which the ions occur of importance since these provide an indication of the amino acid composition of the peptide giving rise to the ion, but so is the mass difference between adjacent ions. This indicates the particular amino acid residue that has been lost and thus provides the sequence information required. The mass differences arising from each of the amino acids are shown in Table 5.6. 

Kentolysin Compared to Heliantholysin. Stoichactis helianthus occurs in the Caribbean region whereas another species, Stoichactis kenti is distributed in the Indo-Pacific area. The latter produces a toxin, kentolysin, that is similar to, but not identical with heliantholysin (6). The amino acid compositions of the two polypeptides show a distinct resemblance but appear to differ significantly in number of residues of lysine, methionine, tyrosine and histidine. IgG from a rabbit immunized against heliantholysin neutralizes both heliantholysin and kentolysin, but neutralization of the homologous toxin is more efficient (Table III). It can be seen that in the concentrations used, the IgG failed to neutralize the related lytic peptides of Condylactis gigantea and Epiactis prolifera. 

The soluble tryptic peptides of 130 mg a chain of Hb-St. Claude were separated on 0.9 x 60 cm columns of Chromobead resin type P (Technlcon Instruments, Dowex 50-X4) at 37°C using the procedure described earlier (16). The method uses a gradient of volatile pyrldlne-acetlc acid buffers of differing molarities and pH as follows first gradient, 666 ml 0.1 M, pH 3.1, and 333 ml 1.0 M, pH 5.0 and second gradient, 166 wl 1.0 M, pH 5.0, and 332 ml 2.0 M, pH 5.0. The amino acid composition of Isolated fragments was determined with a Splnco model 121 automated amino acid analyzer (Beckman Instruments)... 

Figure 3 shows the final chromatogram and activity profile of purified alpha-endopsychosin. The first peak contained most of the PCP displacing activity as measured by its ability to inhibit 3H-PCP. An aliquot of the most active material was hydrolyzed in acid and the amino acid composition was determined using OPA detection. It was determined that the peptide contained approximately 26 amino acids, in close agreement with the molecular weight predicted by Sephadex gel filtration studies. N-terminal analysis revealed that the peptide was blocked at this site. The nature of this blockade is yet to be determined. Studies are under way to determine the amino acid sequence of the peptide. 

Montecucchi PC, de Castiglione R, Piani S, Gozzini L, Erspamer V. Amino acid composition and sequence of dermorphin, a novel opiate-like peptide from the skin of Phyllomedusa sauvagei. Int J Peptide Protein Res 1981 17 275-283. 

Experimental and theoretical approaches are now converging on the polyproline II backbone conformation as the most stable structure for short alanine peptides in water. It becomes of urgent importance to determine the energy differences between polyproline II and other possible backbone conformations, as well as to determine how amino acid composition and sequence affect backbone conformation. 

Measuring protein absorbance at lower wavelengths (205 nm) increases the sensitivity of the assay considerably. Also, as it is the peptide bonds that are absorbing at this wavelength, the assay is subject to much less variation due to the amino acid composition of the protein. 

Figure 12.9 Overview of the production of Refludan (recombinant hirudin). The exact details of many steps remain confidential for obvious commercial reasons. A number of QC checks are carried out on the final product to confirm the product s structure. These include amino acid composition, HPLC analysis and peptide mapping...

Gordon, Martin and Synge18 utilized their new and elegant technique, chromatography, to establish the amino acid composition of gramicidin. They proposed a 24 unit cyclic peptide consisting of six moles each of leucine, and tryptophane, 5 moles of valine, 3 moles of alanine and 2 moles each of glycine and unknown hydroxyamino compound. 

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