Amino acids peptide chain length

Experiments with liposomes, which are more complex stmctures than micelles, point in the same direction. Liposomes consist of one (or several) lipid double layers (see Sect. 10.2), ordered concentrically around an aqueous interior. Blocher et al. (2000) carried out polycondensation reactions of amino acids and peptides using l-palmitoyl-2-oleoyl-.vn-glycero-3-phosphocholine liposomes hydrophobically activated amino acids gave chain lengths of up to 29. The linkage of dipeptides (e.g., H-Trp-Trp-OH) to give Trps-OH, i.e., an octapeptide, was also carried out using liposomes. Thus, a second possibility, as well as adsorption on mineral surfaces, was available for polymer formation via micelles and liposomes. 

Peptide is the name assigned to short polymers of amino acids. Peptides are classified by the number of amino acid units in the chain. Each unit is called an amino acid residue, the word residue denoting what is left after the release of HgO when an amino acid forms a peptide link upon joining the peptide chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four, and so on. After about 12 residues, this terminology becomes cumbersome, so peptide chains of more than 12 and less than about 20 amino acid residues are usually referred to as oligopeptides, and, when the chain exceeds several dozen amino acids in length, the term polypeptide is used. The distinctions in this terminology are not precise. 

This chapter aims to summarize our efforts to investigate the effects of fluorinated amino acid substitutes on the interactions with natural protein environments. In addition to a rather specific example concerning the interactions of small peptides with a proteolytic enzyme, we present a simple polypeptide model that aids for a systematic investigation of the interaction pattern of amino acids that differ in side chain length as well as fluorine content within both a hydrophobic and hydrophilic protein environment. Amino acid side chain fluoiination highly affects polypeptide folding due to steric effects, polarization, and fluorous interactions. 

The binding of metal ions to peptides and proteins is a consequence of these molecules containing a great number of potential donor atoms through both the peptide backbone and amino acid side chains. The complexes formed exist in a variety of conformations that are sensitive to the pH environment of the complex [2,3]. With at least 20 amino acid combinations available, some with coordinating side chains, which can be linked in any particular order and length, the number of ligands that... 

Depending on the nature of the protein and the protease used, progressive proteolysis can liberate bitter peptides from proteins, the bitterness of which is a function of amino acid composition and sequence as well as the peptide chain length (Adler-Nissen, 1986b). An excellent review of the chemistry of bitterness has been published (Roy, 1997) and the reader is directed to this for more details. 

The composition of a protein hydrolysate is conveniently described by the degree of hydrolysis (DH), which is defined as the percentage of peptide bonds cleaved (1). The average peptide chain length (PCL), measured in number of amino acid residues, can be shown to be related to DH by the following equation ... 

In an attempt to find out more about the nature of the secondary binding site in penicillopepsin. Mains et al. (76) analysed the nature of the amino acid side chains at positions removed from the sensitive peptide bond. An abbreviated summary of the results is given in Table VII. The number of hydrophobic and hydrophilic side chains respectively are listed for four amino acids on either side of every peptide bond broken in the B-chain of insulin and in glucagon. The positions are numbered Pi, P2, P/, P2 etc. as defined by Berger and Schechter (103). The choice of four positions was taken from the Frutons work (73) on the specificity of pepsin and the eflFect of chain length on catalytic efficiency. The largest eflFects were observed with substrates having three to four... 

Free radical species that are capable of initiating vinyl polymerization reactions have been identified as Cu -co-ordinated amino-acid radicals, and these are produced in the primary photoreactions of the complex. An examination of the quantum yield and photodecomposition stoicheiometry of Cu (H2Aib)3 (H2Ajb= a-aminoisobutyric acid) as a function of irradiation wavelength and medium conditions has shown that 7r-copper -amidyl radicals are the primary photoproducts. The behaviour of other Cu -peptide complexes suggests that these photochemical parameters are dependent on the peptide chain-length and the number of a-carbon methyl substituents. ... 

The source of the peptides in these complexes can be either "self", i.e., derived from endogenous protons, or fordgn, from pathogenic sources. In inbred mice there are at least 22 allelic forms of heavy chain, each of which is thought to bind peptides with a specific structural motif, e.g., peptide length and position of specific amino acid side chains. The P2-microglobulin chain is invariant. Analysis of natural MHC molecules has led to identification of specific peptide epitopes for several of these alleles. The pq>tide motifs of two of the most well-characterized murine alleles, H-2K and H-2D , have been identified, and the 3- dimensional structures of their ternary complexes have been solved (2,3). 

How long is an a-helix that contains 74 amino acids Compare the length of this a-helix with the length of a fully extended peptide chain containing the same number of amino acids. (The distance between consecutive amino acids in a fully extended chain is 3.5 A.)... 

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