Poly secondary structure

Before analyzing in detail the conformational behaviour of y9-peptides, it is instructive to look back into the origins and the context of this discovery. The possi-bihty that a peptide chain consisting exclusively of y9-amino acid residues may adopt a defined secondary structure was raised in a long series of studies which began some 40 years ago, on y9-amino acid homopolymers (nylon-3 type polymers), such as poly(/9-alanine) 3 [14, 15], poly(y9-aminobutanoic acid) 4 [16-18], poly(a-dialkyl-/9-aminopropanoic acid) 5 ]19], poly(y9-L-aspartic acid) 6 ]20, 21], and poly-(a-alkyl-/9-L-aspartate) 7 [22-36] (Fig. 2.1). 

Polypeptides form various secondary structures (a-heUx, 3-sheet, etc.), depending on solution pHs. We have investigated end-anchored poly(L-glutamic acid) andpoly(L-lysine) in various secondary structures [11,29,35,36], using the analytical method for the steric force... 

Akiyoshi K, Ueminami A, Kurumada S et al (2000) Self-association of cholesteryl-bearing poly(L-lysine) in water and control of its secondary structure by host — guest interaction with cyclodextrin. Macromolecules 33 6752-6756... 

In proteins in particular the peptide bonds contribute to the CD-spectra of the macromolecule. Here, CD-spectra reflect the secondary structure of proteins, which are derived from CD-spectra of model macromolecules with only one defined secondary structure (like poly-L-lysine at given pH values) or based on spectra of proteins with known structures (e.g.,from X-ray crystallography). The amount of a-helices or -sheets in the unknown structure is calculated by linear combination of the reference spectra [150,151]. 

In Section 7.7.3.3, methods for quantitating a-helix and other secondary structural types in peptides were described. These are generally applicable to a series of peptides in which a regular conformation [a-helix, (3-sheet, poly(Pro)II] is in equilibrium with an ensemble of unordered conformations, as evidenced by an isodichroic point observed over a range of temperature, pH, or solvent composition. 

The secondary structure of poly(iV-alkynylamides) is influenced by the position of the chiral center and amide group.The position of the chiral center mainly affects the helical pitch, which becomes short when the chiral center is positioned away from the main chain. The stability of the helical structure is also influenced by the position of the amide group. Based on molecular orbital study, it is concluded that poly(iV-propargylamides) with right-handed helical structure display a plus Cotton effect around 390 nm. This is also confirmed by the exciton chirality method using porphyrin as a chromophore. ... 

The co-polymerization of D-alanine-derived A-propargylamide 22, L-valine-derived 23, and pyrene-based monomer 24 gives helical poly(22 -< o-23-c -24) carrying pyrene. The secondary structure of the co-polymer is tunable by the composition of the optically active amino acid units and solvent, which makes it possible to control the direction of the pyrene groups in the side chain. The interaction between the pyrene groups is small when the co-polymer takes a helical structure. The pyrene groups are regularly positioned in the polymer side chain. The co-polymer emits weak... 

The metalloporphyrin complexes and their derivatives have been studied from the standpoint of model compounds of hemoglobin. The polymer-metalloporphyrin complexes are also formed by the reaction in Scheme 8, and a few qualitative investigations have been made with poly(L-lysine)9,10, poly(L-histidine)11, and poly(vinylimidazole)12 as the polymer ligand. Blauer9 has studied the complex formation of heme with poly(L-lysine) and has discussed the effects of the molecular weight and secondary structure of poly(L-lysine) on complex formation. 

Tliis description combined with Table 2, however, does not necessarily mean that the actual variation of pKa of the relevant group in the material is from ca.10 to ca.5. The actual pKa of the ionic groups in materials could be altered significantly due to the electrostatic interaction between these groups. This electrostatic interaction, on the other hand, could vary significantly according to the conformation that constituent macromolecules take, for example, the secondary structure of poly(amino acid). 

The most stable elements of secondary structure of peptides and proteins are turns, helices, and extended conformations. Within each of these 3D-structures the most commonly found representatives are (3-turns,a-helices, and antiparallel (3-sheet conformations, respectively. y-TurnsJ5 310-helices, poly(Pro) helices, and (3-sheet conformations with a parallel strand arrangement have also been observed, although less frequently. Among the many types of (3-turns classified, type-I, type-II, and type-VI are the most usual, all being stabilized by an intramolecular i <— i+3 (backbone)C=0 -H—N(backbone) H-bond and characterized by either a tram (type-I and type-II) or a cis (type-VI) conformation about the internal peptide bond. In the type-I (3-turn a helical i+1 residue and a quasi-helical 1+2 residue are found, whereas in the type-II (3-turn the i+1 residue is semi-extended and the 1+2 residue is also quasi-helical but left-handed. This latter corner position may be easily occupied by the achiral Gly or a D-amino acid residue. 

The enzyme is very sensitive to the secondary structure of the substrate. Native calf thymus DNA is quite resistant to enzymic attack by spleen exonuclease, being split at less than 4% the rate at which alkali-denatured DNA is split (11). Long deoxyribonucleotides (average chain length 20-50), which still have complementary double-stranded structure, are rather resistant to the enzyme (26). Some limited results obtained with synthetic polyribonucleotides (11) are rather puzzling since poly C was found to be completely resistant, whereas poly A, poly I, and poly U were degraded at comparable rates. In the solvent used (0.15 M acetate buffer-0.01 M EDTA, pH 5.0), poly A and poly C are believed to have... 

Homopolypeptides provide useful secondary structural models for spectroscopic studies on proteins and the ROA spectra of poly(L-lysine) in the three most important conformers are shown in Fig. 7.4. Poly(L-lysine) at alkaline pH... 

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