Secondary Structures of Peptides and Proteins

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. 

SECONDARY STRUCTURES OF PEPTIDES AND PROTEINS method. Amino acid... 

As illustrated in Scheme 134, both distereoisomers of thiazolidine 535 prepared from commercially available amino acid derivatives 533 and 534 can serve as /3-turn mimetics in the secondary structure of peptides and proteins therefore, they play an important role in many molecular recognition events in biological systems <2002TL1197>. A similar application can be found with thiazoline lactams <1999TL477>. 

Discrepancies between retention properties and either summated hydrophobicity or linear hydropathy parameters are expected to become more significant as the molecular size of the solute increases. A number of algorithms are available to predict the secondary structure of peptides and proteins such as the Chou-Fasman [51] method for predicting a-heUx and j8-sheet formation and other procedures [52,53] which determine the probability of heUx formation in a particular solvent environment. These approaches assist in the location of potential hydrophobic areas on the surface of a molecule via characterisation of amphipathic regions. For example, the probability profile shown in Fig. 11 indicates that an amphipathic a-helix can form in the C-terminal region of human )8-endorphin, a peptide which... 

The Merrifield Method 1153 Secondary Structures of Peptides and Proteins 1155... 

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