Structure of Peptides

Naturally occurring peptides show various types of structure. Linear peptides obviously possess two ends, one of which is made up of an amino 

2 These terms, homeomeric peptides and heteromeric peptides, should not be confused with the terms, homopeptide and heteropeptide, which Blout and Linsley (77) used to designate peptides consisting respectively of a single type of amino acid or of several different types of amino acids. 

In addition to linear peptides, one can envisage the existence of cyclic peptides in which there is neither an initial nor terminal amino acid and for which the number of peptide bonds equals the number of amino acids. Of course, one can also postulate the existence of partially cyclic peptides, forming sigma-shaped chains ( r), in which either the terminal or initial amino acid is internally linked in the peptide. Therefore, it is possible to have partially cyclic peptides possessing either a terminal (6 ° ) or an initial amino acid (h,n9) Certain peptides possess other structures, e.g., bicyclic and polycyclic, owing to the presence of nonpeptide linkages between amino acids, in addition to the characteristic a-peptide bond. Examples of such structures are penicillins, peptides of rye ergot. 

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Fig. 1.1 Comparison of the primary structure of peptide and peptoid oligomers...

A //-peptidic parallel sheetiike conformation with characteristic intermolecular 14-membered H-bonded rings was first observed in the crystal structure of -peptide Boc-/ -HVal-/ -HAla-/l -HLeu-OMe 116 (Fig. 2.28A) [10]. However, the struc-... 

It is important to note that the secondary and tertiary structure of peptides to which they are attached may subsequently help in controUing the reactivity of... 

Hydrogels Based on [l-Sheet Structures of Peptides and Polypeptides. 146... 

PROTEIN STRUCTURE OF PEPTIDE DEFORMYLASES Three-dimensional Structure Metal-binding Site... 

Engelhard, V.H. (1994) Structure of peptides associated with class I and class II MHC molecules. Annu. Rev. Immunol. 12, 181-207. 

The characteristic properties of peptides result from the presence of a chain of several or many amide bonds. A first problem is that of numbering, and here Fig. 6.1 taken from the IUPAC-IUB rules may help. A second and major aspect of the structure of peptides is their conformational behavior. Three torsion angles exist in the backbone (Fig. 6.2). The dihedral angle co (omega) describes rotation about C-N,

rotation about N-C , and ip (psi) describes rotation about C -C. Fig. 6.2 represents a peptide in a fully extended conformation where these angles have a value of 180°. 

Figure 1 Peptide pheromone structures determined by NMR. (a) Structure of peptide pheromone (PinA) from Lactobacillus plantarum required for piantaricin biosynthesis. (b) Structure of peptide pheromone (ComC) from Streptococcus pneumonia required for competence deveiopment. ...

The availability of high-resolution structures of peptides EKG, T3-785, IBP, and G991-G1032, which include residues other than Pro and Hyp in the X and Y positions, offers the opportunity to investigate the conformation and interactions of side chains from residues typically found within the collagen triple helix. In the peptide with an EKG tripeptide sequence, the Lys and Glu residues did not form direct intermolecular or intramolecular ion pairs, even though such pairs are sterically feasible. ... 

Figure 6.17 Part structure of peptide drug. Reproduced from [22] with permission of John WUey and Sons Ltd.

In this volume many investigators report on their own studies in conformationally directed drug design. The common theme of all the chapters is the importance of the conformational structure of peptide and nucleic acid in the design of drugs that are either peptide- or nucleic-acid-based or that interact with peptides or nucleic acids. We anticipate that at the present rate of progress significant therapeutic advances will result from... 

Today, it is well-known that peptides or proteins exhibit various kinds of taste. Our group has been researching on the relationship between taste and structure of peptides, BPIa (Bitter peptide la, Arg-Gly-Pro-Pro-Phe-Ile-Val) (7 as a bitter peptide, Om-p-Ala-HCl (OBA), Om-Tau-HCl as salty peptides(2j, and "Inverted-Aspartame-Type Sweetener" (Ac-Phe-Lys-OH) as a sweet peptide(5). The relationship between taste and chemical structure was partly made clear. Since commercial demand for these flavor peptides is increasing, we need to develop new synthetic methods which can prepare these peptides in large scale. We developed the following two methods (1) protein recombination method as a chemical method, (2) enzymatic synthesis using chemically modified enzyme as a biochemical method. 

Due to their substantial size and peptidic nature, inhibitors from this class were not suitable for clinical application. Nevertheless, the structural information derived from many crystal structures of peptidic inhibitors bound to the HIV PR active site was critical for subsequent modeling and design of the next generation of peptidomimetic and nonpeptidic inhibitors of HIV PR. 

Finds crystal structure of peptides bound to Rhizopus pepsin... 

In my talk I surveyed recent advances in the methodology and selected 2D-IR spectra of secondary structures. The results promise to provide structurally based kinetic probes for conformational dynamics, sharp tests of anharmonic potential surfaces and novel information regarding the transient and equilibrium vibrational dynamics of peptides. The heterodyned 2D-IR approach has proven useful in determining structures of peptides in solution and the anharmonic nature of the potential surfaces of peptides and secondary structures [1-10], as have polarized photon echo [2,6,10-12] or pump-probe techniques [4,13-16]. 

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