Dipeptide diagram

Fig. 1. Conformational energy diagram for the alanine dipeptide (adapted from Ramachandran et al., 1963). Energy contours are drawn at intervals of 1 kcal mol-1. The potential energy minima for p, ofR, and aL are labeled. The dependence of the sequential d (i, i + 1) distance (in A) on the 0 and 0 dihedral angles (Billeter etal., 1982) is shown as a set of contours labeled according to interproton distance at the right of the figure. The da (i, i + 1) distance depends only on 0 for trans peptide bonds (Wright et al., 1988) and is represented as a series of contours parallel to the 0 axis. Reproduced from Dyson and Wright (1991). Ann. Rev. Biophys. Chem. 20, 519-538, with permission from Annual Reviews.

The sections presented above provide an account of the separate topics into which translation can be divided. These act as an introduction to the current section, in which a description of the individual reactions in peptide synthesis is presented in a single diagram, i.e. a diagram that encapsulates the whole process (Figure 20.22). An analysis of each separate reaction provides a simple explanation of the interactions that are required in a sequential manner to form the various complexes in the pathway, the activities of which result in the synthesis of, initially, a dipeptide but then a growing peptide. The repetition of the formation of the complexes for each amino acid results in the synthesis of the final peptide, as dictated by the base sequence in the mRNA. 

Figure 2.8. Diagram of a dipeptide. The diagram shows a dipeptide of glycine in the standard conformation 180°, 180°. To a first approximation, all atoms seen in the dipeptide backbone are found within the plane of the paper. For a dipeptide of glycine, the only atoms not within the plane are the side chain hydrogens. The unit begins at the first Ca and goes to the second Ca. Both c > and xp are defined as positive for clockwise rotation when viewed from the nitrogen and carbonyl carbon positions toward the Ca.

In this three-period experiment, milligram amounts of an unknown dipeptide will be examined by the procedures that we have just discussed. In Figure 6-6, a flow diagram of the experiment is provided to aid your understanding of the various steps. 

Figure 6-6 Flow diagram for sequence determination of a dipeptide.

The NCA coupling method is conceptually simple and elegant. This method is now used in efficient large scale production of peptides, for example for the preparation of semi-synthetic dipeptides Enalapril and Lisinopril (Ref. 247). The synthesis of Ala-Pro which is the key building block to synthesize Enalapril is diagrammed in scheme 195. 

Ramachandran s stereochemical plot diagram) of dipeptides has been widely used to predict the secondary structures of proteins [306-309]. It is well known that the calculations on the polypeptides are limited by the number of atoms and hence high level ab initio and DFT calculations have been possible recently only. Several theoretical calculations with different levels of accuracy have been made on the polypeptides to study the < )- 1> plot distribution, H-bonding interactions, and stability [1-4, 308-322]. In the stability of polypeptides and proteins, H-bond plays an important role in the formation of the secondary structures such as the a-helix, (3-sheet, etc., and higher-order structures [1-4]. Quantum chemical calculations on some of the secondary structures in peptides and proteins ((3-sheets, (3-turns, and y-turns) at the HF and MP2 levels have been performed with special emphasis to the H-bonded structures... 

Fig. 19. (a) Observed 15N chemical shift diagram of poly(L-alanine) in the solid state, (b) Calculated 15N shielding diagram of A-acetyl-r.-alanine methylamide (taking hydrogen bonds with two formamide molecules), as a dipeptide model of poly(L-alanine), by means of the FPT-INDO method. 

Chymotrypsin is formed in the pancreas, just as is trypsin, in the form of inactive chymotrypsinogen. Activation is performed by trypsin. The process runs through a series of intermediates which are also enzymically active. As shown in the diagram on page 149, the activation amounts to a double scission of a cyclic peptide, eliminating two dipeptides in the process. 

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