Oligopeptides bond angles

Fig. 7.22 Comparison of calculated and observed (x-ray) mean N-C(a)-C bond angles for oligopeptides. Regions of and , of the most populated regions (N>3) of a set of oligopeptides selected as described in the reference quoted above.

The computation of stable conformations of oligopeptides then involves three different problems First, the geometry (bond lengths and bond angles) of the chain must be known, and the functional form (and the values of the parameters) of U and V must be determined. Second, the sum U + V must be minimized to locate the various local minima. Third, the vibrational (conformational) entropy of each minimum within a reasonable range of the global one, that is, within about 1 kcal/mol, must be calculated to locate the global minimum of G. 

Although the basic methodology for calculating structures of oligopeptides is now in place, there is still room for improvement of potential functions, not only in the parameters used but also in the forms of the functions themselves. In the near future, we can expect to see the introduction of anhar-monicity in bond angle bending, a treatment involving many-body interactions (rather than pairwise interactions), polarization (and possibly distributed multipoles) to treat electrostatics, and improved treatment of hydration. In addition, we will undoubtedly see considerably more use of parallelism in computer hardware and software. 

Though this peptide has considerably increased conformational flexibility over the cyclic peptide tentoxin, it contains two backbone and side chain modifications which confer increased conformational rigidity to the molecule when compared with backbone non-mod1fied oligopeptides. It is helpful to recall that the conformation of a peptide is determined by its overall three-dimensional structure (14). If the bond angles and bond... 

A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the oi-amino group of one amino acid and the a-carboxyl group of another. The peptide bond has partial double bond character and is nearly always in the trans configuration. The backbone conformation of a polypeptide is specified by the rotation angles about the Ca-N bond phi, (j>) and Ca-C bond psi, amino acid residues. The sterically allowed values of 0 and yr are visualized in a Ramachandran plot. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. 

Figure 6 Perspective drawing of terminally blocked L-alanine, the backbone of which may be considered a prototype of a section of an oligopeptide chain. The dashed lines indicate the limits of the alanine residue. The Greek letters designate the backbone dihedral angles.22 For larger side chains, the dihedral angles for rotation about the side-chain bonds are designated by x1. X2, and so on.22...

Peptide bonds are planar and can be either in the trans or in the cis conformation with respect to the two successive C positions. These conformations are equivalent to dihedral angles trans state is strongly favored for peptide bonds that do not involve proline residues. The cis conformation has not been detected in unstructured, linear oligopeptides, and the equilibrium population of the cis form is believed to be less than 0.1% (Brandts et al., 1975, Jorgensen and Gao, 1988). Very few nonproline cis peptide bonds have been found in native, folded proteins by X-ray crystallography (Stewart et al, 1990 MacArthur and Thornton, 1991). 

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