Peptide bond restricted rotation

Amino acids are combined (linked together) through peptide bonds (-C-N-) (Figure 8.1) the peptide bond formed is planar (flat), due to the delocalisation of electrons that form the partial double bond, restricting rotation about the bond. The rigid peptide dihedral angle, co (the bond between C and N), is always close to 180°. The dihedral angles phi (the bond between N and Ca) and psi (the bond between Ca and C) can only have a number of possible values, and so effectively control the protein s three-dimensional structure. 

Peptide bond resonance has several important consequences. First, it restricts free rotation around the peptide bond and leaves the peptide backbone with only two degrees of freedom per amino acid group rotation around... 

While conformation II (Fig. 2.34) of Uke-y -amino acids is found in the 2.614-helical structure, conformation I, which similarly does not suffer from sy -pen-tane interaction, should be an appropriate alternative for the construction of sheet-like structures. However, sheet-like arrangement have not been reported so far for y-peptides composed of acyclic y " -amino acid residues. Nevertheless, other conformational biases (such as a,/9-unsaturation, cyclization between C(a) and C(y)) have been introduced into the y-amino acid backbone to restrict rotation around ethylene bonds and to promote extended conformation with formation of sheets in model peptides. Examples of such short chain y-peptides forming antiparallel (e.g. 152 [208]) and parallel (e.g. 153-155 [205, 208]) sheet-hke structures are shown in Fig. 2.38. 

With the exception of the terminal residues, every amino acid in a peptide is involved in two peptide bonds (one with the preceding residue and one with the following one). Due to the restricted rotation around the C-N bond, rotations are only possible around the N-C and C -C bonds (2). As mentioned above, these rotations are described by the dihedral angles ( ) (phi) and ]> (psi). The angle describes rotation around the N-C bond / describes rotation around Ca-C—i.e., the position of the subsequent bond. 

Two features that affect secondary protein structure (molecular shape) include the rigid, planar geometry and restricted rotation of the peptide bond, and interchain or intrachain hydrogen bonding of the type C=0-H-N. The a helix and the pleated sheet are common protein shapes. 

Resonance stabilization of an amide accounts for its enhanced stability, the weak basicity of the nitrogen atom, and the restricted rotation of the C—N bond. In a peptide, the amide bond is called a peptide bond. It holds six atoms in a plane the C and O of the carbonyl, the N and its H, and the two associated a carbon atoms. 

The peptide unit so formed is a planar, rigid structure since there is restricted rotation about the C-N bond. This means that two isomers should be possible—a ds and a trans. 

Although rotation about the amide bonds is restricted, rotation about the other a bonds in the protein backbone is not. As a result, the peptide chain can twist and bend into a variety of different arrangements that constitute the secondary stmcture of the protein. 

The positions of the C and Cp atoms from the CG model are used to position the N and C backbone atoms so that the correct chirality is maintained (o-amino acids). To restrict the rotational freedom, a strong constraint was used, namely that neighbouring residues must have a planar peptide bond. Harmonic potentials were added between neighbouring backbone atoms, the equilibrium distances of which were taken from average distances calculated from the PDB structures. The C atoms were then immobilised by setting their masses to infinity, and a short molecular dynamics simulation was then run to relax the system. 

D. There is restricted rotation about the peptide bond. 

The amide bond that links different amino acids together in peptides is no different from any other amide bond (Section 24.4). Amide nitrogens are nonbasic because their unshared electron pair is delocalised by interaction with the carbonyl group. This overlap of the nitrogen p orbital with the p orbitals of the carbonyl group imparts a certain amount of double-bond character to the C-N bond and restricts rotation around it. As indicated by the stereo views of alanylserine and serylalanine shown in the previous section, the amide bond is planar and the N-H is oriented 180° to the C=0. 

The polypeptide backbone can only bend in a very restricted way. The peptide bond itself is a hybrid of two resonance structures, one of which has double bond character, so that the carboxyl and amide groups that form the bond must, therefore, remain planar (see Fig. 7.3.). As a consequence, the peptide backbone consists of a sequence of rigid planes formed by the peptide groups (see Fig. 7.3). However, rotation within certain allowed angles (torsion angles) can occur around the bond between the a-carbon and the a-amino group and around the bond between the a-carbon and the carbonyl group. This rotation is subject to steric constraints that maximize the... 

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