Peptide bonds planar structure

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

The peptide bond is characterized by a fixed planar structure, as was discovered by X-ray crystallography of peptides more than 60 years ago. The arrangement of the atoms in the peptide bond is due to resonance stabilisation the lowest-energy state of the system is that in which the four atoms forming the peptide linkage lie in a plane, while the C-N bond has partial double bond character. 

Peptides and proteins are composed of amino acids polymerized together through the formation of peptide (amide) bonds. The peptide bonded polymer that forms the backbone of polypeptide structure is called the a-chain. The peptide bonds of the a-chain are rigid planar units formed by the reaction of the oc-amino group of one amino acid with the a-carboxyl group of another (Figure 1.1). The peptide bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the oc-carbon atom, however, are true single bonds with considerable freedom of movement. 

As described in the beginning of this chapter, the peptide bond is rigid, polar, and prefers a planar structure with hydrogen of the amino group and oxygen of the carbonyl almost trans. It is easily understood that this conformational preference and rigidity has profound implications to the tertiary and quaternary structure of proteins and similarly on the binding of smaller peptides to receptors. 

The nature of the covalent bonds in the polypeptide backbone places constraints on structure. The peptide bond has a partial doublebond character that keeps the entire six-atom peptide group in a rigid planar configuration. The N—C and Ca—C bonds can rotate to assume bond angles of (p and ip, respectively. 

The x-ray diffraction studies of the crystals of small peptides showed that the peptide bond is planar and trans (anti) (Figure 1.3). The same structure has been found for all peptide bonds in proteins, with a few rare exceptions. This planarity results from a considerable delocalization of the lone pair of electrons of the nitrogen onto the carbonyl oxygen. The C—N bond is consequently shortened, and it has double-bond character (equation 1.2). Twisting of the bond breaks it and loses the 75 to 90 kJ/mol (18 to 21 kcal/mol) of delocalization energy. 

In effect, protein structure determination is a search for the conformation of a molecule whose chemical composition is known. For this reason, conformational angles about single bonds are not constrained during refinement, and they should settle into reasonable values. Spectroscopic evidence abundantly implies that peptide bonds are planar, and some refinements constrain peptide geometry. If unconstrained, peptide bonds should settle down to within one to two degrees of planar. 

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. 

The C-N peptide bond has an interesting property It is planar and very rigid. This special geometry of the peptide bond makes it very stable and ideal to maintain the structure of proteins. 

A heuristic potential term to keep peptide bonds and aromatic ring structures planar is given by the improper dihedral term... 

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