Peptide bonds planar geometry

The geometry of the peptide bond is planar and the mam chain is arranged m an anti conformation (Section 27 7)... 

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. 

Figure 10.1 Basic polypeptide geometry. The upper panel shows a short peptide sequence of three amino acids joined by two peptide bonds. A relatively rigid planar structure, indicated by dashed lines, is formed by each peptide bond. The relative positions of two adjacent peptide bond planes is determined by the rotational dihedral angles

Resonance structures like these are commonly cited as leading to the planar geometry of the peptide bond and nucleic acid bases. 

The planar geometry of the peptide bond is analogous to the planar geometry of ethylene (or any other alkene), where the double bond between sp hybridized carbon atoms makes all of the bond angles -120° and puts all six atoms in the same plane. 

Examination of the geometry of the protein backbone reveals several important features. First, the peptide bond is essentially planar (Figure 3.23). Thus, for a pair of amino acids linked by a peptide bond, six atoms he in the same plane the a-carbon atom and CO group from the first amino acid and the NH group and a-carbon atom from the second amino acid. The nature of the chemical bonding within a peptide explains this geometric preference. The peptide bond has considerable double-bond character, which prevents rotation about this bond. 

Bryce and Bax have proposed a method which exploits the correlated nature of RDCs for structural elements of planar geometry, such as the one-bond CVCf, Ci-Ni+1 and Nj+i-Hj couplings in peptide bonds of proteins, or suitably chosen combinations of Dhi ci J rn cr, I c2 cr nd Dhi H2 couplings in... 

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