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Backbone of peptide chain
The document discusses the structure and properties of peptide bonds that link amino acids in proteins, including bond distances and configurations. It explains the significance of the 'trans' configuration, which is predominantly observed due to stearic clashes in the 'cis' configuration, especially in proline-containing linkages. The document also introduces the concept of torsion angles (phi and psi) and the Ramachandran plot, which illustrates allowed combinations of these angles based on steric constraints.
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Backbone of peptide chain
- 1. Dr. Kalpeshkumar CNakarani Tutor cum Second year Resident Backbone linkages of Peptide chain
- 2. General The –COOHgroup of one amino acid can be joined to the –NH2 group of another amino acid by a covalent bond called as peptide bond. Thus it is the peptide linkage which holds various amino acids together in a specific sequence and number.
- 3. Dimensions of fullyextended polypeptide chain Bond distance N-H bond 0.100 nm C=O bond 0.123 nm C-N bond 0.132 nm N-Cα bond 0.147 nm Cα-C bond 0.153 nm Cα-Cα distance 0.360 nm
- 4. Peptide bond Peptidebond is planar • Thus for a pair of amino acid linked by a peptide bond, six atoms lie in the same plane. • Ca, C, O, N, H, Ca
- 5. Peptide bond ispartial Double bond Peptide bond resonates between a single bond and double bond Partial double bond Proof of Partial double bond • In peptide bond C-N distance is 0.132 nm • But • C-N = 149 nm • C=N = 127 nm
- 6. Considering peptide asa ‘partial double bond’ – 2 configurations are possible ‘Trans’ Configuration ‘Cis’ Configuration
- 7. Considering peptide asa ‘partial double bond’ – 2 configurations are possible ‘Trans’ Configuration ‘Cis’ Configuration Allmost all peptide bonds (99.6%) are in ‘trans’ configuration because stearic clashes between groups attached to the Ca atoms do not arise in trans configuration as groups are far apart Stearic clashes arise in ‘cis’ configuration as groups will be near. Rarely occurs (0.4 %) Mostly occurs in X-Pro linkages
- 8. Considering peptide asa ‘partial double bond’ – 2 configurations are possible ‘Cis’ Configuration Stearic clashes arise in ‘cis’ configuration as groups will be near. Rarely occurs (0.4 %) Mostly occurs in X-Pro linkages Because the N of Proline is bonded to 2 tetrahedral carbon atoms limiting the stearic differences between the ‘trans’ and ‘cis’ forms E.g. Ribonuclease A It contains 4 proline, 2 are in ‘trans, and rest 2 are in ‘trans/cis’
- 9. Torsion angles (Dihedralangles) (Between -180 to +180) N-Ca bond (Φ) The angle of rotation is known as phi (Φ) Phi (Φ) Rotation Ca-C bond (Ψ) The angle of rotation is known as psi (Ψ) Psi (Ψ) Rotation • View from previous to next • Keep previous bond at “12 o’clock” position • Measure its angle with next bond • If Clockwise +ve value • If anti clockwise -ve value
- 10. Possible Φ andΨ angles GM Ramchandran recognized that many combinations are forbidden because of stearic collisions between atoms Explanation Video Allowed Φ and Ψ values can be seen on a plot known as ‘Ramchandran plot’.
- 13.
Editor's Notes
- #10 In contrast to peptide bond, which is partial double bond, phi and psi are purely single bond