1. Hierarchical Structure of Proteins
Figure 6-1 part 2

2. Hierarchical Structure of Proteins
Secondary structure (2°):
A description of (typically regular or repeating) local geometric features of the protein backbone
Dominated by hydrogen bonds between the backbone (carbonyl and amide nitrogen)
or beta strand/sheet
Figure 6-1 part 2

3. Hierarchical Structure of Proteins
Tertiary structure (3°):
A description on a larger scale of how the protein is folded: how the secondary structure elements are combined
Dominated by side chain interactions
Figure 6-1 part 3

4. Hierarchical Structure of Proteins
Quaternary structure (4°): How multiple protein chains assemble together (where applicable)
Figure 6-1 part 4

5. Amide resonance in the protein backbone
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6. Amide resonance in the protein backbone
one of the most essential features of the polypeptide backbone
recognized by Pauling, based on chemical insight, before the 3D structures of proteins were known
that, and an understanding of hydrogen bonding, allowed him (and Corey) to predict that the polypeptides would be folded up in regular ways that would satisfy the hydrogen bonding requirements of the backbone; predicted both a-helix and b-sheets
the resulting rigidity of the protein backbone, is likely a key reason why this particular structure evolved as a way to make well-defined structures; compared to organic polymers for instance
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7. The peptide bond shown in the trans configuration (w=180)
Text, Fig. 6-2
Figure 6-2

8. The peptide bond shown (not quite exactly right) in the cis configuration (w=0)
The cis configuration strongly disfavored due to steric clash, except when proline is the i+I residue. In the case of proline, the steric collision is not much worse in cis compared to trans (note that there is a substituent on the amide N for proline that presents a potential steric problem even in trans). Proline is cis about 10% of the time.
Figure 6-2

9. A series of rigid peptide planes in a polypeptide: note that the peptide plane contains atoms from both the preceding and following amino acids
Text, Fig. 6-3
Figure 6-3

10. A series of rigid peptide planes in a polypeptide: note that the peptide plane contains atoms from both the preceding and following amino acids
i i i+1
Figure 6-3

11. The configuration of the protein backbone is described by two ‘dihedral’ angles at each Ca position
Ignoring the possibility of cis peptide bonds, these angles practically describe the whole structure of the protein backbone
Figure 6-4

12. The configuration of the protein backbone is described by two ‘dihedral’ angles at each Ca position
The first dihedral or torsion angle, phi, describes the angle about the bond preceding the Ca atom.
The second angle, psi, describes the angle about the bond following the Ca position.
Figure 6-4

13. Potential collisions between backbone atoms before and after the Ca atom restrict the allowable angles for phi and psi
This was first studied systematically by Ramachandran
Text, Fig. 6-5
Figure 6-5

14. A Ramachandran plot shows which combinations of phi and psi are energetically permissible
The flat, perfectly staggered configuration (which turns out to not be so favorable) would be 180°, 180°.
Figure 6-6

15. Within the allowable regions of the Ramachandran plot, there are special configurations that, when applied repeatedly, give rise to regular structure with hydrogen bonding between backbone atoms
a-helix
Figure 6-7

16. Within the allowable regions of the Ramachandran plot, there are special configurations that, when applied repeatedly, give rise to regular structure with hydrogen bonding between backbone atoms
b-sheets
Figure 6-7

17. 3.6 residues per turn of the helix (helix is right-handed)
a-helix
3.6 residues per turn of the helix (helix is right-handed)
100° turn around the helix axis per residue
Hydrogen bonding from the carbonyl group of residue i to the amide nitrogen of residue i+4
Note that the carbonyls point towards the C-term and the amide hydrogens point towards the N-term
Figure 6-9a

18. antiparallel and parallel b-sheets
Text, Fig. 6-9
Figure 6-9a

19. A typical twisting b-sheet
Figure 6-12