1. Lab2-Peptides

3. Proteins = Sum of aminoacids

4. One amino acid X is equipped with two minimal peptide bonds: The C terminus COOH becomes COCH3, the N terminus NH2 becomes NHCH3. For instance, alanine dipeptide is CH3CONHCH(CH3)CONHCH3 or
Ace-Ala-NMe

5. PES (potential energy surface) of one aminoacid

9. 21 proteinogenic aminoacids

10. Proteins – the machinery of life

11. Helices

12. Sheets

13. Loops and turns

14. OPLS energy hierarchy of Ace-Ala-Ala-NMe

15. Conformers of
Ace-Ala-Ala-NMe

16. Dihedral angles of Ace-Ala-Ala-NMe

18. Alpha-helix or helix 13

19. Dipole momentum
destabilizes helix
NH3+
COO-
Addition of certain
aminoacids
neutralize dipole momentum

20. Alpha-helix G (goes up) and H (goes down) of myoglobin (C=O bonds form Christmas tree structure)
Alpha-helix breakers: glycine (yellow), proline (green)
N (red circle) doesn’t form H bond

21. γ-turn (C7)
Separated by 2 bonds
(b) β-turn (C10)
Separated by 3 bonds
(c) α-turn (C13)
Separated by 4 bonds
(d) π-turn (C16)
Separated by 5
bonds
Type I β-turns,
(b) type II′ β-turns,
(c) type VI β-turns

23. f y Steric interference Structure Fully extended 180
Antiparallel b-sheet
-139
135
Parallel b-sheet
-119
113
Right-handed a-helix
-57
-47
Left-handed a-helix 60
310 helix
-49
-26
p-helix
-70
Steric interference

24. Planarity of peptide bond?
Peptide bond rotational energies and angular frequency distribution. The histogram represents the angular frequency distribution of
3.938 proteins.
The red points are energies derived from Maxwell-Boltzmann relations. The line is the function  A sin2 ω for A = 30 kcal mol-1. (Pauling, Corey)
The black and gray points are peptide bond rotational energies for proteins and peptides, respectively, and were derived from Maxwell-Boltzmann relations.