Lab2-Peptides.

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Presentation transcript:

Lab2-Peptides

Proteins = Sum of aminoacids

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

PES (potential energy surface) of one aminoacid

21 proteinogenic aminoacids

Proteins – the machinery of life

Helices -49 -26 -57 -47 -57 -70

Sheets

Loops and turns

OPLS energy hierarchy of Ace-Ala-Ala-NMe

Conformers of Ace-Ala-Ala-NMe

Dihedral angles of Ace-Ala-Ala-NMe

Alpha-helix or 3.6 helix 13

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

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

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

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

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.