Protein Structure and Tertiary Structure Determination

Relative Orientation of Peptide Groups

• The relative orientation of peptide groups is specified by the torsion angles, specifically the phi ($\phi$) and psi ($\psi$) angles:
  • $\phi$ (phi): rotation around the C\alpha-N bond
  • $\psi$ (psi): rotation around the C\alpha-C bond
• These angles determine how the polypeptide backbone is folded.

Torsion Angles

• When both peptide groups are in the same plane and the polypeptide chain is stretched out, the torsion angles are defined as 180°.
• Viewing from the C\alpha, rotating clockwise increases the angle.
• Note that most combinations of $\phi$ and $\psi$ angles are sterically impossible due to spatial constraints.

Ramachandran Plot

• The Ramachandran plot visually represents permissible $\phi$ and $\psi$ combinations.
• Key regions include:
  • Alpha (α) helix
  • Beta (β) sheets (both parallel and antiparallel)
  • PII helix
• Most allowed combinations occupy specific regions where steric clashes are minimized.

Secondary Structures

• Common secondary structures include:
  • Alpha Helix (α):
  • Stabilized by hydrogen bonds between the main chain.
  • Characterized by specific $\phi$ and $\psi$ angles: $\phi = -57°$, $\psi = -47°$.
  • Has 3.6 residues per turn and a pitch of 5.4 Å.
  • Beta Sheets (β):
  • Can be parallel or antiparallel.
  • Average structure has 6 strands and forms H-bonds between peptide chains.
  • Pleated appearance with a typical distance of 7.0 Å between the strands.
  • Type II Polyproline Helix (PII):
  • Characterized by unique dihedral angles which lend a distinct structure to the polypeptide.

Irregular Structures

• Include turns and loops, which provide flexibility and structure to proteins.
• Reverse Turn (β Bend):
  • Two types exist: Type I and Type II, facilitating connections between sections of the polypeptide chain.

Tertiary Structure Determination

• Determined using techniques like:
  • X-ray Crystallography:
  • Requires purified protein to form crystals that diffract X-ray beams.
  • Data from diffraction patterns lead to an electron density map that can be used to refine the 3-D structure of proteins, including side chains.
  • NMR Spectroscopy: Provides a complementary approach to visualize protein structure.

Summary of X-Ray Crystallography Steps

1. Purify protein.
2. Produce a crystal.
3. Collect diffraction data.
4. Create electron density map.
5. Fit the polypeptide sequence into the electron density map to derive the full structure.