L7/C4: Protein Structure

Biochemistry I

Primary Structure

Amino acid sequence, linear order of AA’s

Secondary Structure

local spatial alignment of amino acid backbone without regard to side chains

• a-helix, b-strands/sheets, random coil, and b-turns

Tertiary Structure

The 3D structure of an entire polypeptide, fold, biological function and catalytic mechanism

Quaternary Structure

the manner in which the tertiary structures of two or more polypeptide chains of a protein interact, spatial arrangements of subunits (folded chains)

In the 1930s-1940s, who determined the structure of the peptide bond by X-ray?

Linus Pauling and Robert Corey

What 4 things did Linus Pauling and Robert Corey find out about the peptide bond?

• 40% double bond character ( the amide or peptide bond is 0.13 A shorter than C_a-N bond

• C=O is 0.02 A longer than those for ketones and aldehydes

• Planar conformation maximizes pi-bonding overlap

• resonance gives 85 kJ/mol stability when bond is planar

Peptide bonds are planar. Are most peptide bonds trans or cis?

Most peptide bonds are trans, 10% that follow proline may be cis

What is the dihedral angle for a trans peptide bond?

180^o or -180 (same thing)

What is the dihedral angle in a cis peptide bond?

0^o

What is the most common type of helix?

the a-helix

Residues per turn (n) in a standard a-helix

3.6

Helical rise per residue (d) in a a-helix

1.5 A

Helical pitch (p) of an a-helix

5.4A

• p = n x d = 3.6×1.5 A

Hydrogen bonding pattern in an a-helix

C=O of the nth residue points towards the N-H of the (N+4)th residue

What aa don’t occur in an a Helix?

Proline and Glycine

Proline characteristics

• introduces destabilizing kink in helix

• nitrogen atom is part of rigid ring

• rotation about N-Ca bond not possible

Glycine characteristics

• high conformational flexibility

• increases the instability of coiled structures

The N_m Helix Nomenclature: N

the number of repeating units per turn

The N_m Helix Nomenclature: m

the number of atoms that complete the cyclic system that is enclosed by the hydrogen bond

What is the designation for an a-helix?

N_m= 3.6₁₃

Three helix types

• 2.2₇ Ribbon

• 3₁₀-helix

• pi-helix 4.1₁₆

The 2.2₇ Ribbon