Protein Structure

Core Concepts

Primary structure: the covalent blueprint

The primary structure is the linear sequence of amino acids joined by peptide bonds, written N-terminus to C-terminus. With 20 standard amino acids, a chain of n residues has 20ⁿ possible sequences. The gene encodes the sequence, and the sequence determines everything else: the chain folds into the most stable shape for that sequence.

The planar peptide bond: the backbone's rigid unit

The peptide bond has partial double-bond character because the lone pair on the amide nitrogen is delocalized onto the carbonyl oxygen:

R–C(=O)–NH–R' ↔ R–C(O^-)=N⁺H–R'

This resonance makes the C–N bond about 40% double-bonded, so it is planar and cannot rotate freely (the measured C–N distance is ~1.33 Å, between single, ~1.47 Å, and double, ~1.27 Å). Rotation is limited to the two flanking single bonds — N–Cα (phi, φ) and Cα–C (psi, ψ). Almost all peptide bonds are trans, with the two α-carbons on opposite sides to avoid steric clash; cis bonds are rare, mostly before proline.

Secondary structure: α-helix and β-sheet

• α-Helix: the backbone winds into a right-handed helix with 3.6 residues per turn and a 5.4 Å pitch, stabilized by H-bonds between the C=O of residue i and the N–H of residue i+4. Side chains point outward. Glycine destabilizes helices (too flexible); proline breaks them (its ring locks the backbone, and it has no N–H to donate).
• β-Sheet: extended segments (β-strands) line up side by side, hydrogen-bonded between the C=O of one strand and the N–H of a neighbor. Strands run the same direction (parallel) or opposite (antiparallel); antiparallel sheets have more linear, stronger H-bonds. β-sheets form the core of silk and membrane β-barrel channels.
• β-Turn: a four-residue hairpin that reverses chain direction; glycine (small) and proline (rigid) are common there.

The Ramachandran plot

A Ramachandran plot shows which (φ, ψ) combinations are sterically allowed; most are forbidden because backbone atoms collide. Allowed regions cluster in wedges: the α-helix region near (φ ≈ −57°, ψ ≈ −47°) and the β-sheet region near (φ ≈ −120°, ψ ≈ +120°). Glycine, with only a hydrogen side chain, is allowed almost everywhere; proline is restricted because its ring constrains φ. Checking structures against Ramachandran plots is standard validation.

Tertiary structure: the folded chain

Tertiary structure is the complete 3D arrangement of one polypeptide, driven mainly by the hydrophobic effect — nonpolar side chains cluster in the interior, away from water. Additional forces then lock the shape in place:

• Hydrogen bonds between side chains and backbone,
• Salt bridges between oppositely charged side chains (e.g., Lys⁺…Asp⁻),
• Disulfide bonds: covalent S–S links from oxidation of two cysteines, Cys–SH + HS–Cys → Cys–S–S–Cys, the only covalent cross-links in most proteins,
• Van der Waals contacts in the tightly packed core.

Globular proteins (enzymes, antibodies) fold compactly with the hydrophobic core buried; fibrous proteins (collagen, keratin) are extended and structural.

Quaternary structure: assembly of subunits

Quaternary structure is the arrangement of two or more folded chains (subunits) into a functional complex. Hemoglobin is the classic example: two α and two β subunits assemble into an α₂β₂ tetramer that binds oxygen cooperatively. The same forces that stabilize tertiary structure hold subunits together.

Common Confusions