The formation of protein structure

Lecture 2

Primary structure determines folding

A protein’s amino acid sequence contains all the information needed to fold into its native 3D structure, as shown by ribonuclease refolding experiments.

Ribonuclease denaturation/refolding

Urea disrupts non‑covalent interactions; mercaptoethanol breaks disulphide bonds. Removing both allows the protein to spontaneously refold and regain activity, proving sequence dictates structure.

Secondary structure

Local regular arrangements (α‑helices and β‑sheets) stabilized by hydrogen bonds between backbone N–H and C=O groups; side chains project outward.

α‑helix

Right‑handed helix stabilized by hydrogen bonds between residue i and i+4. Side chains radiate outward, influencing helix interactions.

310 helix

Less common helix where residue i hydrogen bonds with i+3; tighter and narrower than α‑helix.

β‑sheet

Formed by hydrogen bonding between adjacent strands. Can be parallel or antiparallel. Side chains alternate above and below the sheet.

Tertiary structure

Overall 3D fold stabilized by hydrogen bonds, hydrophobic interactions, electrostatic interactions, van der Waals forces, and sometimes disulphide bonds.

Hydrogen bonds in proteins

Form between electronegative atoms (O, N) and hydrogen. Strongest when linear; influence structural directionality.

Hydrophobic effect

Non‑polar residues cluster in the protein core to avoid disrupting water structure. Major driver of folding and globular protein formation.

Electrostatic interactions

Attractions between charged groups. Stronger in hydrophobic environments due to low dielectric constant.

Van der Waals forces

Weak interactions from transient atomic polarization; thousands collectively stabilize protein structure.

Disulphide bonds

Covalent links between cysteines. Form in oxidizing extracellular environments; stabilize secreted proteins.

Fibrous proteins

Structural proteins such as collagen. Collagen’s triple helix relies on glycine for tight packing and proline for bends. In animals, collagen is essential for connective tissues; deficiency leads to fragility (e.g., scurvy).

Globular proteins

Compact proteins with hydrophobic cores and hydrophilic surfaces. Their shape and surface chemistry determine function.

Myoglobin

Globular oxygen‑binding protein in muscle. In animals, especially diving mammals and athletic species, high myoglobin concentration allows extended oxygen storage.

Protein structure diagrams

Ribbon diagrams show α‑helices (cylinders), β‑strands (arrows), and loops. Topology diagrams flatten the structure to show connectivity.

Motifs

Super‑secondary structures such as βαβ units, α‑helical hairpins, and Greek key motifs. Not independently stable but functionally important.

Domains

Independently folding units within a protein; often globular and functionally distinct.

Multidomain proteins

Single polypeptide containing multiple domains that may function together or independently.

Quaternary structure

Arrangement of multiple polypeptide subunits; stabilized by the same interactions as tertiary structure.

HIV protease

Dimeric enzyme with two subunits; quaternary structure is essential for catalytic activity.

Antibodies

Tetrameric proteins (2 heavy + 2 light chains) used for immune recognition. Each B‑cell produces a unique antibody.

Epitope

Specific region of an antigen recognized by an antibody.

Immunoglobulin domain

Conserved structure of antibody domains: two β‑sheets (4‑strand and 3‑strand) stabilized by a disulphide bond; common in many extracellular animal proteins.