Lecture 4 - Non-globular proteins and misfolding

What is meant by protein oligomers and their types?

• Homo-oligomers: subunits with the same sequence.

• Hetero-oligomers: subunits with different sequences.

• Named by number of subunits: dimer (2), trimer (3), tetramer (4), pentamer (5), decamer (10), dodecamer (12), higher-order n-mers (e.g., 24mer, 60mer).

How do globular proteins differ from non-globular proteins?

• Globular proteins: well-folded, spherical, distinct secondary/tertiary structures, often enzymes.

• Non-globular proteins: fibrous/filamentous, structural roles (keratin, silk, collagen, cytoskeletal proteins).

What are protein fibres and their roles?

• Globular proteins assembling into fibrous quaternary arrangements.

• Examples: cytoskeletal proteins, flagellae, pili, filamentous viruses.

• Properties: strong, dynamic, interact with proteins/DNA.

What is the cytoskeleton and its key classes?

• Present in all cells, links membrane to nucleus, provides stability, templates cell wall construction.

• Dynamic, responds to environment.

• Classes:

  • Microfilaments (Actin)

  • Intermediate filaments (Keratins, Vimentin, Lamins)

  • Microtubules (Tubulin)

How do actin filaments behave dynamically?

• Actin binds/hydrolyses ATP.

• ATP-actin → high affinity, polymerises at + ends.

• ADP-actin → low affinity, depolymerises at – ends.

• ADP exchanged for ATP in free actin

• Generates force for motility.

• Regulated by proteins: profilin/gelsolin (sequester actin), myosin motors, branching proteins, capping proteins.

What are intermediate filaments and their types?

• Long coiled-coil proteins, sometimes with globular domains.

• Functions: adhesion, organisation, muscle fibres.

• Types:

  • I & II: keratins

  • III: vimentin, desmin

  • IV: α-internexin, synemin

  • V: lamins

  • VI: nestin, filensin

What is the structure and role of keratin?

• α-keratin: hair, nails, claws, feathers, skin.

• β-keratin: reptile scales, tortoise shells.

• Coiled-coil stabilised by hydrophobic interactions and disulphides.

• Dimers → tetramers → filaments.

How does vimentin form filaments?

• Coiled-coil → dimer → anti-parallel tetramer.

• Eight tetramers → unit-length filament → fibrous filaments.

• Anchors organelles (nucleus, ER, mitochondria).

What roles do α-internexin and nestin play?

• α-internexin: structural element of axons.

• Nestin: radial growth of axons.

• Both are coiled-coil proteins.

What is the role of lamins in the nucleus?

• Provide nuclear structure, interact with nuclear membrane.

• Sensitive to stretch → mechanosensing.

• Coiled-coil domain + terminal head.

How are microtubules structured and regulated?

• α/β tubulin dimers, directional (+ end = β, – end = α).

• Elongation faster at + end.

• Bind/hydrolyse GTP.

• Protofilaments → 13-protofilament helical tubes.

• Nucleated at MTOCs (γ-tubulin ring complexes, centrosome).

• Drugs: Taxol stabilises GDP-tubulin, blocks depolymerisation → cancer therapy.

• MAPs regulate stability, motors (dynein/kinesin) traffic vesicles.

What proteins form muscle sarcomeres?

• Actin, Myosin, Troponin, Tropomyosin, Titin.

• Titin: largest protein, prevents over-extension.

What are cilia and flagella?

• Cilia: microtubule-based extensions, motility (e.g., mucus movement), sensory roles.

• Flagella: longer, dynamic, motility in eukaryotes and prokaryotes.

• Bacterial flagella: protein helical filaments, motors spin CW/CCW, controlled by signals.

How do filamentous viruses use protein fibres?

• Found in all domains (e.g., bacteriophage, tobacco mosaic virus, influenza).

• Globular capsid proteins form helical filaments.

• Protect genetic material, host receptors at filament ends.

What are pili and fimbriae?

• Pili: conjugative appendages, pilin protein (globular + α-helix), helical arrangement, transfer ssDNA (antibiotic resistance).

• Fimbriae: surface attachment via adhesins, virulence, biofilm formation.

• Curli fibres: amyloid fibres in enterobacteria, biofilm role.

What is collagen’s structure and importance?

• 30% of human protein, ECM (extracellular matrix)

• Triple helix: two α1 chains + one α2 chain.

• Rich in glycine, proline, hydroxyproline.

• Cross-linked via lysine oxidation.

• Diseases: scurvy, Ehlers-Danlos, epidermolysis bullosa.

• Cosmetics: fillers, creams (cannot cross skin).

What is the composition of silkworm silk?

• Fibroin (70–80%): heavy/light variants, GSGAGA repeats, β-sheets, disulphide links.

• Sericin (20–30%): serine-rich, β-sheet, hydrogen bonds to fibroin.

• Produced by silkworms, spiders, lacewings, hymenoptera.

What are the types and properties of spider silk?

• Types: ampullate (dragline), flagelliform (elastic spiral), tubuliform (cocoon), aciniform (prey wrapping), aggregate.

• Properties: strength, ductility, tensile strength, density.

• Structure: spidroins (glycine/alanine repeats, β-strands + disordered regions).

• Variants: MaSp1, MaSp2, Flag.

• Produced as soluble precursors, spun from glands.

What are intrinsically disordered proteins (IDPs)?

• Lack regular tertiary structure.

• May be whole proteins or domains.

• Still stable/active.

• Can undergo order/disorder transitions in response to signals.

• Important in signalling, regulation.

Why is protein folding important?

• Correct folding vital to protein function

What diseases are linked to protein misfolding?

• Alzheimer’s (β-amyloid plaques).

• Parkinson’s (α-synuclein).

• ALS (motor neuron proteins).

• Huntington’s (polyQ repeats).

• Prion diseases (CJD, BSE).

• Type II diabetes.

• Misfolded proteins often form β-sheets → amyloids.

What happens in protein misfolding/ aggregation?

• Mis-folding into predominantly beta-sheet structures

• Proteins susceptible to this: alpha-synuclein, beta-amyloid and prions

• Misfolded proteins can template formation of aggregates from normally folded proteins - infectious agent

What are amyloids and how are they detected?

• Cross-β-sheet aggregates.

• Can template misfolding → infectious-like.

• Stained with Congo red.

• Found in diseases and microbial biofilms.

How did BSE highlight prion infection?

• 1987: cattle brain damage identified.

• 1990s: 180,000 cattle infected, 4.4 million slaughtered.

• 1996: human variant CJD linked to infected meat.

• Only affected those with specific polymorphism.

• Infectious agent: prion protein,