Misfolding & Disease

Amyloid Fibril Formation Kinetics

Summary

Amyloid fibril formation follows nucleation-dependent polymerization kinetics characterized by a sigmoidal time course. The process involves primary nucleation (formation of initial seeds), elongation (fibril growth), and secondary nucleation (surface-catalyzed seed formation). Understanding these kinetics is crucial for developing therapeutic interventions against neurodegenerative diseases.

Key Points

  • 1Amyloid formation follows sigmoidal kinetics: lag phase → growth phase → plateau
  • 2Primary nucleation creates initial seeds; secondary nucleation amplifies on fibril surfaces
  • 3The lag phase can be eliminated by seeding with preformed fibrils
  • 4Oligomeric intermediates are often more cytotoxic than mature fibrils
  • 5Prion-like seeding enables templated propagation of specific fibril conformations

Amyloid fibrils are highly ordered protein aggregates characterized by a cross-β structure, where β-strands run perpendicular to the fibril axis. Their formation underlies devastating neurodegenerative diseases including Alzheimer's, Parkinson's, and ALS.

The Sigmoidal Kinetics

Amyloid formation exhibits characteristic sigmoidal kinetics with three distinct phases:

1. Lag Phase

  • Initially, no detectable fibrils form

    • - Represents the time required for nucleation—formation of the first stable aggregation seeds

  • Duration is highly concentration-dependent
  • Can be eliminated by adding preformed "seeds"

    • 2. Growth Phase

  • Exponential increase in fibril mass
  • Both elongation and secondary nucleation contribute
  • Thioflavin T fluorescence increases dramatically
  • Maximum rate of monomer consumption

    • 3. Plateau Phase

  • Fibril formation reaches equilibrium

    • - Monomer concentration drops to critical concentration (Cr)

  • Dynamic equilibrium between association and dissociation

    • Nucleation Mechanisms

    Primary Nucleation

    The formation of initial nuclei from monomers alone:

    - Homogeneous primary nucleation: Occurs in solution

    - Heterogeneous primary nucleation: Catalyzed by surfaces (lipid membranes, air-water interface)

  • Requires overcoming a high energy barrier
  • Rate-limiting step in unseeded reactions

    • Secondary Nucleation

    New nuclei form on existing fibril surfaces:

  • Monomers bind to fibril sides

    • - Surface-catalyzed nucleation produces new growing ends

  • Dramatically accelerates aggregate multiplication
  • Dominates kinetics after initial nuclei form

    • Fibril Fragmentation

    Mechanical or spontaneous breakage of fibrils:

  • Creates new growing ends
  • Can be dominant secondary process in some systems
  • Rate depends on fibril length and mechanical stress

    • The Master Equation

    Fibril formation kinetics can be described by integrated rate laws:

    Key parameters:

    - k_n: Primary nucleation rate constant

    - k+: Elongation rate constant

    - k_2: Secondary nucleation rate constant

    - n_c: Critical nucleus size (typically 2-4 monomers)

    The relative contribution of each process shapes the kinetic profile and determines:

  • Lag time duration
  • Slope of growth phase
  • Sensitivity to seeding

    • Concentration Dependence

    The kinetics are exquisitely sensitive to protein concentration:

    - Above critical concentration (Cr): Fibrils grow spontaneously

    - Below Cr: Existing fibrils dissolve; no new formation

    - Super-critical concentrations: Dramatically shortened lag phases

    - Scaling relationships: Lag time often scales as [monomer]^(-1/2) to [monomer]^(-2)

    Structural Intermediates

    The pathway involves multiple conformational species:

    Oligomers

  • Small, soluble aggregates (2-50 monomers)

    • - Often more toxic than mature fibrils

  • May be on-pathway or off-pathway
  • Transient and difficult to characterize

    • Protofibrils

  • Early fibrillar structures
  • Thinner than mature fibrils
  • May lack full cross-β organization

    • Mature Fibrils

  • Fully formed cross-β structure
  • Typically 10-15 nm diameter
  • Can be many micrometers long

    • Seeding and Prion-Like Propagation

    Preformed fibril seeds can:

  • Eliminate the lag phase entirely
  • Template the specific polymorph structure
  • Spread between cells in disease contexts

    • - Exhibit strain-like behavior—different conformations propagate faithfully

    This prion-like behavior has profound implications for disease progression and potentially for inter-individual transmission.

    Therapeutic Implications

    Understanding kinetics guides drug development:

    1. Inhibiting primary nucleation: Prevents disease initiation

    2. Blocking secondary nucleation: Slows aggregate multiplication

    3. Stabilizing native state: Shifts equilibrium away from aggregation

    4. Sequestering oligomers: Reduces toxic species

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