Bcm3121

• Folding


  Process by which a polypeptide chain acquires its 3D structure
• Aggregation


  Process by which unfolded polypeptides associate with each other in a disordered manner
• Folding intermediates


  • Can aggregate with other unfolded polypeptides
  • Both folding and aggregation depend on hydrophobic interactions

  
• Normal aggregates


  Structurally disordered
• Amyloid fibrils


  • A special type of aggregate with an ordered conformation that is not the native state
  • Pathogenic
• ΔG


  Free energy, energy available for work
• ΔH


  Enthalpy, a measure of bond formation (-) or a measure of bond breaking (+)
• T


  Temperature, oK
• ΔS


  Entropy, a measure of increasing chaos (+) or a measure of decreasing chaos (-)
• For a spontaneous process, ΔG must be (-)
• Folding Thermodynamics


  • Each point on curve represents a different polypeptide conformation
  • Each conformation has a different DG
  • A curve is only one of many possible folding paths
• Folding Landscape


  • Many different unfolded and partially folded states
  • Different folding pathways lead to one native state
  • Intermediates can persist in local free energy minima
  • Requires energy to escape minimum
• Native State is the Global Minimum on the Folding Landscape
• Folding/Aggregation Landscape


  • Multiple intermolecular contacts in aggregates can make them more stable than individual native states
  • Amyloid aggregates are the most stable
• First ~30 amino acids of the polypeptide chain present within the ribosome is constrained (the N-terminus emerges first)

  
• In vitro, the E. coli cytosol contains ~340 mg/ml of macromolecules (proteins, nucleic acids, ribosomes, etc.)
• Proteins in isolated (pure) systems may not behave as they do in the cell

  
• Molecular crowding


  A condition where a significant volume of a solution (cytoplasm) is occupied with things other than water
• Molecular crowding increases association constants (ka) and decreases dissociation constants (kd)
• Molecular chaperones


  Proteins that assist the covalent folding/unfolding & assembly/disassembly of other macromolecular structures

  
• Heat shock proteins (HSPs)

  Highly conserved, present in all organisms, upregulated in response to stress

  
• HSPs behave as chaperones to repair denatured proteins or promote their degradation after heat shock
• HSPs were discovered by Ritossa from Italy in Drosophilia melanogaster larvae that were exposed to "heat shock" in 1962
• Functions of HSPs


  • Folding of proteins in various intracellular compartments
  • Maintenance of structural proteins
  • Refolding of misfolded proteins
  • Translocation of proteins across membranes and into various cellular compartments
  • Prevention of protein aggregation
  • Degradation of unstable proteins