Tertiary Structures

• Tertiary structure: all non-covalent bondings that make up the overall 3D shape of a protein. How the secondary structure interacts
• Globular Proteins: proteins that are soluble; the most common protein classifcation and most variable
• Native conformation - shape of a protein when biologically active
• Which non-covalent interaction dominates tertiary structure?

  Hydrophobic interactions
• Salt bridges are unlikely in tertiary structure unless ions are very close to each other due to…

  angle differences
• Right handed alpha helicies dominate
• Common super secondary structures include…

  • B-a-B loop
  • B-Barrel
  • and are known for presence in GFP derived proteins
• Polar side chains are exposed in globular proteins due to their hydrophillic nature.

  Non-polar side chains will be hidden due to hydrophobic interactions
• Dielectric constant epsilon

  • In water is ~ 80
  • inside a protein is ~ 4.0
• Fibrous proteins - like a-keratin

  • long and narrow a-helicies most common
  • around 450 amstrongs or 300 residues
• Coiled coil motif - 2 helices wrapped around one another stabilized by tertiary interactions and disulfide bonds

  • tertiary interactions like hydrophobic interactions and ionic interactions common.
  • polar sides usually exterior
• Amphipathic Helicies - for intramembranous proteins

  • Hydrophillic exterior
  • Hydrophobic Interior
  • Ionic charges divide interior and exterior

  
• Disordered proteins - proteins that have regions of instable structure


  PESQK - disordered regions

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  CWIYFMHN are structure promoting

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  AGTRD are indifferent
• Domain - structural patterns that are independently stable and fold independently
• Motif - common combinations of secondary structure
• Sigmoidal - all or noting, exists in two states
• Things that can affect denaturation

  • Solvent
  • pH
  • Ionic Strength
  • Pressure
  • Temperature
• Levinthal’s paradox - proteins cannot fold completely by random tests of structure
• Folding is spontaneous as dictated by its -dG
• When dH and dS are not in accordance with favorability, the reaction then depends on temperature
• Disulfide bridges form when cysteine residues react with one another to create crosslinks
• Intermediate state - transition state between native and unfolded state
• Micelle Proteins - Proteins that form micelles (insoluble colloids) in the cell membrane.