PROTEIN PHYSICS

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PROTEIN PHYSICS

• A. V. Finkelstein
• O. B. Ptitsyn
• LECTURE 5
• www.nd.edu/aasztalo

Andrea Asztalos, 2007 June 20
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Chemical Bonds

• Covalent Bond 50 - 100kcal/mol
• Ionic Bond 5 - 80kcal/mol
• Hydrogen Bond 3 - 6kcal/mol
• Hydrophobic Interaction 0.5 - 3kcal/mol (not a
  bond per se)
• Van der Waals Interaction 1kcal/mol

Van der Waals int. lt Hydrogen Bond lt Ionic Bond
lt Polar Covalent Bond lt Non-polar Covalent Bond
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Hydrophobic Effect
HYDRO PHOBICITY - fear of water

• Nonpolar molecules H2, CH4, CH3CH2CH3, Ala,
  Val, Leu, Gly, Met, Pro,

• Polar molecules CH3CH2OH, Asp, Ser,

Frozen hydrogen bonds Minimum enthalpy structures
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Hydrophobic Interaction
Hydrophobic Interaction - driven by surface
minimization
CLATHRATE
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Experimental Observations
At T25C
Crystallization or Hydrophobic effect?
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Temperature Dependence
Hydrophobicity increases till 140C
Hydrophobic molecules become more sticky
After T140C T?S gt 0, the hydrophobic effect
decreases
High heat capacity (CpdH/dT) (melting of the
ordered water)
Transferring pentane from liquid pentane to water
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Molecular Size Dependence
0.02 0.025 kcal/(moleÅ)-1 of accessible
nonpolar area
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Questions Remarks

• What does it mean physically, that one amino acid
  has a higher hydrophobicity than another one?
• Is there one clathrate or many small ones? It
  depends on the number of water molecules between
  two nonpolar molecules
• The hydrophobic effect is responsible 90 to form
  a compact protein
• The final polishing is done by the van der
  Waals interactions, H-bonds and ionic bonds