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lecture5_large - Protein Structure and Function Lecture 5:...

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1 Protein Structure and Function Lecture 5: Intra- and intermolecular forces Handouts Phenomenological theories Empirical description of behavior van der Waals equation of state (1873) Mie interaction potential (1903) Many functional forms and parameters fit data Quantum theory in 1920s provided rigorous foundation. ¾ Electron cloud distribution determines interaction ¾ All interactions are essentially electrostatic in orgin () ( ) 2 /( PaV Vb R T +− = / / nm wr A r B r =− +
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2 Interaction types Coulomb (electrostatic) ¾ Ion-ion ¾ Ion-dipole van der Waals ¾ Dipole-dipole ¾ Induced dipole (dispersion, London forces) Hydrogen bonding Solvation (hydration) ¾ Electrostatic screening, hydrogen bonding ¾ Hydrophobic effect ± Cavity cost, entropic origin ij ij qq r ε < Electrostatic interactions CH 2 CH 2 CH 2 CH 2 NH 3 + Asp 189 CH 2 O O OC H 2 H Ser Xaa N Yaa O H Ionic Polar δ + δ - δ - δ +
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3 Permanent dipole CH 3 CH 2 Cl δ + δ - δ + δ - Interaction types Coulomb (electrostatic) ¾ Ion-ion ¾ Ion-dipole van der Waals ¾ Dipole-dipole ¾ Induced dipole (dispersion, London forces) Hydrogen bonding Solvation (hydration) ¾ Electrostatic screening, hydrogen bonding ¾ Hydrophobic effect ± Cavity cost, entropic origin
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4 vdW, transient dipolar interaction Figures taken from: http://www.chemguide.co.uk/atoms/bonding/hbond.html#top http://www.super-tech.ro/teoretic.html Lennard-Jones Potential E
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lecture5_large - Protein Structure and Function Lecture 5:...

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