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PROTEIN PHYSICS LECTURES 3-4 Elementary interactions: Van der Waals & H-bonds

PROTEIN PHYSICS LECTURES 3-4 Elementary interactions: Van der Waals & H-bonds. In vacuum. Main-chain: f ( N-C a ) , y (C a -C’). w = 180 o w = 0 o. 2.8A < r min (C…C) = 3.0A strong repulsion. s t r o n g r e p u

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PROTEIN PHYSICS LECTURES 3-4 Elementary interactions: Van der Waals & H-bonds

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  1. PROTEIN PHYSICS LECTURES 3-4 Elementary interactions: Van der Waals & H-bonds

  2. In vacuum

  3. Main-chain: f (N-Ca) , y (Ca-C’)

  4. w = 180o w = 0o 2.8A < rmin(C…C) = 3.0A strong repulsion

  5. s t r o n g r e p u l s i o n weak attraction weak attraction r0(N…N)=3.1A

  6. GLY

  7. ALA

  8. >ALA: g-atoms

  9. PRO (f = -70o) Before PRO

  10. ALA, etc. GLY only

  11. HYDROGEN BONDS WATER molecule: H-bond energy:5 kcal/mol ICE sublimation: (12 kcal/mol - 2 kcal/mol[vdW])/2 10 kcal/mol[CH3-CH2-OH] - 5 kcal/mol[CH3-O-CH3] (HO)-1/3-H+1/3::::: O-2/3-H2+2/3: e1/3 2/3  (-1/2-1/4+21/3) ~ 6 kcal/mol

  12. HYDROGEN BONDS WATER molecule: H-bond energy:5 kcal/mol ICE sublimation: (12 kcal/mol - 2 kcal/mol[vdW])/2 10 kcal/mol[CH3-CH2-OH] - 5 kcal/mol[CH3-O-CH3] (HO)-1/3-H+1/3::::: O-2/3-H2+2/3: e1/3 2/3  (-1/2-1/4+21/3) ~ 6 kcal/mol

  13. HYDROGEN BONDS WATER molecule: H-bond energy:5 kcal/mol ICE sublimation: (12 kcal/mol - 2 kcal/mol[vdW])/2 10 kcal/mol[CH3-CH2-OH] - 5 kcal/mol[CH3-O-CH3] (HO)-1/3-H+1/3::::: O-2/3-H2+2/3: e1/3 2/3  (-1/2-1/4+21/3) ~ 6 kcal/mol

  14. ICE

  15. MODEL OF “FORMED” and “BROKEN” H-BONDS IN WATER IS VERY ROUGH O-H O--H ::: O

  16. PEPTIDE GROUP ALSO FORMS H-BONDS ACCEPTOR DONOR

  17. FORMATION OF H-BOND IN VACUUM ENERGY Edecreases EXCHANGE OF H-BONDS IN WATER ENERGY E = const ENTRORY S~ln(pos.) increases FREE ENERGY F=E-TSdecreases: water moves Just because H-bonds have large energy, only their ENTROPIC part plays a role in water surrounding

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