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

4. In vacuum

5. Main-chain:
f (N-Ca) ,
y (Ca-C’)

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

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

8. GLY

9. ALA

10. >ALA:
g-atoms

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

12. ALA, etc GLY only

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. 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

15. 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

17. ICE

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

19. PEPTIDE GROUP ALSO FORMS H-BONDS
ACCEPTOR
DONOR

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