PROTEIN PHYSICSPROTEIN PHYSICS

LECTURES 3-4LECTURES 3-4

Elementary interactions:Elementary interactions:Van der WaalsVan der Waals

&&H-bondsH-bonds

In vacuumIn vacuum

Main-chain:Main-chain:N-CN-C))(C(C-C’)-C’)

2.8A < rmin(C…C) = 3.0A

strong repulsion

strong repulsion

weak

attraction

weak

attraction

r0(N…N)=3.1A

GLYGLY

ALAALA

>ALA:>ALA:

-atoms

PRO (PRO ( = -70 = -70oo))

Before PROBefore PRO

ALA, etc. GLY onlyALA, etc. GLY only

WATERWATER molecule: molecule:

HYDROGEN BONDSHYDROGEN BONDS

H-bond energy:H-bond energy: 5 kcal/mol5 kcal/molICE ICE sublimation: sublimation: ((12 kcal/mol - 2 kcal/mol12 kcal/mol - 2 kcal/mol[vdW][vdW]))/2/2 10 kcal/mol10 kcal/mol[CH[CH33-CH-CH22-OH]-OH] - 5 kcal/mol - 5 kcal/mol[CH[CH33-O-CH-O-CH33]]

(HO)(HO)-1/3-1/3-H-H+1/3+1/3 ::::: ::::: OO-2/3-2/3-H-H22+2/3+2/3: : 11//3 3

22//3 3 (- (-11//22--11//44+2+211//33))

~ 6 kcal/mol~ 6 kcal/mol

WATERWATER molecule: molecule:

HYDROGEN BONDSHYDROGEN BONDS

H-bond energy:H-bond energy: 5 kcal/mol5 kcal/molICE ICE sublimation: sublimation: ((12 kcal/mol - 2 kcal/mol12 kcal/mol - 2 kcal/mol[vdW][vdW]))/2/2 10 kcal/mol10 kcal/mol[CH[CH33-CH-CH22-OH]-OH] - 5 kcal/mol - 5 kcal/mol[CH[CH33-O-CH-O-CH33]]

(HO)(HO)-1/3-1/3-H-H+1/3+1/3 ::::: ::::: OO-2/3-2/3-H-H22+2/3+2/3: : 11//3 3

22//3 3 (- (-11//22--11//44+2+211//33))

~ 6 kcal/mol~ 6 kcal/mol

WATERWATER molecule: molecule:

HYDROGEN BONDSHYDROGEN BONDS

H-bond energy:H-bond energy: 5 kcal/mol5 kcal/molICE ICE sublimation: sublimation: ((12 kcal/mol - 2 kcal/mol12 kcal/mol - 2 kcal/mol[vdW][vdW]))/2/2 10 kcal/mol10 kcal/mol[CH[CH33-CH-CH22-OH]-OH] - 5 kcal/mol - 5 kcal/mol[CH[CH33-O-CH-O-CH33]]

(HO)(HO)-1/3-1/3-H-H+1/3+1/3 ::::: ::::: OO-2/3-2/3-H-H22+2/3+2/3: : 11//3 3

22//3 3 (- (-11//22--11//44+2+211//33))

~ 6 kcal/mol~ 6 kcal/mol

ICEICE

MODEL OF “FORMED” and “BROKEN”MODEL OF “FORMED” and “BROKEN”H-BONDS IN WATER IS VERY ROUGHH-BONDS IN WATER IS VERY ROUGH

O-H O-H O--H ::: OO--H ::: O

PEPTIDE GROUP PEPTIDE GROUP ALSO FORMS ALSO FORMS

H-BONDSH-BONDS

DONORDONOR

ACCEPTORACCEPTOR

ENERGY ENERGY EE = = const const ENTRORY ENTRORY SS~ln(pos.) ~ln(pos.) increasesincreasesFREE ENERGY FREE ENERGY F=E-TSF=E-TS decreasesdecreases: water moves: water moves

Just because H-bonds have large energy, Just because H-bonds have large energy, only their ENTROPIC part only their ENTROPIC part plays a role in water surrounding plays a role in water surrounding

EXCHANGE OF H-BONDS IN WATEREXCHANGE OF H-BONDS IN WATER

FORMATION OF H-BOND IN VACUUMFORMATION OF H-BOND IN VACUUM

ENERGY ENERGY EE decreasesdecreases