covalent interactions

non-covalent interactions+

=structural stability of (bio)polymers in the operative molecular environment

1

Energy, entropy and reaction

coordinate (Q) of molecular folding

process

covalent interactions

non-covalent interactions

not dependent on solvent

Van der Waals

Rotational

Vibrational

influenced by solvents

electrostatic

interactions

hydrogen bonds

solvent dependent

hydrophobic

Interactions

direct interations with

solvents

disulfide bridges

in proteins:

2

3

non-covalent interactions

not dependent on solvent

Van der Waals

Rotational

Vibrational

influenced by solvents

electrostatic

interactions

hydrogen bonds

solvent dependent

hydrophobic

Interactions

direct interations with

solvents

in proteins:

4

5

energy contribution not dependent on molecular

environment

6

energy contribution not dependent on molecular

environment

7

energy contribution not dependent on molecular

environment

8

energy contribution not dependent on molecular

environment

9

energy contribution not dependent on molecular

environment

10

energy contribution not dependent on molecular

environment

11

influenced by solvent

 • electrostatic interactions• dipolar interactions• hydrogen bonding

122a. enthalpy and entropy in protein folding

hydrogen bond

13

hydrogen bond

2a. enthalpy and entropy in protein folding

14

hydrogen bond

2a. enthalpy and entropy in protein folding

electrostatic interactions

15

16

17

solvent dependent • hydrophobic interactions• direct interations with solvents

The vdW surface of a molecule (shown in red) is defined as the surface of the union of balls representing all atoms, with radii set to the vdW radii.

The accessible surface of the same molecule (shown in green) is the surface generated by the center of a sphere rolling on the vdW surface. The radius of this sphere is usually set to 1.4 Angstroms, the radius of a water molecule. The molecular surface (shown in magenta) is the lower envelope generated by the rolling sphere. It differs from the vdW surface in that some areas are inaccessible to the rolling sphere.

The accessible surface of a protein is defined as the van der Waals envelope of the molecule expanded by the radius of the solvent sphere about each atom center (Lee, B and Richards, FM. The interpretation of protein structure: estimation of static accessibility. J. Mol. Biol., 55, 379-400 (1971)

18

19

20

TOTAL CONFORMATIONAL ENERGY

E=Ea+Er+Ees+El+Et+Ef+EH+EHf

Ea attractiveEr repulsiveEes electrostatic potential El bond lenght changesEt bond angle changesEf torsional potentialEH hydrogen bondEhf hydrophobic interactions

FORCE FIELD21

222a. enthalpy and entropy in protein folding

from http://www.lanl.gov/bmsi/Individual%20Research/Werner/WernerFolding.html

from http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olhydrophobprot.html

thermodynamics of protein folding

232a. enthalpy and entropy in protein folding