covalent interactions
+
non-covalent interactions
=
structural stability of (bio)polymers in the
operative molecular environment
Energy, entropy and
reaction coordinate
(Q) of molecular
folding process
1
covalent interactions
in proteins:
disulfide bridges
non-covalent interactions
not dependent on solvent influenced by solvents

Van der Waals

Rotational

Vibrational

electrostatic
solvent dependent

interactions

hydrogen bonds
hydrophobic
Interactions

direct interations with
solvents
2
3
in proteins:
non-covalent interactions
not dependent on solvent influenced by solvents

Van der Waals

Rotational

Vibrational

electrostatic
solvent dependent

interactions

hydrogen bonds
hydrophobic
Interactions

direct interations with
solvents
4
energy contribution not dependent
on molecular environment
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
influenced by solvent
• electrostatic interactions
• dipolar interactions
• hydrogen bonding
11
hydrogen bond
2a. enthalpy and entropy in protein folding
12
hydrogen bond
2a. enthalpy and entropy in protein folding
13
hydrogen bond
2a. enthalpy and entropy in protein folding
14
electrostatic interactions
15
16
solvent dependent
• hydrophobic interactions
• direct interations with solvents
17
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)
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.
18
19
20
TOTAL CONFORMATIONAL ENERGY
E=Ea+Er+Ees+El+Et+Ef+EH+EHf
Ea
Er
Ees
El
Et
Ef
EH
Ehf
attractive
repulsive
electrostatic potential
bond lenght changes
bond angle changes
torsional potential
hydrogen bond
hydrophobic interactions
FORCE FIELD
21
thermodynamics of protein folding
from http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olhydrophobprot.html
from http://www.lanl.gov/bmsi/Individual%20Research/Werner/WernerFolding.html
2a. enthalpy and entropy in protein folding
22
2a. enthalpy and entropy in protein folding
23