Post on 04-Jan-2016
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