INTERACTIONS IN PROTEINS AND THEIR ROLE IN
STRUCTURE FORMATION
Levels of protein structure organization
Dominant forces in protein folding
• Electrostatic forces
• Hydrogen bonding and van der Waals interactions
• Intrinsic properties
• Hydrophobic forces
• Conformational entropy (opposes folding)
Can we say that there are „dominant” forces in protein folding?
Hardly. Proteins are only marginally stable (5 – 20 kBT/molecule). For comparison: water-water H-bond has about 5 kcal/mol (9 kBT/molecule) Consequently, even the tiniest force cannot be ignored.
However, different types of interactions play different roleHydrophobic interaction: compactnessLocal interactions: chain stiffnessHydrogen bonds: architecture
Local and nonlocal interactions
Long-range vs. short-range interactions
nij
ij rE
1 n<=3: long range interactions
n>3: short-range interactions
Long-range: electrostatic (charge-charge, charge-dipole, and dipole-dipole) interactions
Short-range: van der Waals repulsion and attraction, hydrophobic interactions
Electrostatic interactions
• Lots of like-charges (e.g., side-chain ionization by pH decrease/increase) destabilize protein structure
• Increase of ionic strength destabilizes protein structure
• 5 – 10 kcal/mol / counter-ion (salt-bridge) pair
• A protein contains only a small number of salt bridges, mainly located on the surface (nevertheless, they can be essential).
Example of a surface salt bridge: salt bridge triad between Asp8, Asp12 and Arg110 on the surface of barnase
Replacement of charged residues with hydrophobic residues can increase the stability by 3-4 kcal/mol. Example: ARC
repressor
Wild type: salt triad between R31, E36, and R40
Mutant: hydrophobic packing between M31, Y36, and L40
Potentials of mean force
Maksimiak et al., J.Phys.Chem. B, 107, 13496-13504 (2003)
Masunov & Lazaridis, J.Am.Chem.Soc., 125, 1722-1730 (2003)
Hydrogen-bonding and van der Waals forces
Aw+Bw
An+Bn
(AB)w
(AB)n
G1=-2.40 kcal/mol
G3=+3.10 kcal/mol
Free energies of N-methylamide dimerization in water (w) and CCl4 (n) solution and transfer between these solvents
Local interactions are largely determined by Ramachandran map
Conformations of a terminally-blocked amino-acid residue
C7eq
C7ax
E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)
Energy maps of Ac-Ala-NHMe and Ac-Gly-AHMe obtained with the ECEPP/2 force field
Energy curve of Ac-Pro-NHMe obtained with the ECEPP/2 force field
L-Pro-68o
Energy minima of therminally-blocked alanine with the ECEPP/2 force field
Hydrophobic forces
Sobolewski et al., J.Phys.Chem., 111, 10765-10744 (2008)
Dependence of the PMF and cavity contribution to the PMF of two methane molecules on temperature (Sobolewski et al., PEDS, 22, 547-552 (2009)
S. Miyazawa & R.L. Jernigan, R. L. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18:534-552, 1985.
C M F I L V W Y A G T S Q N E D H R K P
P
K
R
H
D
E
N
Q
S
T
G
A
Y
W
V
L
I
F
M
C
Color map of the MJ table
Conformational entropy