INTERACTIONS IN PROTEINS AND THEIR ROLE IN STRUCTURE FORMATION
Jan 20, 2016
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