Transcript Struktura i Energetyka Białek

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 role
Hydrophobic interaction: compactness
Local interactions: chain stiffness
Hydrogen bonds: architecture
Local and nonlocal interactions
Long-range vs. short-range interactions
1
Eij  n
rij
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
Free energies of N-methylamide dimerization in water (w) and CCl4
(n) solution and transfer between these solvents
Aw+Bw
(AB)n
DG4=+0.62 kcal/mol
DG3=+3.10 kcal/mol
An+Bn
DG1=-2.40 kcal/mol
DG3=+3.10 kcal/mol
(AB)w
Local interactions are largely determined
by Ramachandran map
Conformations of a terminally-blocked amino-acid residue
E
Zimmerman, Pottle, Nemethy, Scheraga,
Macromolecules, 10, 1-9 (1977)
C7eq
C7ax
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
fL-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.
Color map of the MJ table
P
K
R
H
D
E
N
Q
S
T
G
A
Y
W
V
L
I
F
M
C
C M F
I
L V W Y A G T S Q N E D H R K P
Conformational entropy