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