Protein design is a key factor for subunit-subunit association

Abstract

Fundamental questions about role of the quaternary structures are addressed by using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer interactions revealed by atomic force experiments. Force curves during association and dissociation processes are characterized by sudden jumps followed by smooth behavior and form hysteresis loops. Furthermore, the process is reversible in a finite range of temperature stabilizing the dimer, and the width of the hysteresis loop increases as the design procedure improves: i.e., stabilizes the dimer more. It is shown that, in the interface between the two monomeric subunits, the design procedure naturally favors those amino acids whose mutual interaction is stronger.

Figure 1

Native dimer. (a) Structure and numbering (indicated on each bead) of the type of the bead (as in column 1 of Table 1). (b) Inner (squares)- and inter (dots)-chain contacts. In both figures, the chains A and B are represented in light and dark color, respectively. In our model, the sequences A and B are chosen not to be necessarily equal to explore the relevance of the symmetry of the sequence for protein aggregation.

Figure 2

Energy of the model protein plotted as a function of the distance d between subunits.

Figure 3

Subunit dissociation (dark line) and reassociation forces (light line) as resulting from CMD simulations in which the two centers of mass of the two subunits are kept at fixed distance r. The forces are measured after equilibrium at temperature 0.06 ɛ has been reached. Multiple points, very close to each other, indicate repeated calculations and give an estimate of the error bar for the various measured forces. The static force, indicated by the black line, is the force between the monomers immediately after they are separated out at distance r from their native state. The force vs. r curve then is fitted with the function F^fit(r) = γ{(ρ/r)^α₁ − (ρ/r)^α₂} (best fit parameters γ = 20.8 ɛ, ρ = 2.4 σ₀, α₁ = 22.8, and α₂ = 8.5, correlation coefficient among fitted and calculated values equal to 0.9998).

Figure 4

Distributions of inter- (light shadow) and intramonomeric interactions (dark shadow) normalized to the total number of contacts at r = 15.5 Å (native state) (a), r = 23.4 Å (b), and r = 30.6 Å (c). Notice that stronger interactions are favored at the subunit–subunit interface with respect to the intramonomer interactions.

Figure 5

Monomer deformation (distance of a monomer from the corresponding native structure, averaged over the two monomers) as a function of the distance r at T = 0.05 ɛ (a), T = 0.15 ɛ (b), and T = 0.01 ɛ (c).

Figure 6

Comparison between the optimized structures of one subunit folded as in the native protein dimer (darkline) and as independent monomer (lightline). Residues at the interface are indicated with circles.

Figure 7

Dissociation and reassociation forces for two dimers with the same native state but different pairs of sequences: one obtained with an optimal design (a) and the other with a poor design quality (b). Hysteresis loop width correlates well with the degree of dimer stability.