Propagating conformational changes over long (and short) distances in proteins

Abstract

The problem of the propagation of conformational changes over long distances or through a closely packed protein is shown to fit a model of a ligand-induced conformational change between two protein states selected by evolution. Moreover, the kinetics of the pathway between these states is also selected so that the energy of ligand binding and the speed of the transition between conformational states are physiologically appropriate. The crystallographic data of a wild-type aspartate receptor that has negative cooperativity and a mutant that has no cooperativity but has native transmembrane signaling are shown to support this model.

Figure 1

(a) The backbone atoms in the α4 helix, shown at the left, compared with the backbone atoms of the α1 helix, shown at the right, for the wild-type protein. The red line is the apoprotein and the yellow line is the protein with aspartate bound. (b) The same comparison as a, but for the S68A receptor.

Figure 2

Side chains in the helices α1 and α4 that shift relative to each other on binding aspartate.

Figure 3

The alternative pathways for the ligand-induced change. The extremes represent pathways in which (i) the apoprotein isomerizes to conformation B (= ), which then binds substrate  (top); (ii) the ligand binds to the apoprotein conformation that then isomerizes to form the final bound-ligand conformation ( → → ) (bottom); or (iii) the protein isomerizes to a conformation somewhere in between  and  and then binds to the ligand and reaches the final state ( → → → ) (middle). Glossary: A = , the conformation of the protein in the absence of ligand. B = , the conformation of the protein in the presence of ligand. C = , an intermediate conformation containing elements of A and B. AS = , BS = , CS = , the ligand bound to the protein in the A, B, and C conformations, respectively. K_obs = the observed affinity constant of the receptor = K_tAB⋅K_SB. K_tAB = [B]/[A]. K_tAC = [C]/[A]. K_tCB = [B]/[C].

Figure 4

The energetics of the conformation changes when a ligand binds to a protein. Conformational states are shown as potential wells depicting the changing energetics of small displacement from the most stable conformation of that well. The conformation A is the most stable conformation of the apoprotein, but B exists at a higher energy state, its amount depending on the kinetics and K_tAB. The presence of a ligand will stabilize conformation B but will destabilize the A conformation because S has very little attraction to the apo conformation.

Figure 5

Possible mechanisms for ligand-induced changes in the aspartate receptor. On the right is a wedge mechanism in which a ligand is attracted into a position between rigid side chains and deflects one helix downwards relative to the other. On the left is an attraction shift mechanism in which the binding of a ligand attracts hydrogen bonds, leading to a shifting of hydrogen bonds and causing the downward shift of helix α4 relative to helix α1.