Protein conformational dynamics allow promiscuity, but at the same time dynamics can spell specificity. Proteins are often able to bind specifically to more than one partner at the same binding site, a property that has been termed ‘promiscuity’. The partners are often related, and belong to the same family; however, their conformations may vary to some extent. Alternatively, they may belong to different families but share a protein-protein recognition domain, or a motif. Promiscuity is possible because of protein flexibility. In the case of EphA4, the multiple conformations that pre-exist in the free state allow EphA4 to bind nine ephrin ligands.
To understand how conformational dynamics can allow for both promiscuity and specificity, let us consider ubiquitin, for which there are ample data relating to the ‘conformational selection and population shift’ binding mechanism that we have proposed [4
]. Similar to EphA4, a large number of conformations has been observed experimentally for ubiquitin, both in solution and in the crystal form, in the unbound state and bound to a range of ligands. In solution, NMR experiments identified an ensemble of 40 conformers. Each of the 40 were mapped to one of the crystal structure conformations in the unbound state or bound to a ligand[5
], illustrating that these 40 conformations reflect the inherent population rather than being induced by the ligand. While all conformations were observed simultaneously in solution, this is not the case in the static crystal structure environment, which ‘traps’ a certain favored conformation that has a higher abundance under the crystallization conditions. After mutual conformation selection by ubiquitin and the ligand, minor adjustments of the interactions (induced fit) may take place[6
The dynamics and the distribution of possible conformations of a protein are encoded in the sequence; these combined with specific residues at the binding site encode binding specificity. It was proposed that the population shift may occur prior to ligand-receptor binding, when the receptor is 1 to 2 nm from ubiquitin[7
]. Conformational transitions are typically described by the free energy landscape. As Figure illustrates, the energies of the EphA4 conformational substates are separated by low (within open or closed conformation basins) or high (between open or closed conformation basins) barriers. The ligands match these subtly different conformations. Thus, ligands may have altered binding affinities, allowing specificity across substates. Previously it was shown that the binding affinities of EphA4 with ephrin-A1, ephrin-A2, ephrin-A4, ephrin-A5, and ephrin-B2 are 1.2 µm, 2.3 µm, 36 nm, 360 nm, and 10.8 µm, respectively [1
], indicating varied selectivity towards various ligands in solution. In vivo
, however, the affinities may change.
Figure 1 The populations are dynamic and are affected by various factors, including binding. Ligand binding could allosterically affect a second binding site. Because different ligands can allosterically lead to different (second site) conformations and these (more ...)