Use of Molecular‐Dynamics Simulation for Optimizing Protein Stability: Consensus‐Designed Ankyrin Repeat Proteins

In earlier work, two highly homologous (87% sequence identity) ankyrin repeat (AR) proteins, E3_5 and E3_19, were studied using molecular‐dynamics (MD) simulation. Their stabilities were compared, and it was found that the C‐terminal capping unit is unstable in the protein E3_19, in agreement with CD experiments. The different stabilities of these two very similar proteins could be explained by the different charge distributions among the AR units of the two proteins. Here, another AR protein, N3C, with yet another charge distribution has been simulated using MD, and its stability was analyzed. In agreement with the experimental data, the structure of N3C was found to be less stable than that of E3_5, but, in contrast to E3_19, secondary structure was only slightly lost, while structurally N3C is closer to E3_19 than to E3_5. The results suggest that a homogeneous charge distribution over the repeat units does enhance the stability of design AR proteins in aqueous solution, which, however, may be modulated by the bulkiness of amino‐acid side chains involved in the mutations.