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Crystal structural analysis of protein–protein interactions drastically destabilized by a single mutation

¹ Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
² PRESTO, Japan Science and Technology Agency (JST), Tokyo 113-8510, Japan

(RECEIVED October 28, 2007; FINAL REVISION March 25, 2008; ACCEPTED March 25, 2008)

The complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein–protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 Ala, which corresponds to a change of 7.7 kcal·mol^–1 in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 Å resolution by X-ray crystallography. The complex was similar to the wild-type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel-like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel-like structure of hydrated water molecules.

Keywords: protein–protein interaction; barnase; barstar; mutation; water-mediated interaction

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