Thermophilic Adaptation of Protein Complexes Inferred from Proteomic Homology Modeling

SummaryAs protein complexes must remain in their native conformations at habitat temperatures, thermal adaptation requires adjustment of their parts and interactions between them. Based on independent sets of structural templates and sequences of 127 complete prokaryotic proteomes with optimal growth temperatures from 8°C to 100°C, we performed proteomic homology modeling of complexes and analyzed peculiarities in their traits related to thermal adaptation. We explore compositional determinants of thermostability of protein complexes based on the model of stability including negative and positive components of design. We show that positively charged amino acids play an important role in protein complexes, working in negative design against misfolded conformations and aberrant assemblies and contributing to positive design by stabilizing both the native interface and the overall structure of the complex. Aggregation propensity of interfaces is higher than that of surfaces and the difference between them increases with optimal growth temperature securing native complexes in hot environments.

► Proteomic homology modeling ► Role of negative design in thermostability of protein complexes ► Differential aggregation propensity is a new characteristic of protein-protein interfaces ► Negative design is provided by positive charges in protein complexes