Abstract
Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.
Highlights
Species Thermotoga maritima MSB8 Thermus thermophilus HB8 Escherichia coli K-12 MG1655 Bacillus subtilis subsp. subtilis str. 16 Pseudomonas aeruginosa PAO1
It seems no universal trend of variation exits between thermophilic and mesophilic organisms and Wilcoxon statistical tests showed that there is no significant difference of protein chain length and interface size between thermophilic and mesophilic protein complexes, while the expression levels are not directly comparable between species because they are relative values among genes inside one species
The energy change is different: at the high temperature condition, the binding energy for the highly expressed protein complexes has obviously larger change after evolution than the lowly expressed proteins, while at the normal temperature condition, the binding energy change after evolution has no obvious difference between the highly and lowly expressed protein complexes. These results indicate that the protein interface stability has been preferentially optimized to avoid misinteraction for the highly expressed protein complexes at the high temperature condition that corresponds to the higher evolutionary pressure in thermophiles, while the protein interface stability has no preferential optimization for the highly expressed protein complexes at the normal temperature condition that corresponds to the lower evolutionary pressure in mesophiles
Summary
Species Thermotoga maritima MSB8 Thermus thermophilus HB8 Escherichia coli K-12 MG1655 Bacillus subtilis subsp. subtilis str. 16 Pseudomonas aeruginosa PAO1. We calculated the inter-chain interface size for the protein complexes from two thermophiles and three mesophiles. We found that highly expressed protein complexes incline to have larger interfaces than lowly expressed ones in thermophiles while this trait is not manifested in mesophiles. Since the inter-chain interface of a protein complex is related to its thermostability and the interaction of its subunits[10,11], the observed trend that highly expressed protein complexes have larger subunit interfaces revealed a positive correlation between the thermostability of protein complexes and their abundance. To seek the underlying mechanism of this correlation, we simulated the evolution of protein interface stability by using lattice models and found differences in evolutionary speed and energy change between high and normal temperature conditions, which highlighted a higher selection pressure for avoiding misinteractions between highly expressed proteins. Our results provided valuable information for understanding the molecular mechanisms that govern protein-protein interaction
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