Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions.

Tomoki Akiyama, Naoki Kunishima, Sayaka Nemoto, Kazuki Kazama, Masako Hirose, Yuki Sudo, Yoshinori Matsuura, Hisashi Naitow, Takeshi Murata

Proteins 2021 Mar

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It is known that a hyperthermostable protein tolerable at temperatures over 100°C can be designed from a soluble globular protein by introducing mutations. To expand the applicability of this technology to membrane proteins, here we report a further thermo-stabilization of the thermophilic rhodopsin from Thermus thermophilus JL-18 as a model membrane protein. Ten single mutations in the extramembrane regions were designed based on a computational prediction of folding free-energy differences upon mutation. Experimental characterizations using the UV-visible spectroscopy and the differential scanning calorimetry revealed that four of ten mutations were thermo-stabilizing: V79K, T114D, A115P, and A116E. The mutation-structure relationship of the TR constructs was analyzed using molecular dynamics simulations at 300 K and at 1800 K that aimed simulating structures in the native and in the random-coil states, respectively. The native-state simulation exhibited an ion-pair formation of the stabilizing V79K mutant as it was designed, and suggested a mutation-induced structural change of the most stabilizing T114D mutant. On the other hand, the random-coil-state simulation revealed a higher structural fluctuation of the destabilizing mutant S8D when compared to the wild type, suggesting that the higher entropy in the random-coil state deteriorated the thermal stability. The present thermo-stabilization design in the extramembrane regions based on the free-energy calculation and the subsequent evaluation by the molecular dynamics may be useful to improve the production of membrane proteins for structural studies. © 2020 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.

Citation

Tomoki Akiyama, Naoki Kunishima, Sayaka Nemoto, Kazuki Kazama, Masako Hirose, Yuki Sudo, Yoshinori Matsuura, Hisashi Naitow, Takeshi Murata. Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions. Proteins. 2021 Mar;89(3):301-310