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Influence of high temperature and high pressure on the Nip7 proteins from the hyperthermophilic archaea P. abyssi and P. furiosus: molecular dynamics simulation analysis
K.E. Medvedev, K.V. Gunbin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia, kirill-medvedev@yandex.ru

Y.N. Vorobjev
Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia

D.A. Afonnikov
Institute of Cytology and Genetics SB RAS, Novosibirsk State University, Novosibirsk, Russia, ada@bionet.nsc.ru

High temperature and hydrostatic pressure are severe for living cells. However so me organisms can survive and pro liferate at deep-sea hydrothermal vents with high temperatures (above 100C) and pressures (hundreds times greater than atmospheric). The mo lecular mechanis ms of the adaptation of these organisms to extreme environments remain unclear. In this work we apply co mparat ive analysis of the mo lecular dynamics simulat ion o f Nip7 proteins fro m the hyperthermophilic archaea P. abyssi and P. furiosus species. P. furiosus it inhabits shallow hydrothermal vents, it can exist under pressures not above 20 MPa (~200 atm; 1 atm0.1MPa). P. abyssi exists at the depth of about 2200 m (~22 MPa) but it can tolerate pressures up to 50 MPa. Nip7 proteins are invo lved in riboso mal biogenesis, participate in 27S pre-rRNA processing and exosome function [1, 2]. It contains two domains, C-terminal PUA do main, invo lved in non-specific RNA-binding, and N-terminal supposed to be invo lved in proteinprotein interact ion wit h exosome. Recent ly, we observed that Nip7 proteins accumulates radical amino acid subst itutions at high rates during P. furiosus species divergence fro m deep-sea commo n ancestor with P. abyssi [3]. Here, we investigated changes o f the Nip7 polypept ide chain conformat ion and solvent accessibilit y at different pressures (0.1 - 300 MPa) and temperatures (300 and 373 K).


Both proteins do not unfo ld under all evaluated temperature/pressure condit ions. We found that high temperature increase fluctuations of the polypept ide chain of both proteins. High pressure does not affect structure fluctuation but result in conformational changes of the proteins. Interestingly, the RMSD of the P. abyssi Nip7 model fro m the X-ray structure decrease with increasing pressure and temperatures. Obtained data demonstrated that the RNA-binding domain of the Nip7 protein is more flexible than N-terminal one. This flexibilit y may provide C-terminal do main funct ionalit y: non-specific binding o f the po ly-U/po ly-AU RNA sequences. N-terminal do main demonstrates stable hydrophobic core and flexible loop regions. Addit io nally we found that segment of the Nip7 sequence 45-55 (helices 2-3) demonstrate high structure fluctuatio n with increasing temperature in proteins fro m both species. Interestingly, the sequence of this segment is highly conserved in archaeal Nip7 proteins. We suggested that hydrophobic patch formed by this segment may be invo lved in protein-protein interact ions. Our data also suggests that the interactions of these proteins wit h so lvent are different and could be important for adaptation to high-pressure condit io ns at the protein structure level. This work was supported by RFBR grant No. 11-04-01771, RAS program Bio sphere Origin and Evo lut ion, RAS program .II.6.8, SB RAS Integration projects 39 and 130. 1. P. P. Coltri et al. (2007). Structural insights into the interaction o f the Nip7 PUA do main with polyuridine RNA. Biochemistry, 46:14177-14187. 2. J.S. Luz et al. (2010). Identificat ion of archaeal proteins that affect the exosome funct ion in vitro. BMC biochemistry, 11:22. 3. K.V. Gunbin et al. (2009). Molecular evo lut ion of the hyperthermophilic archaea of the Pyrococcus genus: analysis o f adaptation to different environmental condit ions. BMC genomics, 10:639.