Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

BMC Structural Biology

Dmitry A Afonnikov⁵  Nikolay A Kolchanov²  Elena V Boldyreva⁴  Yuri N Vorobjev³  Nikolay A Alemasov¹  Kirill E Medvedev¹ 

[1] Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia;NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow 123182, Russia;Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk 630090, Russia;Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk 630090, Russia;Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia

关键词: Salt bridges;    Adaptation;    High pressure;    Nip7 protein;    Molecular dynamics simulation;   

Others  :  1090719
DOI  :  10.1186/s12900-014-0023-z

 received in 2014-07-06, accepted in 2014-10-03,  发布年份 2014

【 摘 要 】

Background

The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures.

Results

The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.

Conclusions

The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

【 授权许可】

   
2014 Medvedev et al.; licensee BioMed Central Ltd.

【 图 表 】

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