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

Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA - BMC Struct. Biol. (2014)

Bottom Line: Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.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.Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. albatros@bionet.nsc.ru.

ABSTRACT

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.

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The RMSDL values for the NIP7-ABY and NIP7-FUR proteins averaged for all the trajectories and runs. Red triangles highlight the positions at which the RMSDL parameter significantly depends on model type.
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Figure 8: The RMSDL values for the NIP7-ABY and NIP7-FUR proteins averaged for all the trajectories and runs. Red triangles highlight the positions at which the RMSDL parameter significantly depends on model type.

Mentions: Analysis of the influence temperature exerts on the RMSDL in the two models shows that the local structure deviates significantly from the crystal 2P38:A for 77 of the 143 positions we analyzed (53%). Pressure exerts a significant influence on the RMSDL at only 9 positions of the protein (6%), while protein type exerts a significant influence on the conformational deviations of the polypeptide chain for 91 positions, 63% (FigureĀ 8).


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

Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA - BMC Struct. Biol. (2014)

The RMSDL values for the NIP7-ABY and NIP7-FUR proteins averaged for all the trajectories and runs. Red triangles highlight the positions at which the RMSDL parameter significantly depends on model type.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209456&req=5

Figure 8: The RMSDL values for the NIP7-ABY and NIP7-FUR proteins averaged for all the trajectories and runs. Red triangles highlight the positions at which the RMSDL parameter significantly depends on model type.
Mentions: Analysis of the influence temperature exerts on the RMSDL in the two models shows that the local structure deviates significantly from the crystal 2P38:A for 77 of the 143 positions we analyzed (53%). Pressure exerts a significant influence on the RMSDL at only 9 positions of the protein (6%), while protein type exerts a significant influence on the conformational deviations of the polypeptide chain for 91 positions, 63% (FigureĀ 8).

Bottom Line: Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.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.Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. albatros@bionet.nsc.ru.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus