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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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Dependencies of the Cαatoms RMSDs relative to the starting structure on the MD simulation step. Points indicate RMSD values (Y axis) at the simulation time (X axis) averaged over 5 trajectory runs. Whiskers indicate the 95% confidence intervals. (A) RMSD for NIP7-ABY model at 50 MPa and 300 and 373 K. (B) RMSD for NIP7-FUR model at 50 MPa and 300 and 373 K.
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Figure 2: Dependencies of the Cαatoms RMSDs relative to the starting structure on the MD simulation step. Points indicate RMSD values (Y axis) at the simulation time (X axis) averaged over 5 trajectory runs. Whiskers indicate the 95% confidence intervals. (A) RMSD for NIP7-ABY model at 50 MPa and 300 and 373 K. (B) RMSD for NIP7-FUR model at 50 MPa and 300 and 373 K.

Mentions: Figure 2 shows changes in the root mean – square deviations (the RMSDs) of the protein Cα atoms relative to the starting structures during the MD simulations for the trajectories at 50 MPa. From Figure 2 it follows that the structures achieve equilibrium starting from about 10 ns of the trajectory periods. The deviations from the starting structure are about 2 Å for the NIP7-ABY model, they are about 2.25 Å for the NIP7-FUR model.


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)

Dependencies of the Cαatoms RMSDs relative to the starting structure on the MD simulation step. Points indicate RMSD values (Y axis) at the simulation time (X axis) averaged over 5 trajectory runs. Whiskers indicate the 95% confidence intervals. (A) RMSD for NIP7-ABY model at 50 MPa and 300 and 373 K. (B) RMSD for NIP7-FUR model at 50 MPa and 300 and 373 K.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Dependencies of the Cαatoms RMSDs relative to the starting structure on the MD simulation step. Points indicate RMSD values (Y axis) at the simulation time (X axis) averaged over 5 trajectory runs. Whiskers indicate the 95% confidence intervals. (A) RMSD for NIP7-ABY model at 50 MPa and 300 and 373 K. (B) RMSD for NIP7-FUR model at 50 MPa and 300 and 373 K.
Mentions: Figure 2 shows changes in the root mean – square deviations (the RMSDs) of the protein Cα atoms relative to the starting structures during the MD simulations for the trajectories at 50 MPa. From Figure 2 it follows that the structures achieve equilibrium starting from about 10 ns of the trajectory periods. The deviations from the starting structure are about 2 Å for the NIP7-ABY model, they are about 2.25 Å for the NIP7-FUR model.

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