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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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Graphs showing the dependencies on different conditions of MD simulations for the solvent-accessible residue areas. (A) total; (B) polar; (C) hydrophobic. Pressure is plotted along the X, the SAS area in Å2 along the Y axis. Whiskers indicate the 95% confidence intervals. Blue, the NIP7-ABY model, 300 K; green, the NIP7-FUR model, 300 K; red, the NIP7-ABY model, 373 K; brown, the NIP7-FUR model, 373 K.
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Figure 4: Graphs showing the dependencies on different conditions of MD simulations for the solvent-accessible residue areas. (A) total; (B) polar; (C) hydrophobic. Pressure is plotted along the X, the SAS area in Å2 along the Y axis. Whiskers indicate the 95% confidence intervals. Blue, the NIP7-ABY model, 300 K; green, the NIP7-FUR model, 300 K; red, the NIP7-ABY model, 373 K; brown, the NIP7-FUR model, 373 K.

Mentions: We compute for each trajectory the average values of solvent accessibility of the residues for the entire protein (SASt), also separately for the polar (SASp) and hydrophobic (SASh) surface fractions. We calculate the mean and standard error of these parameters over five runs for each protein model and pressure-temperature values set. The results are given in Figure 4(A-C).


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)

Graphs showing the dependencies on different conditions of MD simulations for the solvent-accessible residue areas. (A) total; (B) polar; (C) hydrophobic. Pressure is plotted along the X, the SAS area in Å2 along the Y axis. Whiskers indicate the 95% confidence intervals. Blue, the NIP7-ABY model, 300 K; green, the NIP7-FUR model, 300 K; red, the NIP7-ABY model, 373 K; brown, the NIP7-FUR model, 373 K.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Graphs showing the dependencies on different conditions of MD simulations for the solvent-accessible residue areas. (A) total; (B) polar; (C) hydrophobic. Pressure is plotted along the X, the SAS area in Å2 along the Y axis. Whiskers indicate the 95% confidence intervals. Blue, the NIP7-ABY model, 300 K; green, the NIP7-FUR model, 300 K; red, the NIP7-ABY model, 373 K; brown, the NIP7-FUR model, 373 K.
Mentions: We compute for each trajectory the average values of solvent accessibility of the residues for the entire protein (SASt), also separately for the polar (SASp) and hydrophobic (SASh) surface fractions. We calculate the mean and standard error of these parameters over five runs for each protein model and pressure-temperature values set. The results are given in Figure 4(A-C).

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