Limits...
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.

Show MeSH

Related in: MedlinePlus

Nip7 protein structure. (A) 3D representation of the P. abyssi protein structure (2P38:A) [23]. The secondary structure elements are lettered and colored (helices red, β-strands blue, turns green). The N-terminal domain left, C-terminal domain right. Amino acid residues assumed to bind an RNA molecule [23] shown as ball and stick representation. (B) Alignment of the P. abyssi and P. furiosus sequences. The substitutions in the P. furiosus relative to the P. abyssi protein are on gray background. Distinguished are the following types of substitutions resulting in replacement of: a polar residue in P. abyssi by a nonpolar in P. furiosus (red); a charged P. abyssi amino acid by an uncharged in P. furiosus at retained polarity (green); polar amino acid in P. furiosus by nonpolar in P. abyssi (pink); P. furiosus charged side group by an uncharged (lilac); those resulting in oppositely charged residues (blue). Secondary structure is shown below sequences according to 2P38:A: the helices are indicated in red rectangles, blue arrows indicate β-strands. Residues belonging to the interior of the protein according to the GetArea web-server [27] are shown in bold letters. The symbol *denotes amino acids involved in RNA binding [23]. The N-terminal domain beneath the row of position numbers, blue; the C-terminal domain, red.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Nip7 protein structure. (A) 3D representation of the P. abyssi protein structure (2P38:A) [23]. The secondary structure elements are lettered and colored (helices red, β-strands blue, turns green). The N-terminal domain left, C-terminal domain right. Amino acid residues assumed to bind an RNA molecule [23] shown as ball and stick representation. (B) Alignment of the P. abyssi and P. furiosus sequences. The substitutions in the P. furiosus relative to the P. abyssi protein are on gray background. Distinguished are the following types of substitutions resulting in replacement of: a polar residue in P. abyssi by a nonpolar in P. furiosus (red); a charged P. abyssi amino acid by an uncharged in P. furiosus at retained polarity (green); polar amino acid in P. furiosus by nonpolar in P. abyssi (pink); P. furiosus charged side group by an uncharged (lilac); those resulting in oppositely charged residues (blue). Secondary structure is shown below sequences according to 2P38:A: the helices are indicated in red rectangles, blue arrows indicate β-strands. Residues belonging to the interior of the protein according to the GetArea web-server [27] are shown in bold letters. The symbol *denotes amino acids involved in RNA binding [23]. The N-terminal domain beneath the row of position numbers, blue; the C-terminal domain, red.

Mentions: The 3D structure of P. abyssi Nip7 protein is known (PDB ID 2P38; Figure 1A). The protein polypeptide chain is 166 amino acids long of which 155 residues are represented in the 3D structure. The protein consists of two α-β domains [23], Figure 1. The N-terminal domain (residues 1–90) is composed of five antiparallel β-strands surrounded by three α-helices and one 310 helix. There is an assumption that archaeal Nip7 may interact with exosome via its N-terminal domain, thereby controlling the exosome function [22]. However, the molecular mechanism of this interaction is unknown.


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)

Nip7 protein structure. (A) 3D representation of the P. abyssi protein structure (2P38:A) [23]. The secondary structure elements are lettered and colored (helices red, β-strands blue, turns green). The N-terminal domain left, C-terminal domain right. Amino acid residues assumed to bind an RNA molecule [23] shown as ball and stick representation. (B) Alignment of the P. abyssi and P. furiosus sequences. The substitutions in the P. furiosus relative to the P. abyssi protein are on gray background. Distinguished are the following types of substitutions resulting in replacement of: a polar residue in P. abyssi by a nonpolar in P. furiosus (red); a charged P. abyssi amino acid by an uncharged in P. furiosus at retained polarity (green); polar amino acid in P. furiosus by nonpolar in P. abyssi (pink); P. furiosus charged side group by an uncharged (lilac); those resulting in oppositely charged residues (blue). Secondary structure is shown below sequences according to 2P38:A: the helices are indicated in red rectangles, blue arrows indicate β-strands. Residues belonging to the interior of the protein according to the GetArea web-server [27] are shown in bold letters. The symbol *denotes amino acids involved in RNA binding [23]. The N-terminal domain beneath the row of position numbers, blue; the C-terminal domain, red.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Nip7 protein structure. (A) 3D representation of the P. abyssi protein structure (2P38:A) [23]. The secondary structure elements are lettered and colored (helices red, β-strands blue, turns green). The N-terminal domain left, C-terminal domain right. Amino acid residues assumed to bind an RNA molecule [23] shown as ball and stick representation. (B) Alignment of the P. abyssi and P. furiosus sequences. The substitutions in the P. furiosus relative to the P. abyssi protein are on gray background. Distinguished are the following types of substitutions resulting in replacement of: a polar residue in P. abyssi by a nonpolar in P. furiosus (red); a charged P. abyssi amino acid by an uncharged in P. furiosus at retained polarity (green); polar amino acid in P. furiosus by nonpolar in P. abyssi (pink); P. furiosus charged side group by an uncharged (lilac); those resulting in oppositely charged residues (blue). Secondary structure is shown below sequences according to 2P38:A: the helices are indicated in red rectangles, blue arrows indicate β-strands. Residues belonging to the interior of the protein according to the GetArea web-server [27] are shown in bold letters. The symbol *denotes amino acids involved in RNA binding [23]. The N-terminal domain beneath the row of position numbers, blue; the C-terminal domain, red.
Mentions: The 3D structure of P. abyssi Nip7 protein is known (PDB ID 2P38; Figure 1A). The protein polypeptide chain is 166 amino acids long of which 155 residues are represented in the 3D structure. The protein consists of two α-β domains [23], Figure 1. The N-terminal domain (residues 1–90) is composed of five antiparallel β-strands surrounded by three α-helices and one 310 helix. There is an assumption that archaeal Nip7 may interact with exosome via its N-terminal domain, thereby controlling the exosome function [22]. However, the molecular mechanism of this interaction is unknown.

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