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Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.

Rázga F, Koca J, Mokdad A, Sponer J - Nucleic Acids Res. (2007)

Bottom Line: Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA).The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads.In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.

ABSTRACT
Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42-44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

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Essential dynamics of Kt-42+rGAC rRNA system. Schematic (left) and surface (right) representations of the leading essential dynamics motions, double arrows indicate oscillations. (A) The initial displacement of the Head stemming from the rearrangement of Hinge2 (purple) observed during the first 5 ns of simulation and causing the permanent increase of the inter-helical angle by ca 25° (initial geometry in black, final in red). (B) Anisotropic anharmonic oscillation of rGAC pivoting at Kt-42 (Hinge1) (purple, EDA mode 1). (C) Internal breathing of rGAC (EDA mode 2) not contributing to the overall motion of rGAC and involving mainly the dynamics of non-canonical base pairs (see Supplementary Data). (D) Fluctuations of rGAC around Hinge2 (purple, EDA mode 3) characterized as anisotropic oscillatory bending of the duplex containing the upper part of helix 42 and helix 43. (E) Twisting of rGAC (EDA mode 4) stemming from twisting inherent to Kt-42 (35) and twisting in the Hinge2 region.
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Figure 2: Essential dynamics of Kt-42+rGAC rRNA system. Schematic (left) and surface (right) representations of the leading essential dynamics motions, double arrows indicate oscillations. (A) The initial displacement of the Head stemming from the rearrangement of Hinge2 (purple) observed during the first 5 ns of simulation and causing the permanent increase of the inter-helical angle by ca 25° (initial geometry in black, final in red). (B) Anisotropic anharmonic oscillation of rGAC pivoting at Kt-42 (Hinge1) (purple, EDA mode 1). (C) Internal breathing of rGAC (EDA mode 2) not contributing to the overall motion of rGAC and involving mainly the dynamics of non-canonical base pairs (see Supplementary Data). (D) Fluctuations of rGAC around Hinge2 (purple, EDA mode 3) characterized as anisotropic oscillatory bending of the duplex containing the upper part of helix 42 and helix 43. (E) Twisting of rGAC (EDA mode 4) stemming from twisting inherent to Kt-42 (35) and twisting in the Hinge2 region.

Mentions: We carried out 31 ns MD simulation of the Kt-42+rGAC rRNA of H. marismortui. During the first 5 ns the molecule gradually changed its initial (X-ray) arrangement to a new stable geometry. The relaxation changes the initial position of helices 43/44 by ca. 25° with respect to helix 42 (Figure 2A). After the initial transition is completed, the overall RMSD fluctuates in the range of 5–11 Å and 1–5 Å versus the starting and averaged structures, respectively (Figure S1). This initial structural transition is pivoting around the junction between helices 42 and 43/44, specifically base triples G1158 = C1209/A1188 and G1159 = C1208/A1189. We suggest that this structural transition reflects the relaxation of the system in the absence of the adjacent ribosomal elements. The initial relaxation does not lead to any changes in base pairing or isostericity of the simulated molecule.Figure 2.


Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.

Rázga F, Koca J, Mokdad A, Sponer J - Nucleic Acids Res. (2007)

Essential dynamics of Kt-42+rGAC rRNA system. Schematic (left) and surface (right) representations of the leading essential dynamics motions, double arrows indicate oscillations. (A) The initial displacement of the Head stemming from the rearrangement of Hinge2 (purple) observed during the first 5 ns of simulation and causing the permanent increase of the inter-helical angle by ca 25° (initial geometry in black, final in red). (B) Anisotropic anharmonic oscillation of rGAC pivoting at Kt-42 (Hinge1) (purple, EDA mode 1). (C) Internal breathing of rGAC (EDA mode 2) not contributing to the overall motion of rGAC and involving mainly the dynamics of non-canonical base pairs (see Supplementary Data). (D) Fluctuations of rGAC around Hinge2 (purple, EDA mode 3) characterized as anisotropic oscillatory bending of the duplex containing the upper part of helix 42 and helix 43. (E) Twisting of rGAC (EDA mode 4) stemming from twisting inherent to Kt-42 (35) and twisting in the Hinge2 region.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919483&req=5

Figure 2: Essential dynamics of Kt-42+rGAC rRNA system. Schematic (left) and surface (right) representations of the leading essential dynamics motions, double arrows indicate oscillations. (A) The initial displacement of the Head stemming from the rearrangement of Hinge2 (purple) observed during the first 5 ns of simulation and causing the permanent increase of the inter-helical angle by ca 25° (initial geometry in black, final in red). (B) Anisotropic anharmonic oscillation of rGAC pivoting at Kt-42 (Hinge1) (purple, EDA mode 1). (C) Internal breathing of rGAC (EDA mode 2) not contributing to the overall motion of rGAC and involving mainly the dynamics of non-canonical base pairs (see Supplementary Data). (D) Fluctuations of rGAC around Hinge2 (purple, EDA mode 3) characterized as anisotropic oscillatory bending of the duplex containing the upper part of helix 42 and helix 43. (E) Twisting of rGAC (EDA mode 4) stemming from twisting inherent to Kt-42 (35) and twisting in the Hinge2 region.
Mentions: We carried out 31 ns MD simulation of the Kt-42+rGAC rRNA of H. marismortui. During the first 5 ns the molecule gradually changed its initial (X-ray) arrangement to a new stable geometry. The relaxation changes the initial position of helices 43/44 by ca. 25° with respect to helix 42 (Figure 2A). After the initial transition is completed, the overall RMSD fluctuates in the range of 5–11 Å and 1–5 Å versus the starting and averaged structures, respectively (Figure S1). This initial structural transition is pivoting around the junction between helices 42 and 43/44, specifically base triples G1158 = C1209/A1188 and G1159 = C1208/A1189. We suggest that this structural transition reflects the relaxation of the system in the absence of the adjacent ribosomal elements. The initial relaxation does not lead to any changes in base pairing or isostericity of the simulated molecule.Figure 2.

Bottom Line: Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA).The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads.In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.

ABSTRACT
Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42-44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

Show MeSH
Related in: MedlinePlus