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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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Related in: MedlinePlus

Base tetrad A1207/G1160 … G1190/C1186 at the helix 42/rGAC junction. The overall X-ray geometry (A), the trans H/SE A1207/G1160 base pair with dynamical water insertion (B left), the trans WC/WC G1190/C1186 base pair assisted either by water or ion (B right) and the unusual G1190/G1160 base pair (X-ray structure, C left). A similar A1192/C1182 contact is shown (C right). Extended analysis of base pairing dynamics is given in Supplementary Data.
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Figure 3: Base tetrad A1207/G1160 … G1190/C1186 at the helix 42/rGAC junction. The overall X-ray geometry (A), the trans H/SE A1207/G1160 base pair with dynamical water insertion (B left), the trans WC/WC G1190/C1186 base pair assisted either by water or ion (B right) and the unusual G1190/G1160 base pair (X-ray structure, C left). A similar A1192/C1182 contact is shown (C right). Extended analysis of base pairing dynamics is given in Supplementary Data.

Mentions: The junction between helix 42 and helix 43/44 comprises the bases localized at the border between the extended Kt-42 NC-stem and the rGAC, namely base triads G1158 = C1209/A1188 and G1159 = C1208/A1189 and tetrad A1207/G1160 … G1190/C1186 (Figures 1 and 3). This Hinge2 represents the pivoting point of the initial displacement of rGAC. Then it becomes the center of the directional (anisotropic) oscillations (Figure 2D) of the angle between the upper part of helix 42 and rGAC. The intrinsic Hinge2 bendability is not localized as in case of Kt-42, where the motion is pivoting around a single H-bond of the A-minor interaction (35). For Hinge2, the structural dynamics of the A-minor interaction, triad and tetrad (see Supplementary Data) are not coupled with either the initial displacement of rGAC or the subsequent EDA mode 3 dynamics.Figure 3.


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)

Base tetrad A1207/G1160 … G1190/C1186 at the helix 42/rGAC junction. The overall X-ray geometry (A), the trans H/SE A1207/G1160 base pair with dynamical water insertion (B left), the trans WC/WC G1190/C1186 base pair assisted either by water or ion (B right) and the unusual G1190/G1160 base pair (X-ray structure, C left). A similar A1192/C1182 contact is shown (C right). Extended analysis of base pairing dynamics is given in Supplementary Data.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Base tetrad A1207/G1160 … G1190/C1186 at the helix 42/rGAC junction. The overall X-ray geometry (A), the trans H/SE A1207/G1160 base pair with dynamical water insertion (B left), the trans WC/WC G1190/C1186 base pair assisted either by water or ion (B right) and the unusual G1190/G1160 base pair (X-ray structure, C left). A similar A1192/C1182 contact is shown (C right). Extended analysis of base pairing dynamics is given in Supplementary Data.
Mentions: The junction between helix 42 and helix 43/44 comprises the bases localized at the border between the extended Kt-42 NC-stem and the rGAC, namely base triads G1158 = C1209/A1188 and G1159 = C1208/A1189 and tetrad A1207/G1160 … G1190/C1186 (Figures 1 and 3). This Hinge2 represents the pivoting point of the initial displacement of rGAC. Then it becomes the center of the directional (anisotropic) oscillations (Figure 2D) of the angle between the upper part of helix 42 and rGAC. The intrinsic Hinge2 bendability is not localized as in case of Kt-42, where the motion is pivoting around a single H-bond of the A-minor interaction (35). For Hinge2, the structural dynamics of the A-minor interaction, triad and tetrad (see Supplementary Data) are not coupled with either the initial displacement of rGAC or the subsequent EDA mode 3 dynamics.Figure 3.

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