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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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Kt-42+rGAC rRNA system. (A) Base pairing in the simulated Kt-42+rGAC system (helices 42–44 from the 23S rRNA of H. marismortui) using standard nomenclature (54). The two flexible regions are marked as rectangles and the individual helices are marked as H42, H43 and H44. Strand connectivity is not highlighted to keep the figure readable. (B) Secondary structure of the Kt-42+rGAC. (C) Schematic representation of the Kt-42+rGAC showing its modularity with five consecutive segments (C-stem, Hinge1, NC-stem, Hinge2 and Head) with very distinct intrinsic mechanical properties and dynamics (see the text). Two flexible Hinges (circles) link three rigid segments (C-stem, NC-stem and Head). Arrows indicate the direction of preferred motions at both Hinges.
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Figure 1: Kt-42+rGAC rRNA system. (A) Base pairing in the simulated Kt-42+rGAC system (helices 42–44 from the 23S rRNA of H. marismortui) using standard nomenclature (54). The two flexible regions are marked as rectangles and the individual helices are marked as H42, H43 and H44. Strand connectivity is not highlighted to keep the figure readable. (B) Secondary structure of the Kt-42+rGAC. (C) Schematic representation of the Kt-42+rGAC showing its modularity with five consecutive segments (C-stem, Hinge1, NC-stem, Hinge2 and Head) with very distinct intrinsic mechanical properties and dynamics (see the text). Two flexible Hinges (circles) link three rigid segments (C-stem, NC-stem and Head). Arrows indicate the direction of preferred motions at both Hinges.

Mentions: The starting geometry of helices 42–44 of Domain II of 23S rRNA of Haloarcula marismortui was taken from the X-ray structure of the 50S subunit of H. marismortui (PDB file 1JJ2) (5). Helix 42 forms the kink-turn motif (Kt-42) (46) while helices 43 and 44 form the GTPase-associated center rRNA (rGAC). The whole rRNA system named as Kt-42+rGAC was simulated as single-stranded RNA molecule containing 84 nucleotides (nt); residues 1140–1223 using H. marismortui numbering (Figure 1). The system can be roughly divided into two parts: Kt-42 with the attached stems (residues 1140–1157 and 1210–1223) and the rGAC (helices 43/44; residues 1158–1209, Figure 1C). The V-shaped Kt-42 contains the canonical stem (C-stem), internal loop (Kink) and non-canonical stem (NC-stem). The rGAC comprises a very complex pairing pattern described in detail in Figure 1A using the standard nomenclature (54). The starting structures of helices 42–44 of 23S rRNA of Escherichia coli were taken from PDB files 2AW4 and 2AWB (18) (residues 1036–1119 using E. coli numbering).Figure 1.


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)

Kt-42+rGAC rRNA system. (A) Base pairing in the simulated Kt-42+rGAC system (helices 42–44 from the 23S rRNA of H. marismortui) using standard nomenclature (54). The two flexible regions are marked as rectangles and the individual helices are marked as H42, H43 and H44. Strand connectivity is not highlighted to keep the figure readable. (B) Secondary structure of the Kt-42+rGAC. (C) Schematic representation of the Kt-42+rGAC showing its modularity with five consecutive segments (C-stem, Hinge1, NC-stem, Hinge2 and Head) with very distinct intrinsic mechanical properties and dynamics (see the text). Two flexible Hinges (circles) link three rigid segments (C-stem, NC-stem and Head). Arrows indicate the direction of preferred motions at both Hinges.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Kt-42+rGAC rRNA system. (A) Base pairing in the simulated Kt-42+rGAC system (helices 42–44 from the 23S rRNA of H. marismortui) using standard nomenclature (54). The two flexible regions are marked as rectangles and the individual helices are marked as H42, H43 and H44. Strand connectivity is not highlighted to keep the figure readable. (B) Secondary structure of the Kt-42+rGAC. (C) Schematic representation of the Kt-42+rGAC showing its modularity with five consecutive segments (C-stem, Hinge1, NC-stem, Hinge2 and Head) with very distinct intrinsic mechanical properties and dynamics (see the text). Two flexible Hinges (circles) link three rigid segments (C-stem, NC-stem and Head). Arrows indicate the direction of preferred motions at both Hinges.
Mentions: The starting geometry of helices 42–44 of Domain II of 23S rRNA of Haloarcula marismortui was taken from the X-ray structure of the 50S subunit of H. marismortui (PDB file 1JJ2) (5). Helix 42 forms the kink-turn motif (Kt-42) (46) while helices 43 and 44 form the GTPase-associated center rRNA (rGAC). The whole rRNA system named as Kt-42+rGAC was simulated as single-stranded RNA molecule containing 84 nucleotides (nt); residues 1140–1223 using H. marismortui numbering (Figure 1). The system can be roughly divided into two parts: Kt-42 with the attached stems (residues 1140–1157 and 1210–1223) and the rGAC (helices 43/44; residues 1158–1209, Figure 1C). The V-shaped Kt-42 contains the canonical stem (C-stem), internal loop (Kink) and non-canonical stem (NC-stem). The rGAC comprises a very complex pairing pattern described in detail in Figure 1A using the standard nomenclature (54). The starting structures of helices 42–44 of 23S rRNA of Escherichia coli were taken from PDB files 2AW4 and 2AWB (18) (residues 1036–1119 using E. coli numbering).Figure 1.

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