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Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Bergonzo C, Hall KB, Cheatham TE - J Phys Chem B (2015)

Bottom Line: This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV).The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR.Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

ABSTRACT
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.

No MeSH data available.


Localization of top 10%of Mg2+ ion density (shown ingreen) in the top cluster from the divalent ion environment MD simulations.
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fig5: Localization of top 10%of Mg2+ ion density (shown ingreen) in the top cluster from the divalent ion environment MD simulations.

Mentions: Density-basedgrid analysis was performed on each cluster of thedivalent ion simulations to understand the different influence Mg2+ had on the more compact and less compact U-turn. The localizationof the top 10% of Mg2+ ion density is reported in Figure 5 and Table 5. Figure 5 shows a significant amount of density coordinatingthe phosphates of the UNR motif residues. The association of Mg2+ in this region explains the ability of the U-turn to preferentiallyadopt compact structures, since charged phosphate groups are shieldedfrom each other by the localized charge density of the Mg2+ ion. Interestingly, the localization of associated Mg2+ did not change in the second cluster from divalent ion simulations(gatekeeper structure), despite the less-compact nature of the U-turn(Supporting Figure 6). What did changewas the percent occupancy, or residence time, of the associated Mg2+, which was far lower for most residues in the second lesscompact structure (and is reported in Table 5). We hypothesize that this is a result ofimperfect clustering, and is a combination of Mg2+ ionsbinding and leaving rather than remaining bound for any length oftime. Table 5 alsoidentifies that the majority of density is localized in previouslydescribed binding sites 1 and 3.5 In thesimulations starting from MgFree + 40 mM MgCl2, Mg2+ binding in sites 1 and 3 correlates with RNA sampling theMgBound conformation, while binding in sites 2 and 4 does not (Supporting Figure 7). Supporting Table 3 details the percent occupancy of all atoms consideredpart of binding sites 1–4, and all of these sites have nonzerooccupancy in the simulations.5 Additionally,this table shows the average distance between Mg2+ ionsand their RNA hydrogen-bond acceptors is around 4.0 Å in eachcase, indicating that the Mg2+ ions associate with theRNA through interactions with first shell water molecules and do notdirectly chelate RNA phosphate oxygen atoms.


Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Bergonzo C, Hall KB, Cheatham TE - J Phys Chem B (2015)

Localization of top 10%of Mg2+ ion density (shown ingreen) in the top cluster from the divalent ion environment MD simulations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4634716&req=5

fig5: Localization of top 10%of Mg2+ ion density (shown ingreen) in the top cluster from the divalent ion environment MD simulations.
Mentions: Density-basedgrid analysis was performed on each cluster of thedivalent ion simulations to understand the different influence Mg2+ had on the more compact and less compact U-turn. The localizationof the top 10% of Mg2+ ion density is reported in Figure 5 and Table 5. Figure 5 shows a significant amount of density coordinatingthe phosphates of the UNR motif residues. The association of Mg2+ in this region explains the ability of the U-turn to preferentiallyadopt compact structures, since charged phosphate groups are shieldedfrom each other by the localized charge density of the Mg2+ ion. Interestingly, the localization of associated Mg2+ did not change in the second cluster from divalent ion simulations(gatekeeper structure), despite the less-compact nature of the U-turn(Supporting Figure 6). What did changewas the percent occupancy, or residence time, of the associated Mg2+, which was far lower for most residues in the second lesscompact structure (and is reported in Table 5). We hypothesize that this is a result ofimperfect clustering, and is a combination of Mg2+ ionsbinding and leaving rather than remaining bound for any length oftime. Table 5 alsoidentifies that the majority of density is localized in previouslydescribed binding sites 1 and 3.5 In thesimulations starting from MgFree + 40 mM MgCl2, Mg2+ binding in sites 1 and 3 correlates with RNA sampling theMgBound conformation, while binding in sites 2 and 4 does not (Supporting Figure 7). Supporting Table 3 details the percent occupancy of all atoms consideredpart of binding sites 1–4, and all of these sites have nonzerooccupancy in the simulations.5 Additionally,this table shows the average distance between Mg2+ ionsand their RNA hydrogen-bond acceptors is around 4.0 Å in eachcase, indicating that the Mg2+ ions associate with theRNA through interactions with first shell water molecules and do notdirectly chelate RNA phosphate oxygen atoms.

Bottom Line: This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV).The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR.Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

ABSTRACT
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.

No MeSH data available.