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Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch.

Kelley JM, Hamelberg D - Nucleic Acids Res. (2009)

Bottom Line: Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform.The rate of forming contacts in the unbound form that are similar to that in the bound form is fast.Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA.

ABSTRACT
Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches, normally located in the 5' un-translated region of their mRNAs. Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform. Here, we report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria. We show that the ensemble of conformations of the unbound form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form, and the pseudoknot structure is only fully formed upon binding the metabolite, SAM. The rate of forming contacts in the unbound form that are similar to that in the bound form is fast. Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.

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Distances between N3 of U10 and O4 of U44 (black), O4 of U11 and O4 of U21 (red) and O4 of U12 and N6 of A46 (blue) in the bound form (left column) and unbound form (right column) of the SAM-II riboswitch during the simulations. The colors are consistent with the corresponding interactions shown in Figure 1B.
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Figure 2: Distances between N3 of U10 and O4 of U44 (black), O4 of U11 and O4 of U21 (red) and O4 of U12 and N6 of A46 (blue) in the bound form (left column) and unbound form (right column) of the SAM-II riboswitch during the simulations. The colors are consistent with the corresponding interactions shown in Figure 1B.

Mentions: There are three major hydrogen bonding and electrostatic interactions between SAM and the RNA (Figure 1B) that are intricately involved in stabilizing the pseudoknot structure. The extended structure of SAM also spans three of the interactions made by L1 and the major groove of P2b, as shown in Figure 1B. We have monitored the three interactions formed by L1 and the major groove of the P2b helix in the presence and absence of SAM in order to probe the role of SAM in preserving these interactions and the integrity of the SAM-II pseudoknot structure. Two of the three interactions L1 makes with the major groove of the P2b helix that are between N3 of U10 and O4 of U44 and between O4 of U11 and O4 of U21 directly involve SAM and are well-formed in the complex (off state) throughout the simulation, as shown in Figure 2 (left column). The distance between O4 of U11 and O4 of U21 is used to monitor the second interaction, because the proximity of these two atoms is essential to the formation of the interaction site for the positively charged sulfur group in SAM. The third interaction between O4 of U12 and N6 of A46, also shown in Figure 2 (left column), is quite stable throughout the simulation with some breathing motions taking place. The third interaction does not form any hydrogen bonding interactions with SAM. SAM locks the first two interactions in place and stabilizes the pseudoknot structure. The third interaction seems to naturally follow.Figure 2.


Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch.

Kelley JM, Hamelberg D - Nucleic Acids Res. (2009)

Distances between N3 of U10 and O4 of U44 (black), O4 of U11 and O4 of U21 (red) and O4 of U12 and N6 of A46 (blue) in the bound form (left column) and unbound form (right column) of the SAM-II riboswitch during the simulations. The colors are consistent with the corresponding interactions shown in Figure 1B.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303485&req=5

Figure 2: Distances between N3 of U10 and O4 of U44 (black), O4 of U11 and O4 of U21 (red) and O4 of U12 and N6 of A46 (blue) in the bound form (left column) and unbound form (right column) of the SAM-II riboswitch during the simulations. The colors are consistent with the corresponding interactions shown in Figure 1B.
Mentions: There are three major hydrogen bonding and electrostatic interactions between SAM and the RNA (Figure 1B) that are intricately involved in stabilizing the pseudoknot structure. The extended structure of SAM also spans three of the interactions made by L1 and the major groove of P2b, as shown in Figure 1B. We have monitored the three interactions formed by L1 and the major groove of the P2b helix in the presence and absence of SAM in order to probe the role of SAM in preserving these interactions and the integrity of the SAM-II pseudoknot structure. Two of the three interactions L1 makes with the major groove of the P2b helix that are between N3 of U10 and O4 of U44 and between O4 of U11 and O4 of U21 directly involve SAM and are well-formed in the complex (off state) throughout the simulation, as shown in Figure 2 (left column). The distance between O4 of U11 and O4 of U21 is used to monitor the second interaction, because the proximity of these two atoms is essential to the formation of the interaction site for the positively charged sulfur group in SAM. The third interaction between O4 of U12 and N6 of A46, also shown in Figure 2 (left column), is quite stable throughout the simulation with some breathing motions taking place. The third interaction does not form any hydrogen bonding interactions with SAM. SAM locks the first two interactions in place and stabilizes the pseudoknot structure. The third interaction seems to naturally follow.Figure 2.

Bottom Line: Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform.The rate of forming contacts in the unbound form that are similar to that in the bound form is fast.Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA.

ABSTRACT
Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches, normally located in the 5' un-translated region of their mRNAs. Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform. Here, we report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria. We show that the ensemble of conformations of the unbound form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form, and the pseudoknot structure is only fully formed upon binding the metabolite, SAM. The rate of forming contacts in the unbound form that are similar to that in the bound form is fast. Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.

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