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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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Probability distributions, p(κ), of the effective curvature, κ, of the expression platform in the bound (black) and unbound (red) forms of the of the SAM-II riboswitch. Ensembles of structures of the bound state (right inset) with a curved expression platform and unbound state (left inset) with a less curved expression platform are shown as insets. The structures represent a 5 ns segment of the simulation that matches the conformations at the peaks of the distributions.
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Figure 4: Probability distributions, p(κ), of the effective curvature, κ, of the expression platform in the bound (black) and unbound (red) forms of the of the SAM-II riboswitch. Ensembles of structures of the bound state (right inset) with a curved expression platform and unbound state (left inset) with a less curved expression platform are shown as insets. The structures represent a 5 ns segment of the simulation that matches the conformations at the peaks of the distributions.

Mentions: The expression platform is a key component of bacterial mRNA structure and directs the ribosome to the proper location in order to initiate protein synthesis. The ultimate goal of conformational switching in the SAM-II riboswitch is to initiate or terminate translation due to induced conformational changes in the expression platform that expose or conceal the ribosomal recognition sequence. The AUG start codon, which is not part of the crystal structure, would normally be found downstream, immediately after the 3′-end of the riboswitch. As we have already seen above, the motions of the binding site, L1 and the expression platform are correlated. A hypothesis based on occlusion of the recognition SD sequence in repressing translation was proposed as a result of the pseudoknot structure of the SAM-II riboswitch and chemical probing experiments (10). It was assumed that stabilization of the pseudoknot structure by SAM locks the expression platform in an ensemble of conformations that prevent the bases of the recognition sequence from ultimately interacting with the ribosome. One main observation of the expression platform in the bound form (as shown in Figure 1) is that it is an integral part of the helical structure formed by the P2a/b helix, following the curvature of the helix, in the bound structure. Since the metabolite-bound form of the pseudoknot structure of SAM-II represses translation, it is obvious that this particular conformation would not allow ribosomal assembly or translation to proceed. It is therefore assumed that a different ensemble of conformations of the expression platform would serve as a proper recognition conformation or a proper conformation to initiate translation. We have therefore studied the curvature of the expression platform in the bound and unbound forms of the riboswitch, as shown in Figure 4. In order to calculate the effective curvature, we fitted the phosphorus atoms of six of the last seven phosphate groups to an effective circle.Figure 4.


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

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

Probability distributions, p(κ), of the effective curvature, κ, of the expression platform in the bound (black) and unbound (red) forms of the of the SAM-II riboswitch. Ensembles of structures of the bound state (right inset) with a curved expression platform and unbound state (left inset) with a less curved expression platform are shown as insets. The structures represent a 5 ns segment of the simulation that matches the conformations at the peaks of the distributions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Probability distributions, p(κ), of the effective curvature, κ, of the expression platform in the bound (black) and unbound (red) forms of the of the SAM-II riboswitch. Ensembles of structures of the bound state (right inset) with a curved expression platform and unbound state (left inset) with a less curved expression platform are shown as insets. The structures represent a 5 ns segment of the simulation that matches the conformations at the peaks of the distributions.
Mentions: The expression platform is a key component of bacterial mRNA structure and directs the ribosome to the proper location in order to initiate protein synthesis. The ultimate goal of conformational switching in the SAM-II riboswitch is to initiate or terminate translation due to induced conformational changes in the expression platform that expose or conceal the ribosomal recognition sequence. The AUG start codon, which is not part of the crystal structure, would normally be found downstream, immediately after the 3′-end of the riboswitch. As we have already seen above, the motions of the binding site, L1 and the expression platform are correlated. A hypothesis based on occlusion of the recognition SD sequence in repressing translation was proposed as a result of the pseudoknot structure of the SAM-II riboswitch and chemical probing experiments (10). It was assumed that stabilization of the pseudoknot structure by SAM locks the expression platform in an ensemble of conformations that prevent the bases of the recognition sequence from ultimately interacting with the ribosome. One main observation of the expression platform in the bound form (as shown in Figure 1) is that it is an integral part of the helical structure formed by the P2a/b helix, following the curvature of the helix, in the bound structure. Since the metabolite-bound form of the pseudoknot structure of SAM-II represses translation, it is obvious that this particular conformation would not allow ribosomal assembly or translation to proceed. It is therefore assumed that a different ensemble of conformations of the expression platform would serve as a proper recognition conformation or a proper conformation to initiate translation. We have therefore studied the curvature of the expression platform in the bound and unbound forms of the riboswitch, as shown in Figure 4. In order to calculate the effective curvature, we fitted the phosphorus atoms of six of the last seven phosphate groups to an effective circle.Figure 4.

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.

Show MeSH