Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch

Fuks, Christin; Falkner, Sebastian; Schwierz, Nadine; Hengesbach, Martin

doi:10.3389/fmolb.2022.826505

Cited by 5 publications

(7 citation statements)

References 55 publications

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“…In particular, all base-stacking interactions between consecutive nucleotides and hydrogen-bond interactions between any bases G and C, A and U, or G and U are included ( 48 ). Therefore, the model captures non-native secondary structure interactions as shown in previous work ( 54 , 73 ) and for TERRA25 (see Supplementary Figure S3). Moreover, it has been shown that TIS reproduces experimental thermodynamic and structural data for several different RNA molecules including ribozyme formation or riboswitch folding under a variety of solvent conditions ( 52 , 54 , 73 ).…”

Section: Materials and Methodsmentioning

confidence: 90%

“…TIS, the three-interaction site model developed by Thirumalai and coworkers, is a simple low-resolution model. Its efficiency and accuracy to describe folding has been demonstrated for a variety of RNA molecules ranging in size from larger molecules such as ribozyme ( 52 ) to smaller RNAs like riboswitch ( 54 ), pseudoknot ( 50 ), and hairpin ( 49 ).…”

Section: Introductionmentioning

confidence: 99%

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RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Ugrina,

Burkhart,

Müller

et al. 2023

Nucleic Acids Research

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The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.

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Section: Materials and Methodsmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Ugrina,

Burkhart,

Müller

et al. 2023

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Therefore, the model captures non-native secondary structure interactions as shown in previous work (54,73) and for TERRA25 (see Figure S3). Moreover, it has been shown that TIS reproduces experimental thermodynamic and structural data for several different RNA molecules including ribozyme formation or riboswitch folding under a variety of solvent conditions (52,54,73). With these prerequisites, TIS is ideal to resolve intermediates states and their frequency of occurrence in the folding of rG4 systems.…”

Section: Intermediate States In Tismentioning

confidence: 87%

“…In particular, all basestacking interactions between consecutive nucleotides and hydrogen-bond interactions between any bases G and C, A and U, or G and U are included (48). Therefore, the model captures non-native secondary structure interactions as shown in previous work (54,73) and for TERRA25 (see Figure S3). Moreover, it has been shown that TIS reproduces experimental thermodynamic and structural data for several different RNA molecules including ribozyme formation or riboswitch folding under a variety of solvent conditions (52,54,73).…”

Section: Intermediate States In Tismentioning

confidence: 99%

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Ugrina

Burkhart

Mueller

et al. 2023

Preprint

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The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes. Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two transient, on-pathway intermediates. Since these intermediates are degenerate with two to four alternative conformations per state, RNA quadruplex folding is a multi-pathway process with high conformational entropy.

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“…understood despite studies probing the selectivity 54,57 of the AD to Gdm + . While no theoretical studies on the ligand binding mechanism of ykkC-I exist to date, a coarse-grained study based on the coarse-grained three-interaction site (TIS) shows that the guanidine-AD of the mini-ykkC guanidine-II aptamer exhibits a three-state model composed of (i) an open conformation, (ii) the kissing-loop conformation, and (iii) a novel Mg 2+ -dependent state 73 in the absence of guanidine. Another study, using extensive molecular dynamics (MD) simulations, showed the role of the binding pocket in discriminating between Gdm + and its close relative, urea.…”

Section: Introductionmentioning

confidence: 99%

Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms

Singh,

Reddy

2023

J. Chem. Theory Comput.

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Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm + ) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm + from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm + . We studied the binding of Gdm + to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm + binding. We show that Gdm + binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm + binding propensity, making the Gdm + binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.

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Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch

Cited by 5 publications

References 55 publications

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms

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