The dynamic nature of the four-way junction of the hepatitis C virus IRES

Melcher, Sonya E.; Wilson, Timothy J.; Lilley, David M.J.

doi:10.1261/rna.5130703

Cited by 33 publications

(35 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We have recently made a study of the 2HS 1 2HS 2 four-way junction (helixhelix -(extra unpaired base) -helix-helix -(two extra unpaired bases)) 9 of the hepatitis C virus IRES element. 26 Time-resolved FRET experiments indicate that this junction has approximately equal populations of parallel and antiparallel forms in the presence of divalent metal ions. This junction has been crystallised in an almost side-by-side parallel conformation, 27 suggesting that the crystallisation process has drawn the equilibrium into the parallel form.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Conformational Flexibility of Four-way Junctions in RNA

Hohng

Wilson

Tan

et al. 2004

Journal of Molecular Biology

View full text Add to dashboard Cite

Helical junctions are common architectural features in RNA. They are particularly important in autonomously folding molecules, as exemplified by the hairpin ribozyme. We have used single-molecule fluorescence spectroscopy to study the dynamic properties of the perfect (4H) four-way helical junction derived from the hairpin ribozyme. In the presence of Mg 2þ , the junction samples parallel and antiparallel conformations and both stacking conformers, with a bias towards one antiparallel stacking conformer. There is continual interconversion between the forms, such that there are several transitions per second under physiological conditions. Our data suggest that interconversion proceeds via an open intermediate with reduced cation binding in which coaxial stacking between helices is disrupted. The rate of interconversion becomes slower at higher Mg 2þ concentrations, yet the activation barrier decreases under these conditions, indicating that entropic effects are important. Transitions also occur in the presence of Na þ only; however, the coaxial stacking appears incomplete under these conditions. The polymorphic and dynamic character of the four-way RNA junction provides a source of structural diversity, from which particular conformations required for biological function might be stabilised by additional RNA interactions or protein binding.

show abstract

Section: Discussionmentioning

confidence: 99%

“…(b) An antiparallel 4H junction that exists in the RNaseP RNA. 26 (c) A parallel 2HS 1 2HS 2 junction formed by helices 94 to 97 of the 23 S rRNA in the 50 S ribosomal subunit. 30 The formally unpaired bases are coloured grey in this representation.…”

Section: Discussionmentioning

confidence: 99%

Conformational Flexibility of Four-way Junctions in RNA

Hohng

Wilson

Tan

et al. 2004

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…The HCV IRES contains two regions of tertiary fold corresponding to the four-way junction III abc and the pseudo-knot III ef /IV. Previous data suggested that the isolated four-way junction exists in a dynamic equilibrium between different conformations 38 , but ESMD simulations showed that the four-way junction is stabilized in the context of the entire domain III and that these folded elements are not major sources of flexibility in the entire IRES molecule (Supplementary Note 2, Supplementary Figs S4, S5 and S6).…”

Section: Saxs Experimentsmentioning

confidence: 98%

Structure of the full-length HCV IRES in solution

et al. 2013

View full text Add to dashboard Cite

The 5 0 -untranslated region of the hepatitis C virus genome contains an internal ribosome entry site (IRES) that initiates cap-independent translation of the viral RNA. Until now, the structural characterization of the entire (IRES) remained limited to cryo-electron microscopy reconstructions of the (IRES) bound to different cellular partners. Here we report an atomic model of free full-length hepatitis C virus (IRES) refined by selection against small-angle X-ray scattering data that incorporates the known structures of different fragments. We found that an ensemble of conformers reproduces small-angle X-ray scattering data better than a single structure suggesting in combination with molecular dynamics simulations that the hepatitis C virus (IRES) is an articulated molecule made of rigid parts that move relative to each other. Principal component analysis on an ensemble of physically accessible conformers of hepatitis C virus (IRES) revealed dominant collective motions in the molecule, which may underlie the conformational changes occurring in the (IRES) molecule upon formation of the initiation complex.

show abstract

“…We have previously studied the structure and dynamic properties of the 2HS 2 2HS 1 four-way junction. The structure of a related construct was solved by X-ray crystallography (Kieft et al 2002), but we found that this junction was either a stacked cross with axes perpendicular or a dynamic structure oscillating between parallel and anti-parallel stacked structures (Melcher et al 2003). Interestingly, an anti-parallel conformation was suggested by a single-particle cryo-electron microscopy (cryo-EM) study (Boehringer et al 2005), whereas a parallel conformation was found in the crystal structure (Kieft et al 2002).…”

Section: Introductionmentioning

confidence: 95%

Structure of the three-way helical junction of the hepatitis C virus IRES element

Ouellet¹,

Melcher²,

Iqbal³

et al. 2010

RNA

Self Cite

View full text Add to dashboard Cite

The hepatitis C virus internal ribosome entry site (IRES) element contains a three-way junction that is important in the overall RNA conformation, and for its role in the internal initiation of translation. The junction also illustrates some important conformational principles in the folding of three-way helical junctions. It is formally a 3HS 4 junction, with the possibility of two alternative stacking conformers. However, in principle, the junction can also undergo two steps of branch migration that would form 2HS 1 HS 3 and 2HS 2 HS 2 junctions. Comparative gel electrophoresis and ensemble fluorescence resonance energy transfer (FRET) studies show that the junction is induced to fold by the presence of Mg 2+ ions in low micromolar concentrations, and suggest that the structure adopted is based on coaxial stacking of the two helices that do not terminate in a hairpin loop (i.e., helix IIId). Single-molecule FRET studies confirm this conclusion, and indicate that there is no minor conformer present based on an alternative choice of helical stacking partners. Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold.

show abstract

The dynamic nature of the four-way junction of the hepatitis C virus IRES

Cited by 33 publications

References 39 publications

Conformational Flexibility of Four-way Junctions in RNA

Conformational Flexibility of Four-way Junctions in RNA

Structure of the full-length HCV IRES in solution

Structure of the three-way helical junction of the hepatitis C virus IRES element

Contact Info

Product

Resources

About