Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA

Roderico Acevedo, Declan Evans, Katheryn A. Penrod, Scott A. Showalter

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Protein-nucleic acid interactions are central to a variety of biological processes, many of which involve large-scale conformational changes that lead to bending of the nucleic acid helix. Here, we focus on the nonsequence-specific protein TRBP, whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stranded RNA (dsRNA). Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface. We show through isothermal titration calorimetry experiments that dsRBD2 of TRBP binds dsRNA with a temperature-independent observed binding affinity (KD ∼500 nM). Furthermore, a near-zero observed heat capacity change (ΔCp = 70 ± 40 cal·mol-1·K-1) suggests that large-scale conformational changes do not occur upon binding. This result is bolstered by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of the RNA along its helical axis. Overall, these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in the A-form geometry of dsRNA in solution. These results further support our previous hypothesis, based on extensive gel-shift assays, that TRBP preferentially binds to sites of nearly ideal A-form structure while being excluded from sites of local deformation in the RNA helical structure. The implications of this mechanism for efficient micro-RNA processing will be discussed.

Original languageEnglish (US)
Pages (from-to)2610-2617
Number of pages8
JournalBiophysical journal
Volume110
Issue number12
DOIs
StatePublished - Jun 21 2016

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Double-Stranded RNA
Nucleic Acids
RNA
Biological Phenomena
Calorimetry
Molecular Dynamics Simulation
MicroRNAs
Proteins
Hot Temperature
Gels
Double-Stranded RNA Binding Motif
Temperature

All Science Journal Classification (ASJC) codes

  • Biophysics

Cite this

Acevedo, Roderico ; Evans, Declan ; Penrod, Katheryn A. ; Showalter, Scott A. / Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA. In: Biophysical journal. 2016 ; Vol. 110, No. 12. pp. 2610-2617.
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Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA. / Acevedo, Roderico; Evans, Declan; Penrod, Katheryn A.; Showalter, Scott A.

In: Biophysical journal, Vol. 110, No. 12, 21.06.2016, p. 2610-2617.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA

AU - Acevedo, Roderico

AU - Evans, Declan

AU - Penrod, Katheryn A.

AU - Showalter, Scott A.

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