Specificity of RSG-1.2 Peptide Binding to RRE-IIB RNA Element of HIV-1 over Rev Peptide Is Mainly Enthalpic in Origin

Kumar, Santosh; Bose, Debojit; Suryawanshi, Hemant; Sabharwal, Harshana; Mapa, Koyeli; Maiti, Souvik

doi:10.1371/journal.pone.0023300

Cited by 9 publications

(7 citation statements)

References 49 publications

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“…These Δ H values are much higher than those reported for a Zn-finger-IIB interaction (−7.2 kcal/mol at 298 K) 37 and an in vitro selected peptide, RSG1.2-IIB interaction (−13.9 kcal/mol at 298 K) 38 under similar conditions (temperature, salt, pH). This is likely due to the coupled folding and RNA-binding of the unstructured free ARM, which can contribute significantly to the observed Δ H (and also to the unfavorable T Δ S ).…”

Section: Resultscontrasting

confidence: 59%

Thermodynamics of Rev–RNA Interactions in HIV-1 Rev–RRE Assembly

et al. 2015

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The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev–ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev–IIB complex forms a stable interface, whereas the Rev–IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20–30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev–RRE assembly and disassembly, and consequently its function.

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Section: Resultscontrasting

confidence: 59%

Thermodynamics of Rev–RNA Interactions in HIV-1 Rev–RRE Assembly

et al. 2015

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“…Structural studies have shown an alpha helix at the major groove of RRE–RNA complex, and this interaction is sequence base‐specific with supplementary electrostatic contacts with phosphate backbone . The specificity of RSG‐1.2 peptide binding to RRE‐IIB RNA element of HIV‐1 surpassing REV peptide is enthalpic in origin as reported by previous studies …”

Section: Introductionsupporting

confidence: 67%

Binding and thermodynamics of REV peptide−ctDNA interaction

Upadhyay

2017

Biopolymers

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The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a T of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the T by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔC ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA.

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“…In another study, the binding of the Rev peptide to the HIV-1 RRE RNA is shown to be enthalpy driven as compared to the RSG-1.2 binding to the RRE RNA which is favored entropically. 18 The present study is the next step towards a better understanding of the energetic basis of molecular interactions between RNA and peptides. Here we explore the thermodynamic and solvent dynamic parameters of BIV TAR RNA and Tat interactions through various calorimetric and spectroscopic measurements.…”

Section: Introductionmentioning

confidence: 92%

“…There are many reports revealing the intricacies of the thermodynamic basis of complex formation of RNA and small molecules like aminoglycosides [14][15][16] and peptides. 17,18 The solution structure of BIV TAR RNA and the TAR-Tat complex is well characterized through NMR and molecular dynamics studies. 19,20 Tat binds with BIV TAR RNA in a b-hairpin loop structure in the major groove.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics and solvation dynamics of BIV TAR RNA–Tat peptide interaction

2013

Self Cite

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The interaction of the trans-activation responsive (TAR) region of bovine immunodeficiency virus (BIV) RNA with the Tat peptide is known to play important role in viral replication. Despite being thoroughly studied through a structural point of view, the nature of binding between BIV TAR RNA and the BIV Tat peptide requires information related to its thermodynamics and the nature of hydration around the TAR-Tat complex. In this context, we carried out the thermodynamic study of binding of the Tat peptide to the BIV TAR RNA hairpin through different calorimetric and spectroscopic measurements. Fluorescence titration of 2-aminopurine tagged BIV TAR RNA with the Tat peptide gives their binding affinity. The isothermal titration calorimetric experiment reveals the enthalpy of binding between BIV TAR RNA and the Tat peptide to be largely exothermic with the value of -11.7 (SEM 0.2) kcal mol(-1). Solvation dynamics measurements of BIV TAR RNA having 2-AP located at the bulge region have been carried out in the absence and presence of the BIV Tat peptide using the time correlated single photon counting technique. The solvent cage around the Tat binding site of RNA appears to be more rigid in the presence of the Tat peptide as compared to the free RNA. The displacement of solvent and ions on RNA due to peptide binding influences the entropic contributions to the total binding energy.

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Specificity of RSG-1.2 Peptide Binding to RRE-IIB RNA Element of HIV-1 over Rev Peptide Is Mainly Enthalpic in Origin

Cited by 9 publications

References 49 publications

Thermodynamics of Rev–RNA Interactions in HIV-1 Rev–RRE Assembly

Thermodynamics of Rev–RNA Interactions in HIV-1 Rev–RRE Assembly

Binding and thermodynamics of REV peptide−ctDNA interaction

Thermodynamics and solvation dynamics of BIV TAR RNA–Tat peptide interaction

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