Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington’s Disease (HD) and Spinocerebellar Ataxias (SCAs)

<div><p>In humans, neurodegenerative disorders such as Huntington’s disease (HD) and many spinocerebellar ataxias (SCAs) have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(C<b><u>A</u></b>G) repeats. Moreover, mutant huntingtin protein translated from expanded r(C<b><u>A</u></b>G) also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(C<b><u>A</u></b>G) motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD) simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different <i>syn</i> and <i>anti</i> conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(C<b><u>A</u></b>G) motif.</p></div

Energetics of Preferential Binding of Retinoic Acid-Inducible Gene‑I to Double-Stranded Viral RNAs with 5′ Tri-/Diphosphate over 5′ Monophosphate

Retinoic acid-inducible gene-I (RIG-I) is a cytosolic sensor protein that recognizes viral RNAs and triggers an innate immune response in cells. Panhandle-like base-paired blunt-ended 5′ ppp/pp-dsRNA is a characteristic feature of viral RNAs. Structural studies of RIG-I C-terminal domain bound 5′ ppp/pp-dsRNA complexes show the direct interaction between all the 5′ terminal phosphates (α, β, and γ) and protein, suggesting γ phosphate might be a major recognition determinant for RIG-I binding. Biochemical studies, however, suggest that 5′ pp-dsRNA is the minimal determinant for RIG-I binding and antiviral response. Despite biochemical and structural studies, the origin of viral RNA recognition by RIG-I is an unsolved problem. X-ray structures of RIG-I bound dsRNA not only provide atomic insight into the interaction network but also provide sufficiently good models for computational studies. We report structure-based molecular dynamics (MD) free energy calculations to quantitatively estimate the energetics of RIG-I binding to dsRNA containing 5′ ppp, 5′ pp, and 5′ p. The results suggest that RIG-I weakly discriminates between 5′ ppp-dsRNA and 5′ pp-dsRNA (favoring former) and strongly disfavors 5′ p-dsRNA with respect to the rest. Interestingly, direct interaction between γ phosphate of 5′ ppp-dsRNA and RIG-I is a robust feature of the MD simulations. dsRNA binding to RIG-I is associated with Mg²⁺ dissociation from the 5′ phosphate/s of dsRNA. The higher Mg²⁺ dissociation penalty from 5′ ppp-dsRNA with respect to 5′ pp-dsRNA offsets most of the favorable interaction between RIG-I and γ phosphate of 5′ ppp-dsRNA. This leads to weak discrimination between 5′ ppp-dsRNA and 5′ pp-dsRNA. 5′ p-dsRNA is discriminated strongly because of the loss of interaction with RIG-I

The secondary structure and refined structure of the RNA construct 5´ r(UUGGGCCAGCAGCAGGUCC)₂.

<p>A. The secondary structure of oligonucleotide r(C<u>A</u>G) repeat duplex model that allowed crystal growth. B. The global structure of the RNA including the electron density map at 1.0 σ C. The electron density map of non-canonical A-A pairs at 1.0σ. D. The backbone structure of the RNA construct.</p

Three dimensional structure of the 1x1 nucleotide AA internal loop and its closing base pairs for RNA construct 5´ r(UUGGGCCAGCAGCAGGUCC)₂.

<p>Each of the loop closing pairs has geometry consistent with that of Watson-Crick GC base pairs. The distance values (in Å) are labeled for hydrogen bonds (dashed lines); the C1´-C1´ distances (solid lines).</p

Lowest energy conformation of 5´ r(CCGCAGCGG)_2.

<p>A. The lowest energy conformation of CAG motif obtained after rMD simulation of 5´ r(CCGC<u>A</u>GCGG)_<b>2</b>. B. Ensemble of ten lowest energy structures of 5´ r(CCGC<u>A</u>GCGG)_<b>2</b> obtained after rMD simulation. C. Ensemble of ten lowest energy structures of AA pairs of 5´ r(CCGC<u>A</u>GCGG)_<b>2</b> obtained after rMD simulation.</p

Ball and stick model of nucleic acid.

<p>Ball and stick model of various types of nucleic acid helical forms, showing base inclination angle axis (solid red line); diameter of groove (dashed blue line).</p

Copper(II)-Catalyzed Benzylic C(sp³)–H Aerobic Oxidation of (Hetero)Aryl Acetimidates: Synthesis of Aryl-α-ketoesters

A straightforward method is developed in this paper for the synthesis of α-ketoesters through copper-catalyzed aerobic oxidation of (hetero)­aryl acetimidates using molecular oxygen as a sustainable oxidant. The reaction represents the first example of the direct synthesis of aryl-α-ketoesters from arylacetimidates through the aerobic oxidation of a benzylic C_(sp3)–H (CO) bond in moderate to good yield. This transformation occurs under mild reaction conditions with a wide range of substrates and utilizes a readily available oxidant and catalyst. The synthetic utility of this transformation is demonstrated through scaled-up synthesis. A plausible reaction mechanism is also proposed

Palladium-Catalyzed Regioselective C–H Alkenylation of Arylacetamides via Distal Weakly Coordinating Primary Amides as Directing Groups

Herein we disclose the efficient Pd­(II)-catalyzed and regioselective ortho C–H alkenylation of arylacetamide derivatives, viz. weakly coordinating aliphatic primary amides. This protocol utilizes ubiquitous free primary amides as the directing group and circumvents two troublesome steps of installation and removal of an external auxiliary. This strategy directly enables the incorporation of a synthetically versatile olefin in the products in moderate to good yields with regio- and distereoselectivity. The alkenylated acetamides can be easily manipulated and further transformed into a variety of useful derivatives

Co-opetition, corporate responsibility and sustainability: Why multi-dimensional constructs matter

Purpose: This study aims to set out to develop and validate a new instrument to measure the multi-dimensional nature of co-opetition in corporate responsibility and sustainability (CRS). It is anticipated that this instrument will prove useful to firms wanting to adopt measures that support relevant sustainability strategies. Design/methodology/approach: The scale development concerns three separate components, namely, item generation through expert interviews; a pilot study conducted for scale purification; and a final study for scale confirmation and validation, respectively. The final study comprises 215 firms across 11 sectors in Australia that engage in co-opetitive alliances for CRS activities. Findings: This study empirically validates the distinctiveness of three dimensions (commonality-driven, competition-driven and collaboration-driven) of co-opetition in relation to CRS resulting in a 15-item multi-dimensional scale. The three dimensions were found to be important aspects both in terms of scale validity and organisational consideration. Research limitations/implications: This study proposes a new research area regarding the proposed framework, as well as practical strategies for practitioners when considering co-opetition and their firm’s engagement in CRS activities. Originality/value: Prior studies in similar areas have mainly comprised conceptual or qualitative approaches and do not tend to focus on all three aspects of co-opetition, corporate social responsibility and sustainability