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1. Intrinsically disordered electronegative clusters improve stability and binding specificity of RNA-binding proteins

   Zaharias, S.; Zhang, Z.; Davis, K.; Fargason, T.; Cashman, D.; Yu, T.; Zhang, J. (July 2021, Journal of biological chemistry)

   Musier-Forsyth, Karin (Ed.)

   RNA-binding proteins play crucial roles in various cellular functions, and contain abundant disordered protein regions. The disordered regions in RNA-binding proteins are rich in repetitive sequences, such as poly-K/R, poly-N/Q, poly-A, and poly-G residues. Our bioinformatic analysis identified a largely neglected repetitive sequence family we define as electronegative clusters (ENCs) that contain acidic residues and/or phosphorylation sites. The abundance and length of ENCs exceed other known repetitive sequences. Despite their abundance, the functions of ENCs in RNA-binding proteins are still elusive. To investigate the impacts of ENCs on protein stability, RNA-binding affinity, and specificity, we selected one RNA-binding protein, the ribosomal biogenesis factor 15 (Nop15) as a model. We found that the Nop15 ENC increases protein stability and inhibits nonspecific RNA binding, but minimally interferes with specific RNA binding. To investigate the effect of ENCs on sequence specificity of RNA binding, we grafted an ENC to another RNA-binding protein, Ser/Arg-rich splicing factor 3 (SRSF3). Using RNA Bind-n-Seq, we found that the engineered ENC inhibits disparate RNA motifs differently, instead of weakening all RNA motifs to the same extent. The motif site directly involved in electrostatic interaction is more susceptible to the ENC inhibition. These results suggest that one of functions of ENCs is to regulate RNA binding via electrostatic interaction. This is consistent with our finding that ENCs are also overrepresented in DNA-binding proteins, while underrepresented in halophiles, in which nonspecific nucleic acid binding is inhibited by high concentrations of salts. 

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2. Anionic G•U pairs in bacterial ribosomal rRNAs

   https://doi.org/10.1261/rna.079583.123  

   Westhof, Eric; Watson, Zoe L; Zirbel, Craig L.; Cate, Jamie H.D. (April 2023, RNA)

   Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson-Crick pairs. Another type of G•U pair interacting via their Watson-Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G+3 in the mRNA. In such pairs the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions. 

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3. Evaluation of Thermodynamic Stabilities of in silico Designed Nucleic Acid 3WJ Motifs

   Abby Coffman, Megan Teter (March 2023, ACS SPRING 2023)

   Nucleic Acid (NA) nanotechnology is a rapidly emerging field demonstrating application of polynucleotides as a versatile biopolymer to fabricate nanostructures of various dimensions and shapes in a programmable and highly predictable way. The folding of DNA or RNA strands into a stable double helix configuration mainly relies on the Watson-Crick (Canonical) base pair composition (G=C and A-T or A-U in the case of RNA), base stacking, and metal ion concentrations. The thermodynamic parameters of DNA B-form helix formation and A-form helix of RNA can be computed using empirically defined sets of nearest neighboring parameters encompassed within the 2D structure predicting programs for example mfold, NUPAC. However, these programs are lacking parameters for a hybrid DNA/RNA base pairing and non-canonical base interactions. In this report, we focused our study to evaluate thermodynamic parameters of several in silico designed three-way junction (3WJ) DNA and hybrid DNA-RNA structural elements. The designed 3WJ motifs contain three helical stems linked with 4,3,2,1, and 0 single stranded Thymidine (T) or Uridine (U) nucleotides. We will report assembly efficiency of the 3WJs investigated by gel shift assay and thermodynamic parameters measured by UV-melting technique. Our experiments reveal that the amount of Ts and Us linkages in the three-way junction dictate the stability of the overall 3WJ conformations. This study is important as we expect it will contribute to the existing set of parameters used for NA structure prediction algorithms as well as provide a guidance for rational design of NA nanostructures. 

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4. Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition

   https://doi.org/10.1111/febs.16301  

   Roy, Sayantani; Boral, Soumendu; Maiti, Snigdha; Kushwaha, Tushar; Basak, Aditya J.; Lee, Woonghee; Basak, Amit; Gholap, Shivajirao L.; Inampudi, Krishna K.; De, Soumya (December 2021, The FEBS Journal)

   Human RNA‐binding motif 3 protein (RBM3) is a cold‐shock protein which functions in various aspects of global protein synthesis, cell proliferation and apoptosis by interacting with the components of basal translational machinery. RBM3 plays important roles in tumour progression and cancer metastasis, and also has been shown to be involved in neuroprotection and endoplasmic reticulum stress response. Here, we have solved the solution NMR structure of the N‐terminal 84 residue RNA recognition motif (RRM) of RBM3. The remaining residues are rich in RGG and YGG motifs and are disordered. The RRM domain adopts a βαββαβ topology, which is found in many RNA‐binding proteins. NMR‐monitored titration experiments and molecular dynamic simulations show that the beta‐sheet and two loops form the RNA‐binding interface. Hydrogen bond, pi–pi and pi–cation are the key interactions between the RNA and the RRM domain. NMR, size exclusion chromatography and chemical cross‐linking experiments show that RBM3 forms oligomers in solution, which is favoured by decrease in temperature, thus, potentially linking it to its function as a cold‐shock protein. Temperature‐dependent NMR studies revealed that oligomerization of the RRM domain occurs via nonspecific interactions. Overall, this study provides the detailed structural analysis of RRM domain of RBM3, its interaction with RNA and the molecular basis of its temperature‐dependent oligomerization. 

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5. Trends in trigonal prismatic Ln-[1]ferrocenophane complexes and discovery of a Ho ³⁺ single-molecule magnet

   https://doi.org/10.1039/D0SC01197E  

   Latendresse, Trevor P.; Vieru, Veacheslav; Upadhyay, Apoorva; Bhuvanesh, Nattamai S.; Chibotaru, Liviu F.; Nippe, Michael (April 2020, Chemical Science)

   Lanthanide metallocenophanes are an intriguing class of organometallic complexes that feature rare six-coordinate trigonal prismatic coordination environments of 4f elements with close intramolecular proximity to transition metal ions. Herein, we present a systematic study of the structural and magnetic properties of the ferrocenophanes, [LnFc 3 (THF) 2 Li 2 ] − , of the late trivalent lanthanide ions (Ln = Gd ( 1 ), Ho ( 2 ), Er ( 3 ), Tm ( 4 ), Yb ( 5 ), Lu ( 6 )). One major structural trend within this class of complexes is the increasing diferrocenyl (Fc 2− ) average twist angle with decreasing ionic radius ( r ion ) of the central Ln ion, resulting in the largest average Fc 2− twist angles for the Lu 3+ compound 6 . Such high sensitivity of the twist angle to changes in r ion is unique to the here presented ferrocenophane complexes and likely due to the large trigonal plane separation enforced by the ligand (>3.2 Å). This geometry also allows the non-Kramers ion Ho 3+ to exhibit slow magnetic relaxation in the absence of applied dc fields, rendering compound 2 a rare example of a Ho-based single-molecule magnet (SMM) with barriers to magnetization reversal ( U ) of 110–131 cm −1 . In contrast, compounds featuring Ln ions with prolate electron density ( 3–5 ) don't show slow magnetization dynamics under the same conditions. The observed trends in magnetic properties of 2–5 are supported by state-of-the-art ab initio calculations. Finally, the magneto-structural relationship of the trigonal prismatic Ho-[1]ferrocenophane motif was further investigated by axial ligand (THF in 2 ) exchange to yield [HoFc 3 (THF*) 2 Li 2 ] − ( 2-THF* ) and [HoFc 3 (py) 2 Li 2 ] − ( 2-py ) motifs. We find that larger average Fc 2− twist angles (in 2-THF* and 2-py as compared to in 2 ) result in faster magnetic relaxation times at a given temperature. 

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