Template-Based Modeling of Protein-RNA Interactions

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes

Topological edge and corner states in Bi fractals on InSb

Topological materials hosting metallic edges characterized by integer quantized conductivity in an insulating bulk have revolutionized our understanding of transport in matter. The topological protection of these edge states is based on symmetries and dimensionality. However, only integer-dimensional models have been classified, and the interplay of topology and fractals, which may have a non-integer dimension, remained largely unexplored. Quantum fractals have recently been engineered in metamaterials, but up to present no topological states were unveiled in fractals realized in real materials. Here, we show theoretically and experimentally that topological edge and corner modes arise in fractals formed upon depositing thin layers of bismuth on an indium antimonide substrate. Scanning tunneling microscopy reveals the appearance of (nearly) zero-energy modes at the corners of Sierpi\'nski triangles, as well as the formation of outer and inner edge modes at higher energies. Unexpectedly, a robust and sharp depleted mode appears at the outer and inner edges of the samples at negative bias voltages. The experimental findings are corroborated by theoretical calculations in the framework of a continuum muffin-tin and a lattice tight-binding model. The stability of the topological features to the introduction of a Rashba spin-orbit coupling and disorder is discussed. This work opens the perspective to novel electronics in real materials at non-integer dimensions with robust and protected topological states.Comment: Main manuscript 14 pages, supplementary material 34 page

Characterizing microRNA editing and mutation sites in Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder whose pathogenesis is still unclear. MicroRNAs (miRNAs) are a kind of endogenous small non-coding RNAs that play important roles in the post-transcriptional regulation of genes. Recent researches show that miRNAs are edited in multiple ways especially in central nervous systems. A-to-I editing of RNA catalyzed by Adenosine deaminases acting on RNA (ADARs) happens intensively in brain and is also noticed in other organs and tissues. Although miRNAs are widely edited in human brain, miRNA editing in ASD is still largely unexplored. In order to reveal the editing events of miRNAs in ASD, we analyzed 131 miRNA-seq samples from 8 different brain regions of ASD patients and normal controls. We identified 834 editing sites with significant editing levels, of which 70 sites showed significantly different editing levels in the superior frontal gyrus samples of ASD patients (ASD-SFG) when compared with those of control samples. The editing level of an A-to-I editing site in hsa-mir-376a-1 (hsa-mir-376a-1_9_A_g) in ASD-SFG is higher than that of normal controls, and the difference is exaggerated in individuals under 10 years. The increased expression of ADAR1 is consistent with the increased editing level of hsa-mir-376a-1_9_A_g in ASD-SFG samples compared to normal SFG samples. Furthermore, we verify that A-to-I edited hsa-mir-376a-5p directly represses GPR85 and NAPB, which may contribute to the abnormal neuronal development of ASD patients. These results provide new insights into the mechanism of ASD

Quantum phase transition in magnetic nanographenes on a lead superconductor

Quantum spins, referred to the spin operator preserved by full SU(2) symmetry in the absence of the magnetic anistropy, have been proposed to host exotic interactions with superconductivity4. However, spin orbit coupling and crystal field splitting normally cause a significant magnetic anisotropy for d/f-shell spins on surfaces6,9, breaking SU(2) symmetry and fabricating the spins with Ising properties10. Recently, magnetic nanographenes have been proven to host intrinsic quantum magnetism due to their negligible spin orbital coupling and crystal field splitting. Here, we fabricate three atomically precise nanographenes with the same magnetic ground state of spin S=1/2 on Pb(111) through engineering sublattice imbalance in graphene honeycomb lattice. Scanning tunneling spectroscopy reveals the coexistence of magnetic bound states and Kondo screening in such hybridized system. Through engineering the magnetic exchange strength between the unpaired spin in nanographenes and cooper pairs, quantum phase transition from the singlet to the doublet state has been observed, in consistent with quantum models of spins on superconductors. Our work demonstrates delocalized graphene magnetism host highly tunable magnetic bound states with cooper pairs, which can be further developed to study the Majorana bound states and other rich quantum physics of low-dimensional quantum spins on superconductors.Comment: 13 pages, 4figure

Facile Preparation of Organic Nanoparticles by Interfacial Cross-Linking of Reverse Micelles and Template Synthesis of Subnanometer Au−Pt Nanoparticles

A single- and a double-tailed cationic surfactant with the triallylammonium headgroup formed reverse micelles (RMs) in heptane/chloroform containing a small amount of water. The reverse micelles were cross-linked at the interface upon UV irradiation in the presence of a water-soluble dithiol cross-linker and a photoinitiator. The resulting interfacially cross-linked reverse micelles (ICRMs) of the single-tailed surfactant aggregated in a solvent-dependent fashion, whereas those of the double-tailed were identical in size as the corresponding RMs. The ICRMs could extract anionic metal salts, such as AuCl4− and PtCl62−, from water into the organic phase. Au and Pt metal nanoparticles were produced upon reduction of metal salts. The covalent nature of the ICRMs made the template synthesis highly predictable, with the size of the metal particles controlled by the amount of the metal salt and the method of reduction. Nanoalloys were obtained by combining two metal precursors in the same reaction. Reduction of the ICRM-entrapped aurate also occurred without any external reducing agents, and the gold nanoparticles differed dramatically from those obtained through sodium borohydride reduction. The same template allowed the preparation of luminescent Au4, Au8, and Au13−Au23 clusters, as well as gold nanoparticles several nanometers in size, simply by using different amounts of gold precursor and reducing conditions