Quantum Chemical Studies Of Nucleic Acids Can We Construct A Bridge To The Rna Structural Biology And Bioinformatics Communities?

In this feature article we provide a side-by-side introduction for two research fields quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics Our main aim is to demonstrate that these research areas while largely separated in contemporary literature have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution

Comprehensive survey and geometric classification of base triples in RNA structures

Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. Given 12 geometric base pair families defined by the Leontis–Westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. We searched representative atomic-resolution RNA 3D structures and found instances of 68 of the 108 predicted base triple families. Model building suggests that some of the remaining 40 families may be unlikely to form for steric reasons. We developed an on-line resource that provides exemplars of all base triples observed in the structure database and models for unobserved, predicted triples, grouped by triple family, as well as by three-base combination (http://rna.bgsu.edu/Triples). The classification helps to identify recurrent triple motifs that can substitute for each other while conserving RNA 3D structure, with applications in RNA 3D structure prediction and analysis of RNA sequence evolution

The electronic structure and the nature of the chemical bond in CeO2.

The X-ray photoelectron spectral structure of CeO2 valence electrons in the binding energy range of 0 to ∼50 eV was analyzed. The core-electron spectral structure parameters and the results of relativistic discrete-variational calculations of CeO8 and Ce63O216 clusters were taken into account. Comparison of the valence and the core-electron spectral structures showed that the formation of the inner (IVMO) and the outer (OVMO) valence molecular orbitals contributes to the spectral structure more than the many-body processes. The Ce 4f electrons were established to participate directly in chemical bond formation in CeO2 losing partially their f character. They were found to be localized mostly within the outer valence band. The Ce 5p atomic orbitals were shown to participate in the formation of both the inner and the outer valence molecular orbitals (MOs). A large part in the IVMO formation is taken by the filled Ce 5p1/2, 5p3/2 and O 2s atomic shells, while the Ce 5s electrons participate weakly in the chemical bond formation. The composition and the sequent order of the molecular orbitals in the binding energy range of 0 to ∼50 eV were established. A quantitative scheme for the molecular orbitals of CeO2 was built. This scheme is fundamental for understanding the nature of chemical bonding and also for the interpretation of other X-ray spectra of CeO2. Evaluations revealed that the IVMO electrons weaken the chemical bond formed by the OVMO electrons by 37%.The work was supported by the RFBR grant № 17-03-00277a. M.V. Ryzhkov acknowledges financial support of FASO of Russia ISSC of the Ural Branch of RAS № AAAA-A16-116122810214-9. A.J. Popel acknowledges funding from the UK EPSRC (grant EP/I036400/1) and Radioactive Waste Management Ltd (formerly the Radioactive Waste Management Directorate of the UK Nuclear Decommissioning Authority, contract NPO004411A-EPS02), a maintenance grant from the Russian Foundation for Basic Research (projects 13-03-90916) and CSAR bursary

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org

Complex Random Energy Model: Zeros and Fluctuations

The partition function of the random energy model at inverse temperature $\beta$ is a sum of random exponentials $Z_N(\beta)=\sum_{k=1}^N \exp(\beta \sqrt{n} X_k)$, where $X_1,X_2,...$ are independent real standard normal random variables (= random energies), and $n=\log N$. We study the large $N$ limit of the partition function viewed as an analytic function of the complex variable $\beta$. We identify the asymptotic structure of complex zeros of the partition function confirming and extending predictions made in the theoretical physics literature. We prove limit theorems for the random partition function at complex $\beta$, both on the logarithmic scale and on the level of limiting distributions. Our results cover also the case of the sums of independent identically distributed random exponentials with any given correlations between the real and imaginary parts of the random exponent.Comment: 31 pages, 1 figur

The Spin Structure of the Nucleon

We present an overview of recent experimental and theoretical advances in our understanding of the spin structure of protons and neutrons.Comment: 84 pages, 29 figure