4.7 Article

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p

Joshua A. Imperatore et al.

Summary: The study reveals the conservation and functional importance of the s2m element in the genome of SARS-CoV-2 and other coronaviruses. The s2m element is involved in the dimerization of the viral genome and interacts with host cellular microRNA. These findings suggest that the s2m element could be a potential therapeutic target for COVID-19 and other coronavirus-related diseases.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion

Setu M. Vora et al.

Summary: A study has found that SARS-CoV-2 utilizes its nonstructural protein 1 (Nsp1) to suppress host protein synthesis, but targeting the SL1 region of the SARS-CoV-2 5' untranslated region (5' UTR) can evade Nsp1-mediated translational suppression and hinder viral replication. The findings provide a conservative therapeutic target for COVID-19.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

Francisco Carrascoza et al.

Summary: This paper analyzes the stereochemical quality of predicted RNA three-dimensional models and aims to improve RNA 3D structure modeling approaches by reducing deviations from standard bond lengths and angles, planarity, or chirality.
Article Biochemical Research Methods

Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex

Shun L. Sakuraba et al.

Summary: Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) blocks translation of host mRNAs in infected cells. This study utilized molecular dynamics simulation to investigate the mechanism of viral RNA evasion. Results suggested that the stem loop structure of the viral RNA binds to multiple regions of nsp1, allowing the virus to evade host translation shutoff.

PLOS COMPUTATIONAL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow

Marcin Magnus

Summary: Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods in recent years. However, many tools are still exclusive to a few bioinformatic groups. To make the advancements in RNA structural biology accessible to the broader community of biologists, we developed the rna-tools.online web server, which provides a user-friendly platform for various RNA 3D structure analyses and manipulations.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Kamil Luwanski et al.

Summary: Advancements in experimental and computational techniques have allowed for the exploration of large and complex RNA 3D structures, leading to the discovery of previously unstudied properties and motifs. RNAspider is a web server that automatically identifies, classifies, and visualizes entanglements in RNA tertiary structures.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

Tammy C. T. Lan et al.

Summary: Lan et al. report on the RNA structure ensembles of the entire SARSCoV-2 genome in infected human cells. They identify alternative RNA conformations that play a critical role in promoting high frameshifting rates. These findings provide valuable insights into the biology of coronavirus RNA and can guide the development of RNA-based therapeutics for SARS-CoV-2.

NATURE COMMUNICATIONS (2022)

Review Biochemistry & Molecular Biology

Deep Learning in RNA Structure Studies

Haopeng Yu et al.

Summary: The article discusses the successful applications of deep learning in solving RNA structure problems, including RNA structure prediction, non-canonical G-quadruplex, RNA-protein interactions, and RNA switches. It also provides a general guide to using deep learning for solving RNA structure problems.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Article Biochemical Research Methods

RNAloops: a database of RNA multiloops

Jakub Wiedemann et al.

Summary: Studying the 3D structure of RNA is crucial for understanding its functions and developing therapeutic solutions. However, computational modeling of multi-branched loops has been a weak point in structural bioinformatics. The RNAloops database collects and analyzes these loops, providing search, analysis, and data statistics functionalities.

BIOINFORMATICS (2022)

Article Biochemistry & Molecular Biology

Secondary structure of the SARS-CoV-2 5'-UTR

Zhichao Miao et al.

Summary: The 5'UTR of SARS-CoV-2 contains stable structures, including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants' 5'UTRs revealed a highly conserved structure with few co-variations, confirming the secondary structure model based on probing experiments.

RNA BIOLOGY (2021)

Article Biochemistry & Molecular Biology

RNA sequence and ligand binding alter conformational pro fi le of SARS-CoV-2 stem loop II motif

Ali H. Aldhumani et al.

Summary: This study investigates the stem-loop II motif of SARS-CoV-2 as a potential drug target, highlighting the significant conformational differences caused by nucleotide transversion and ligand binding. The findings provide insights for future drug discovery efforts in targeting noncoding RNA elements.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

Nicholas C. Huston et al.

Summary: This study utilized a novel approach to determine the secondary structure of the SARS-CoV-2 RNA genome, revealing well-folded RNA structures in infected cells. The research also identified unique aspects of the SARS-CoV-2 genome architecture and conserved features across beta-coronaviruses. The presented native, secondary structure of SARS-CoV-2 serves as a roadmap for focused studies on the viral life cycle, primer design, and identification of RNA drug targets against COVID-19.

MOLECULAR CELL (2021)

Article Biochemistry & Molecular Biology

The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation

Antonin Tidu et al.

Summary: This study reveals how SARS-CoV-2 coronavirus evades NSP1 inhibition through the SL1 RNA hairpin, promoting viral translation and necessary for translation of subgenomic RNAs in the late phase of infection. Therapeutic strategies targeting SL1 may affect viral translation at both early and late stages of infection, making SL1 a potential Achilles heel of the virus.
Article Biochemical Research Methods

Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

Sara Ibrahim Omar et al.

Summary: The coronavirus responsible for COVID-19 controls viral protein production through a unique RNA pseudoknot structure, which may be a potential target for treating the disease. Computational modeling revealed multiple possible conformations of the SARS-CoV-2 pseudoknot, providing insight for future experiments and drug discovery efforts. The study also identified unusual structures involving RNA threading through helical junctions, which could aid in understanding and developing treatments for SARS-CoV-2.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs

Lei Sun et al.

Summary: Research on the structure and interactions of SARS-CoV-2 RNA with host proteins has identified potential therapeutic targets and strategies for reducing viral infection, shedding light on new avenues for COVID-19 treatment.
Article Biochemistry & Molecular Biology

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

Ramya Rangan et al.

Summary: This study provides 3D models of SARS-CoV-2 RNA regions based on chemical mapping data and Rosetta's algorithm to develop small molecule antivirals. Modeling convergence supports high accuracy of predicted low energy states, with subsequent experimental validation. Additionally, models of RNA riboswitches are provided, offering new directions for discovering RNA binders.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

Martina Zafferani et al.

Summary: The urgent need to develop novel antivirals has led to the study of small-molecule chemical probes, with a report on amiloride-based small molecules that inhibit viral replication by targeting structured elements within the viral RNA. This represents a potential new avenue for developing specific antivirals targeting the RNA of coronaviruses.

SCIENCE ADVANCES (2021)

Article Chemistry, Multidisciplinary

Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

Sandro Bottaro et al.

Summary: This study predicted the structure and dynamics of RNA stem loops in the 5'UTR of the SARS-CoV-2 genome using extensive molecular dynamics simulations, revealing rich dynamics and specific structural rearrangements. These findings could provide insights into the structural features and functional roles of RNA molecules.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Biochemistry & Molecular Biology

Entanglements of structure elements revealed in RNA 3D models

Mariusz Popenda et al.

Summary: Computational methods for predicting RNA 3D structure are increasingly important in molecular biology and medicine. The RNA-Puzzles initiative evaluates and shares computationally built RNAs, allowing for better understanding of strengths and weaknesses in prediction methods. This study focuses on the issue of entangled RNA fragments in predicted 3D models, proposing a classification system for different types of entanglements.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

The architecture of the SARS-CoV-2 RNA genome inside virion

Changchang Cao et al.

Summary: Researchers have used vRIC-seq technology to reveal the tertiary structure of the SARS-CoV-2 genome in virions, finding an unentangled globule conformation. They also discovered the role of long-range duplexes and higher-order junctions in the sequential packaging of the viral genome, with some mutations potentially contributing to more stable duplex structures.

NATURE COMMUNICATIONS (2021)

Article Genetics & Heredity

A map of the SARS-CoV-2 RNA structurome

Ryan J. Andrews et al.

Summary: The study utilized the bioinformatics approach ScanFold to analyze the RNA structure of SARS-CoV-2, revealing its enrichment in stable and ordered structures, providing a potential resource for RNA drug targets. Enhanced results were obtained through the re-analysis of publicly available datasets, and ScanFold was updated for comparisons with other RNA modeling methods.

NAR GENOMICS AND BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Entanglements of structure elements revealed in RNA 3D models

Mariusz Popenda et al.

Summary: Computational methods for predicting RNA 3D structures have practical applications in molecular biology and medicine, highlighting the need to improve accuracy. The RNA-Puzzles initiative plays a significant role in collecting and evaluating computationally built RNAs, allowing for the analysis of prediction methods. This study focuses on entangled RNA fragments in predicted structures, proposing a classification based on topology and components.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Zhichao Miao et al.

Review Genetics & Heredity

Advances in RNA 3D Structure Modeling Using Experimental Data

Bing Li et al.

FRONTIERS IN GENETICS (2020)

Article Biochemistry & Molecular Biology

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

Omer Ziv et al.

MOLECULAR CELL (2020)

Article Biochemistry & Molecular Biology

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

Christiane Iserman et al.

MOLECULAR CELL (2020)

Article Virology

The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

Junxing Zhao et al.

VIRUSES-BASEL (2020)

Article Biochemistry & Molecular Biology

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

Ilaria Manfredonia et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Anna Wacker et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Cell Biology

New Insights into Ribosome Structure and Function

Amy Jobe et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2019)

Review Virology

Coronavirus genomic RNA packaging

Paul S. Masters

VIROLOGY (2019)

Review Biochemistry & Molecular Biology

Computational modeling of RNA 3D structure based on experimental data

Almudena Ponce-Salvatierra et al.

BIOSCIENCE REPORTS (2019)

Article Biochemical Research Methods

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

Maciej Antczak et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

LCS-TA to identify similar fragments in RNA 3D structures

Jakub Wiedemann et al.

BMC BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

Michal J. Boniecki et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Computational modeling of RNA 3D structures and interactions

Wayne K. Dawson et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Review Multidisciplinary Sciences

Principal component analysis: a review and recent developments

Ian T. Jolliffe et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2016)

Article Biochemical Research Methods

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

Agnieszka Rybarczyk et al.

BMC BIOINFORMATICS (2015)

Article Biochemical Research Methods

Rclick: a web server for comparison of RNA 3D structures

Minh N. Nguyen et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

RNApdbee-a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

Maciej Antczak et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

RNAlyzer-novel approach for quality analysis of RNA structural models

Piotr Lukasiak et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Automated 3D structure composition for large RNAs

Mariusz Popenda et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Improved prediction of RNA tertiary structure with insights into native state dynamics

John Paul Bida et al.

Article Genetics & Heredity

Evolutionary conservation and functional roles of ncRNA

Zhipeng Qu et al.

Frontiers in Genetics (2012)

Article Biochemical Research Methods

ViennaRNA Package 2.0

Ronny Lorenz et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold

Chul Won Lee et al.

FEBS LETTERS (2011)

Article Biochemistry & Molecular Biology

On the significance of an RNA tertiary structure prediction

Christine E. Hajdin et al.

Article Biochemistry & Molecular Biology

Analysis of Four-Way Junctions in RNA Structures

Christian Laing et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Structural lability in stem-loop 1 drives a 5′ UTR 3′ UTR interaction in coronavirus replication

Lichun Li et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Biochemistry & Molecular Biology

The structure of a rigorously conserved RNA element within the SARS virus genome

MP Robertson et al.

PLOS BIOLOGY (2005)

Article Biochemical Research Methods

A comprehensive comparison of comparative RNA structure prediction approaches

PP Gardner et al.

BMC BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)