4.7 Article

Cryo-EM advances in RNA structure determination

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 Biochemical Research Methods

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

Ellen D. Zhong et al.

Summary: cryoDRGN is an algorithm that uses the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It can uncover residual heterogeneity in high-resolution datasets and visualize large-scale continuous motions of protein complexes, while also offering interactive tools for dataset visualization and analysis.

NATURE METHODS (2021)

Article Multidisciplinary Sciences

Computed structures of core eukaryotic protein complexes

Ian R. Humphreys et al.

Summary: By utilizing proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling, we systematically identified and built accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. These models cover nearly 800 previously uncharacterized assemblies, providing comprehensive insights into key processes in eukaryotic cells.

SCIENCE (2021)

Article Multidisciplinary Sciences

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure

Steve L. Bonilla et al.

Summary: Viruses utilize multifunctional structured RNAs to manipulate host biochemistry, and cryo-EM has revealed the structure of viral transfer RNA-like structures and their interactions with enzymes, demonstrating the noncanonical interactions used by viruses to bind host machinery.

SCIENCE (2021)

Review Biochemistry & Molecular Biology

Reprint of Amorphous nickel titanium alloy film: A new choice for cryo electron microscopy sample preparation

Xiaojun Huang et al.

Summary: Cryo-electron microscopy (cryoEM) has become a key method in structural biology. This study introduced a new supporting substrate, the amorphous nickel-titanium alloy (ANTA) film, for cryoEM sample preparation, which showed advantages in electron conductivity and interaction with proteins compared to conventional carbon film, leading to improved particle distribution and reconstruction resolution in experiments.

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2021)

Article Multidisciplinary Sciences

Structural analyses of an RNA stability element interacting with poly(A)

Seyed-Fakhreddin Torabi et al.

Summary: Cis-acting RNA elements, such as the element for nuclear expression (ENE), play a crucial role in stabilizing polyadenylated RNA. Structural studies have identified evolutionarily diverse ENE-like elements, including a subclass known as double ENEs (dENEs). Investigation of a dENE derived from a rice transposable element revealed insights into the directionality and structural changes upon poly(A) binding.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

Ali Punjani et al.

Summary: 3DVA is an algorithm that fits a linear subspace model of conformational change to high-resolution cryo-EM data, enabling the resolution and visualization of detailed molecular motions of proteins. It has been shown to successfully resolve multiple flexible motions in various protein complexes, providing new biological insights from single particle cryo-EM data.

JOURNAL OF STRUCTURAL BIOLOGY (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

Article Multidisciplinary Sciences

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Zhaoming Su et al.

Summary: This study presents cryo-EM structures of the Tetrahymena ribozyme in substrate-free and bound states, revealing new peripheral helical structures and kissing loop pseudoknots. The global architecture is nearly identical, with significant conformational changes and localized shifts in the internal guide sequence and guanosine binding site upon RNA substrate binding. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for cryo-EM-based study of structure-function relationships in ribozymes.

NATURE (2021)

Article Biochemistry & Molecular Biology

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

Kaiming Zhang et al.

Summary: A 6.9 angstrom resolution cryo-EM structure of the SARS-CoV-2 frameshift stimulation element (FSE) was successfully demonstrated in this study, guiding the development of antisense oligonucleotides that impair virus replication. The FSE, crucial for balanced expression of viral proteins, is becoming a key target for drug discovery campaigns against COVID-19.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Multidisciplinary Sciences

Geometric deep learning of RNA structure

Raphael J. L. Townshend et al.

Summary: The study introduces a machine learning approach that can accurately identify RNA structures without assumptions about their defining characteristics, trained with only a small amount of known data. This approach outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction challenges.

SCIENCE (2021)

Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

Review Biology

Imaging and visualizing SARS-CoV-2 in a new era for structural biology

Kendra E. Leigh et al.

Summary: The global impact of the SARS-CoV-2 pandemic has highlighted the importance of scientific research, which has been facilitated by advancements in various scientific fields. Technological improvements in cryo-electron microscopy have allowed for a quicker and more detailed visualization of the virus, aiding in the accelerated development of vaccines and therapeutics.

INTERFACE FOCUS (2021)

Article Biochemical Research Methods

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

Kalli Kappel et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Single-particle cryo-EM at atomic resolution

Takanori Nakane et al.

NATURE (2020)

Article Multidisciplinary Sciences

Atomic-resolution protein structure determination by cryo-EM

Ka Man Yip et al.

NATURE (2020)

Article Multidisciplinary Sciences

Cryo-EM with sub-1 Å specimen movement

Katerina Naydenova et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Topaz-Denoise: general deep denoising models for cryoEM and cryoET

Tristan Bepler et al.

NATURE COMMUNICATIONS (2020)

Letter Cell Biology

Resolving individual atoms of protein complex by cryo-electron microscopy

Kaiming Zhang et al.

CELL RESEARCH (2020)

Review Biophysics

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?

Robert M. Glaeser

ANNUAL REVIEW OF BIOPHYSICS, VOL 48 (2019)

Review Biochemistry & Molecular Biology

Challenges and opportunities in cryo-EM single-particle analysis

Dmitry Lyumkis

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

Article Biochemical Research Methods

The cryo-EM method microcrystal electron diffraction (MicroED)

Brent L. Nannenga et al.

NATURE METHODS (2019)

Review Biochemistry & Molecular Biology

Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions

Radostin Danev et al.

TRENDS IN BIOCHEMICAL SCIENCES (2019)

Article Biochemistry & Molecular Biology

Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA

Daniel B. Haack et al.

Article Multidisciplinary Sciences

Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution

Xiao Fan et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Shuang Li et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Review Biochemistry & Molecular Biology

Computational modeling of RNA 3D structure based on experimental data

Almudena Ponce-Salvatierra et al.

BIOSCIENCE REPORTS (2019)

Article Multidisciplinary Sciences

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

Kaiming Zhang et al.

NATURE COMMUNICATIONS (2019)

Review Anatomy & Morphology

Advances in cryo-electron tomography for biology and medicine

Roman I. Koning et al.

ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER (2018)

Review Chemistry, Physical

Proteins, interfaces, and cryo-EM grids

Robert M. Glaeser

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2018)

Article Biochemistry & Molecular Biology

High resolution single particle cryo-electron microscopy using beam-image shift

Anchi Cheng et al.

JOURNAL OF STRUCTURAL BIOLOGY (2018)

Article Biochemical Research Methods

Reducing effects of particle adsorption to the air-water interface in cryo-EM

Alex J. Noble et al.

NATURE METHODS (2018)

Article Multidisciplinary Sciences

Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant

Yong Zi Tan et al.

NATURE COMMUNICATIONS (2018)

Article Biochemical Research Methods

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

Kalli Kappel et al.

NATURE METHODS (2018)

Editorial Material Biochemical Research Methods

Cryo-electron tomography

Allison Doerr

NATURE METHODS (2017)

Review Biochemistry & Molecular Biology

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

Sebastian M. Fica et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Multidisciplinary Sciences

RNA structure inference through chemical mapping after accidental or intentional mutations

Clarence Y. Cheng et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Biochemistry & Molecular Biology

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

Sebastian M. Fica et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes

Ottilie von Loeffelholz et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)

Review Microscopy

Automated data collection in single particle electron microscopy

Yong Zi Tan et al.

MICROSCOPY (2016)

Article Biochemistry & Molecular Biology

Progress towards an optimal specimen support for electron cryomicroscopy

Christopher J. Russo et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Denoising and covariance estimation of single particle cryo-EM images

Tejal Bhamre et al.

JOURNAL OF STRUCTURAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Structure of a group II intron in complex with its reverse transcriptase

Guosheng Qu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Structure of a group II intron in complex with its reverse transcriptase

Guosheng Qu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

The structural biology of CRISPR-Cas systems

Fuguo Jiang et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Review Biochemistry & Molecular Biology

The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones

Thomas R. Cech et al.

Article Biochemistry & Molecular Biology

New molecular engineering approaches for crystallographic studies of large RNAs

Jinwei Zhang et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Article Multidisciplinary Sciences

Volta potential phase plate for in-focus phase contrast transmission electron microscopy

Radostin Danev et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Ultrastable gold substrates for electron cryomicroscopy

Christopher J. Russo et al.

SCIENCE (2014)

Editorial Material Multidisciplinary Sciences

The Resolution Revolution

Werner Kuehlbrandt

SCIENCE (2014)

Article Biochemistry & Molecular Biology

The molecular recognition of kink-turn structure by the L7Ae class of proteins

Lin Huang et al.

Article Biochemistry & Molecular Biology

Structural Determinants for Geometry and Information Decoding of tRNA by T Box Leader RNA

Jason C. Grigg et al.

STRUCTURE (2013)

Article Biochemistry & Molecular Biology

Spotiton: A prototype for an integrated inkjet dispense and vitrification system for cryo-TEM

Tilak Jain et al.

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Article Multidisciplinary Sciences

Landscape of transcription in human cells

Sarah Djebali et al.

NATURE (2012)

Article Cell Biology

The RNA Worlds in Context

Thomas R. Cech

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy

Richard Henderson et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Cell Biology

Group II Introns: Mobile Ribozymes that Invade DNA

Alan M. Lambowitz et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Electronic detectors for electron microscopy

A. R. Faruqi et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

Zasha Weinberg et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy

PB Rosenthal et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)