Research Highlight |
Featured
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Article
| Open Access
Electrospray-assisted cryo-EM sample preparation to mitigate interfacial effects
ESI-cryoPrep is a cryo-EM specimen preparation method that employs electrospray ionization techniques to deposit charged macromolecule-containing droplets on EM grids. Demonstrated across various protein samples, this approach effectively prevents biomolecule adsorption at air–water or graphene–water interfaces, addressing challenges related to protein denaturation and preferred orientation.
- Zi Yang
- , Jingjin Fan
- & Xiaoyu Zhou
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Brief Communication |
Square condenser apertures for square cameras in low-dose transmission electron microscopy
Square and rectangular beams made with new condenser apertures enable more efficient image capture in low-dose transmission electron microscopy with no compromise to image quality in single-particle cryoelectron microscopy.
- Hamish G. Brown
- , Dan Smith
- & Eric Hanssen
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Article |
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN
TomoDRGN is a deep learning framework designed to model conformational and compositional heterogeneity from cryo-ET datasets on a per-particle basis.
- Barrett M. Powell
- & Joseph H. Davis
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Brief Communication
| Open Access
Square beams for optimal tiling in transmission electron microscopy
A square electron beam improves imaging of large fields of view in transmission electron microscopes by facilitating montage tomography of vitrified specimens with no loss in data quality relative to conventional round beams.
- Eugene Y. D. Chua
- , Lambertus M. Alink
- & Alex de Marco
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This Month |
If at first you don’t succeed
Scientists have successes to celebrate but must also cope with the sting of failures. In the way she handles both, Nobel laureate Katalin Karikó inspires others.
- Vivien Marx
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Article
| Open Access
Serial Lift-Out: sampling the molecular anatomy of whole organisms
Serial Lift-Out creates a series of lamellae from one lift-out volume for cryo-ET, increasing the ease and throughput of cryo-lift-out and enabling the study of molecular anatomy in multicellular systems including C. elegans larvae.
- Oda Helene Schiøtz
- , Christoph J. O. Kaiser
- & Jürgen M. Plitzko
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Method to Watch |
Visual proteomics
Advances will enable proteome-scale structure determination in cells.
- Rita Strack
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Article
| Open Access
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination
An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of predicted structures do not agree with experimentally resolved data. Therefore, care must be taken when using these predictions for informing structural hypotheses.
- Thomas C. Terwilliger
- , Dorothee Liebschner
- & Paul D. Adams
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Brief Communication |
Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models
This manuscript describes a refinement protocol that extends the e2gmm method to optimize both the orientation and conformation estimation of particles to improve the alignment for flexible domains of proteins.
- Muyuan Chen
- , Michael F. Schmid
- & Wah Chiu
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Article
| Open Access
Genetically encoded multimeric tags for subcellular protein localization in cryo-EM
Genetically encoded multimeric particles (GEMs) are 25-nm tags with recognizable structural signatures, which can be used to label specific proteins in mammalian cells to facilitate their subcellular localization in cryo-ET.
- Herman K. H. Fung
- , Yuki Hayashi
- & Julia Mahamid
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Article
| Open Access
OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis
OPUS-DSD is a neural network-based algorithm that reconstructs distinct conformations or continuous dynamics of the macromolecular structural landscape, starting from single-particle cryo-EM data.
- Zhenwei Luo
- , Fengyun Ni
- & Jianpeng Ma
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Article |
CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning
Few methods for three-dimensional structure modeling of nucleic acids from cryo-EM data exist. CryoREAD, a fully automated DNA/RNA atomic structure modeling method based on deep learning, was developed to fill this gap.
- Xiao Wang
- , Genki Terashi
- & Daisuke Kihara
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Research Briefing |
Capturing detailed cellular landscapes by montage cryo-electron tomography
To capture expansive, seamless fields of view from frozen hydrated specimens by cryo-electron tomography, we developed methods for the collection and processing of montage data. This approach enables rapid acquisition of contiguous regions of specimens using a montaged tilt series collection scheme.
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Article |
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting
This article describes a time-resolved cryo-plunger that combines a droplet-based microfluidic mixer with a laser-induced generator of microjets that allows rapid reaction initiation and plunge-freezing of cryo-EM grids. A time resolution of 5 ms was achieved using this approach.
- Stefania Torino
- , Mugdha Dhurandhar
- & Rouslan G. Efremov
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Perspective |
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions
This Perspective introduces the Minimum Information About Disorder Experiments guidelines, which provide a community consensus on the minimum information required to appropriately describe metadata on experimentally and computationally derived structural state(s) of intrinsically disordered proteins or regions.
- Bálint Mészáros
- , András Hatos
- & Norman E. Davey
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Brief Communication |
New measures of anisotropy of cryo-EM maps
This paper proposes two new anisotropy metrics—the Fourier shell occupancy and the Bingham test—that can be used to understand the quality of cryogenic electron microscopy maps.
- Jose-Luis Vilas
- & Hemant D. Tagare
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Article
| Open Access
TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining
TomoTwin is a deep metric learning-based particle picking method for cryo-electron tomograms. TomoTwin obviates the need for annotating training data and retraining a picking model for each protein.
- Gavin Rice
- , Thorsten Wagner
- & Stefan Raunser
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Research Briefing |
Mapping the motion and structure of flexible proteins from cryo-EM data
A deep learning algorithm maps out the continuous conformational changes of flexible protein molecules from single-particle cryo-electron microscopy images, allowing the visualization of the conformational landscape of a protein with improved resolution of its moving parts.
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Article
| Open Access
3DFlex: determining structure and motion of flexible proteins from cryo-EM
3D Flexible Refinement (3DFlex) is a generative neural network model for continuous molecular heterogeneity for cryo-EM data that can be used to determine the structure and motion of flexible biomolecules. It enables visualization of nonrigid motion and improves 3D structure resolution by aggregating information from particle images spanning the conformational landscape of the target molecule.
- Ali Punjani
- & David J. Fleet
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Correspondence |
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps
- Tsukasa Nakamura
- , Xiao Wang
- & Daisuke Kihara
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Analysis
| Open Access
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
An international blind study confirms that smFRET measurements on dynamic proteins are highly reproducible across instruments, analysis procedures and timescales, further highlighting the promise of smFRET for dynamic structural biology.
- Ganesh Agam
- , Christian Gebhardt
- & Thorben Cordes
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Review Article |
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology
This Review describes advances in cryogenic electron tomography on focused ion beam lamellae, highlighting the key benefits of this technology for in situ structural biology and discussing important future directions.
- Casper Berger
- , Navya Premaraj
- & Peter J. Peters
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Editorial |
AlphaFold and beyond
A great deal has happened in the protein structure prediction field since Nature Methods selected this topic as our Method of the Year 2021. Here’s a quick, non-comprehensive update.
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News & Views |
Seeing the wood for the trees
A deep learning approach called DeepPiCt facilitates segmentation and macromolecular identification in the cellular jungle of electron cryotomography data.
- Olivia E. R. Smith
- & Tanmay A. M. Bharat
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Article
| Open Access
Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation
Cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) integrates three-dimensional confocal microscopy with focused ion beam–scanning electron microscopy for efficient preparation of lamellae containing target structures for in situ structural biology with cryo-electron tomography.
- Weixing Li
- , Jing Lu
- & Wei Ji
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Article
| Open Access
ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study
The ELI-TriScope advances cryo-CLEM by focusing light, electron and ion beams on cryopreserved samples for markedly improved preparation of cryo-lamellae containing target structures.
- Shuoguo Li
- , Ziyan Wang
- & Fei Sun
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Comment |
Protein structure prediction has reached the single-structure frontier
Dramatic advances in protein structure prediction have sparked debate as to whether the problem of predicting structure from sequence is solved or not. Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a single structure, instead of a structural distribution, and that this realization is crucial for the next generation of structure prediction algorithms.
- Thomas J. Lane
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Method to Watch |
Fluorescence in structural biology
Advances in fluorescence microscopy and spectroscopy show their promise for applications that complement in situ structural biology methods like cryoelectron tomography.
- Rita Strack
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Article
| Open Access
Uniform thin ice on ultraflat graphene for high-resolution cryo-EM
This paper shows that the uniformity of vitreous ice thickness relies on the surface flatness of the supporting film, and presents a method to use ultraflat graphene as the support for cryo-EM specimen preparation.
- Liming Zheng
- , Nan Liu
- & Hailin Peng
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Research Briefing |
Fast cryo-electron tomography data acquisition to determine molecular structures in situ
To accelerate data acquisition for in situ cryo-electron tomography, we created a method that takes into consideration sample geometry for the robust prediction of sample movement while the microscope stage is tilted. This approach enabled the parallel collection of tens to hundreds of tilt series.
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Brief Communication |
Deep-tissue SWIR imaging using rationally designed small red-shifted near-infrared fluorescent protein
miRFP718nano is a rationally designed small near-infrared fluorescent protein with an emission tail that extends into the short-wave infrared range for improved multiplexed and deep-tissue imaging applications.
- Olena S. Oliinyk
- , Chenshuo Ma
- & Vladislav V. Verkhusha
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Article |
Parallel cryo electron tomography on in situ lamellae
The parallel cryo electron tomography (PACE-tomo) method increases the throughput on in situ samples by parallelizing acquisition. It maximizes the usable sample area on individual lamellae without compromising data quality.
- Fabian Eisenstein
- , Haruaki Yanagisawa
- & Radostin Danev
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Article
| Open Access
Improved AlphaFold modeling with implicit experimental information
This paper presents an iterative procedure where AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions.
- Thomas C. Terwilliger
- , Billy K. Poon
- & Paul D. Adams
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Research Briefing |
Obtaining cryo-EM structures by scanning transmission electron microscopy
Scanning transmission electron microscopy (STEM) techniques reveal atomic-resolution details of organic and inorganic materials. The application of STEM to biological vitrified specimens under low-dose cryogenic imaging conditions demonstrates that STEM also achieves near-atomic-resolution 3D structures of biological macromolecules.
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Article
| Open Access
Single-particle cryo-EM structures from iDPC–STEM at near-atomic resolution
This paper explores the use of scanning transmission electron microscopy (STEM) to vitrified biological samples for biomolecular structure elucidation. Integrated differential phase contrast (iDPC)–STEM imaging of keyhole limpet hemocyanin and tobacco mosaic virus enabled cryo-EM structure determination at 6.5 and 3.5 Å resolution, respectively.
- Ivan Lazić
- , Maarten Wirix
- & Carsten Sachse
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This Month |
Tamir Gonen
MicroED for structure determination without a model and with heavy metal guitar riffs.
- Vivien Marx
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News & Views |
Electron counting takes microED to the next level
New data collection methods enable ab initio protein structure determination by micro-electron diffraction for the first time.
- Kevin D. Corbett
- & Mark A. Herzik Jr
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Article
| Open Access
Ab initio phasing macromolecular structures using electron-counted MicroED data
This article reports sub- and near-atomic structures of triclinic lysozyme and serine protease proteinase K, respectively, providing first demonstrations of ab initio phasing using electron counted MicroED data to solve macromolecular structures.
- Michael W. Martynowycz
- , Max T. B. Clabbers
- & Tamir Gonen
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Research Highlight |
Quantifying radiation damage
Bnet provides a measure of radiation damage suffered by protein crystals during X-ray crystallography.
- Arunima Singh
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Article |
Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly
ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops) enables improved single-particle cryo-EM of RNAs. ROCK was used to generate high-quality structures of three diverse RNAs, including the Tetrahymena group I intron.
- Di Liu
- , François A. Thélot
- & Peng Yin
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Comment |
Fighting SARS-CoV-2 with structural biology methods
High-resolution structural information is critical for rapid development of vaccines and therapeutics against emerging human pathogens. Structural biology methods have been at the forefront of research on SARS-CoV-2 since the beginning of the COVID-19 pandemic. These technologies will continue to be powerful tools to fend off future public health threats.
- Jun Zhang
- & Bing Chen
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Article |
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks
CR-I-TASSER integrates deep neural-network learning with I-TASSER assembly simulations for automated cryo-EM structure determination.
- Xi Zhang
- , Biao Zhang
- & Yang Zhang
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Editorial |
Method of the Year 2021: Protein structure prediction
Deep Learning based approaches for protein structure prediction have sent shock waves through the structural biology community. We anticipate far-reaching and long-lasting impact.
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Comment |
A paradigm shift in structural biology
The release of protein structure predictions from AlphaFold will increase the number of protein structural models by almost three orders of magnitude. Structural biology and bioinformatics will never be the same, and the need for incisive experimental approaches will be greater than ever. Combining these advances in structure prediction with recent advances in cryo-electron microscopy suggests a new paradigm for structural biology.
- Sriram Subramaniam
- & Gerard J. Kleywegt
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Technology Feature |
Method of the Year: protein structure prediction
Nature Methods has named protein structure prediction the Method of the Year 2021.
- Vivien Marx
Automated atomic modeling in cryo-EM maps
Protein–ligand structure prediction
Graphene sandwich for cryo-EM
Contrast enhancement for cryo-ET