Abstract
Structure determination of proteins and macromolecular complexes by single-particle cryo-electron microscopy (cryo-EM) is poised to revolutionize structural biology. An early challenging step in the cryo-EM pipeline is the detection and selection of particles from two-dimensional micrographs (particle picking). Most existing particle-picking methods require human intervention to deal with complex (irregular) particle shapes and extremely low signal-to-noise ratio (SNR) in cryo-EM images. Here, we design a fully automated super-clustering approach for single particle picking (SuperCryoEMPicker) in cryo-EM micrographs, which focuses on identifying, detecting, and picking particles of the complex and irregular shapes in micrographs with extremely low signal-to-noise ratio (SNR). Our method first applies advanced image processing procedures to improve the quality of the cryo-EM images. The binary mask image-highlighting protein particles are then generated from each individual cryo-EM image using the super-clustering (SP) method, which improves upon base clustering methods (i.e., k-means, fuzzy c-means (FCM), and intensity-based cluster (IBC) algorithm) via a super-pixel algorithm. SuperCryoEMPicker is tested and evaluated on micrographs of β-galactosidase and 80S ribosomes, which are examples of cryo-EM data exhibiting complex and irregular particle shapes. The results show that the super-particle clustering method provides a more robust detection of particles than the base clustering methods, such as k-means, FCM, and IBC. SuperCryoEMPicker automatically and effectively identifies very complex particles from cryo-EM images of extremely low SNR. As a fully automated particle detection method, it has the potential to relieve researchers from laborious, manual particle-labeling work and therefore is a useful tool for cryo-EM protein structure determination.
Highlights
X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have been the principal technologies of high resolution structural biology, accounting for over 95% of the current holdings of the Protein Data Bank
In the past few years, major technological advances have fueled a “resolution revolution” in cryo-electron microscopy [1,2,3], and cryo-EM has emerged as a leading structural biology technology capable of determining protein structures to resolutions rivaling X-ray crystallography [4,5,6,7,8,9]
To aid the streamlining of particle picking, we propose a super-fully automated approach (SuperCryoEMPicker) for picking single particles of complex shapes in cryo-EM images, leveraging the new super-clustering technique
Summary
X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have been the principal technologies of high resolution structural biology, accounting for over 95% of the current holdings of the Protein Data Bank. Identification of particles in micrographs (particle picking) is a critical step in structure determination by cryo-EM. The 2D cryo-EM images contain randomly arranged particles along with non-particles—bits of frost, deformed particles, protein aggregates, and so on. These images have high background noise and low contrast due to a limited electron dose used in imaging. A large number of single-particle images need to be picked from cryo-EM micrographs to perform a reliable 3D reconstruction of the underlying protein structure
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