Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy

Punjani, Ali; Brubaker, Marcus A.; Fleet, David J.

doi:10.1109/tpami.2016.2627573

Cited by 55 publications

(45 citation statements)

References 34 publications

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“…The first crossing at a FSC of 0.143 42 was used to determine the resolution at these 100 points, and a histogram of these points was plotted, along with the spread of directional resolution values defined by +/− 1σ from the mean. Sphericity was also used as a measure of the degree of anisotropy.…”

Section: Methodsmentioning

confidence: 99%

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Addressing preferred specimen orientation in single-particle cryo-EM through tilting

et al. 2017

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We present a strategy for tackling preferred particle orientation in single-particle cryogenic electron microscopy (cryo-EM) by employing tilts during data collection, and we quantify the resulting directional resolution and density isotropy using a new 3D Fourier Shell Correlation (FSC) algorithm. These techniques enabled structure determination of the influenza hemagglutinin (HA) trimer, which adopts a highly preferred orientation, to near-atomic resolution. They also improved both isotropy and global resolution for ribosomal biogenesis intermediates, which adopt a moderately preferred orientation. We propose that data collection at tilts is generally applicable to single-particle analysis, and furthermore, that quantitative isotropy estimation should be employed to evaluate cryo-EM density maps.

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Section: Methodsmentioning

confidence: 99%

“…3), the full stack of 158,432 particles from micrographs at 40° tilt from the HA trimer (0° and 40°) analysis was used. CryoSPARC 42 was used to generate an ab initio model. Using a 30 Å low-pass filtered version of this model, the particles were refined using Relion 3D refinement.…”

Section: Methodsmentioning

confidence: 99%

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

et al. 2017

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“…In recent years, several algorithms have been very successful in solving the homogeneous case (no heterogeneity). Clever algorithms and heuristics which reduce the number of comparisons significantly, and efficient use of hardware components such as GPUs have made the recent implementation of these algorithms rather fast [6,19,32,7]. Other approaches to the cryo-EM problem rely on similarity measure between images to align the images before estimating the structure of the molecule [33,34,35,36].…”

Section: Existing Methods In Cryo-em and Related Workmentioning

confidence: 99%

Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM

Lederman

Andén²,

Singer

2020

Inverse Problems

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Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose orientations and positions are unknown. The molecular structures are not rigid objects, but flexible objects involved in dynamical processes. The different conformations are exhibited by different instances of the macromolecule observed in a cryo-EM experiment, each of which is recorded as a particle image. The range of conformations and the conformation of each particle are not known a priori; one of the great promises of cryo-EM is to map this conformation space. Remarkable progress has been made in determining rigid structures from homogeneous samples of molecules in spite of the unknown orientation of each particle image and significant progress has been made in recovering a few distinct states from mixtures of rather distinct conformations, but more complex heterogeneous samples remain a major challenge.We introduce the "hyper-molecule" framework for modeling structures across different states of heterogeneous molecules, including continuums of states. The key idea behind this framework is representing heterogeneous macromolecules as highdimensional objects, with the additional dimensions representing the conformation space. This idea is then refined to model properties such as localized heterogeneity. In addition, we introduce an algorithmic framework for recovering such maps of heterogeneous objects from experimental data using a Bayesian formulation of the problem and Markov chain Monte Carlo (MCMC) algorithms to address the computational challenges in recovering these high dimensional hyper-molecules. We demonstrate these ideas in a prototype applied to synthetic data.

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“…One bottleneck is that a fine discretization comes at the cost of large set of templates, which leads to a computationally expensive procedure. Moreover, methods based on projection-matching were found to degrade significantly in low SNR regimes [20] or when errors occur in the estimation of the density map used for the generation of the clean templates [21]. Examples of joint-reconstruction methods that address 3D ab initio modeling are found in [22], [23].…”

Section: A Standard 3d Refinement Techniquesmentioning

confidence: 99%

Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM

Zehni

Donati

Soubies

et al. 2020

IEEE Trans. on Image Process.

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Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of biomolecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3D refinement, which resolves a highresolution 3D structure from an initial approximate volume by refining the estimation of the orientation of each projection. In this work, we propose a new approach that refines the projection angles on the continuum. We formulate the optimization problem over the density map and the orientations jointly. The density map is updated using the efficient alternating-direction method of multipliers, while the orientations are updated through a semicoordinate-wise gradient descent for which we provide an explicit derivation of the gradient. Our method eliminates the requirement for a fine discretization of the orientation space and does away with the classical but computationally expensive templatematching step. Numerical results demonstrate the feasibility and performance of our approach compared to several baselines.

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Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy

Cited by 55 publications

References 34 publications

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM

Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM

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