National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM080139
米国
引用
ジャーナル: Nat Methods / 年: 2021 タイトル: Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM. 著者: Muyuan Chen / Steven J Ludtke / 要旨: Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual ...Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and compositional states. While numerous methods are available for computational classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present e2gmm, a machine learning algorithm to determine a conformational landscape for proteins or complexes using a three-dimensional Gaussian mixture model mapped onto two-dimensional particle images in known orientations. Using a deep neural network architecture, e2gmm can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on both simulated data and three biological systems to explore compositional and conformational changes at a range of scales. The software is distributed as part of EMAN2.
生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス)
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実験情報
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構造解析
手法
クライオ電子顕微鏡法
解析
単粒子再構成法
試料の集合状態
particle
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試料調製
緩衝液
pH: 7
凍結
凍結剤: ETHANE
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電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
撮影
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 e/Å2
電子線
加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系
照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD
実験機器
モデル: Titan Krios / 画像提供: FEI Company
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画像解析
最終 再構成
解像度のタイプ: BY AUTHOR / 解像度: 5.0 Å / 解像度の算出法: OTHER 詳細: 10000 particles are used to reconstruct each frame of the continuous movement. The maps are filtered to 5A for visualization. 使用した粒子像数: 10000