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新算法显著改善单粒子冷冻电镜重构
作者:小柯机器人 发布时间:2020/12/2 20:51:06

加拿大多伦多大学David J. Fleet、Ali Punjani研究小组的一项最新研究发现非均匀细化、自适应正则化可改善单粒子冷冻电镜(cryo-EM)重构。相关论文于2020年11月30日发表在《自然-方法学》杂志上。

研究人员介绍了非均匀优化,这是一种基于交叉验证优化的算法,该算法会在优化时自动对3D密度图进行正则化,以解决空间变化问题。与常见的位移不变正则算法不同,非均匀细化可系统地消除无序区域的噪声,同时保留了可用于对齐粒子图像的信号,在许多情况下可显著提高分辨率和三维(3D)重构的质量。研究人员获得了小至100 kDa多种膜蛋白的高分辨率重建结构,证明了cryo-EM在此类对结构生物学和药物发现至关重要的靶标筛选中可明显提高有效性。cryoSPARC软件包实现了非均匀优化。

据了解,cryo-EM被广泛用于研究生物大分子,这些大分子具有无序、柔韧性或部分占有区域。例如,膜蛋白经常与局部无序的去污剂胶束和脂质纳米颗粒混合的形式存于溶液。这样的空间可变性会对假定刚性的现有迭代优化算法产生负面影响,影响计算3D重建。

附:英文原文

Title: Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

Author: Ali Punjani, Haowei Zhang, David J. Fleet

Issue&Volume: 2020-11-30

Abstract: Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package. Membrane proteins exhibit spatial variation in rigidity and disorder, which poses a challenge for traditional cryo-EM reconstruction algorithms. Non-uniform refinement accounts for this spatial variability, yielding improved 3D reconstruction quality even for small membrane proteins.

DOI: 10.1038/s41592-020-00990-8

Source: https://www.nature.com/articles/s41592-020-00990-8

期刊信息

Nature Methods:《自然—方法学》,创刊于2004年。隶属于施普林格·自然出版集团,最新IF:28.467
官方网址:https://www.nature.com/nmeth/
投稿链接:https://mts-nmeth.nature.com/cgi-bin/main.plex