New Opportunities Created by Single-Particle Cryo-EM: The Mapping of Conformational Space.
New Opportunities Created by Single-Particle Cryo-EM: The Mapping of Conformational Space.
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DOI：
10.1021/acs.biochem.8b00064
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发表时间：
2018-02-13
期刊：
影响因子：
2.9
通讯作者：
Frank J
中科院分区：
文献类型：
--
作者：
Frank J
我们有证据表明，从一些冷冻EM研究，分子在溶液中存在的构象状态的连续分布，远远大于离散的最大似然分类，如Relion的标准方法确定的数量。1这个发现，如果它成立，当我们希望研究一个进行性分子机器时，特别有趣，这个机器要么积极地与功能配体和能量配额一起“运行”，（GTP和ATP）在没有配体的情况下在热平衡中提供或“闲置”，因为它承诺有机会在实验上揭示自由能景观和功能途径，而无需任何模型假设。在与威斯康星州密尔沃基大学的Abbas Ourmazd小组的合作中，我的小组在过去的七年中开发了一种用于从大量的低温EM单粒子快照中连续映射状态的方法。2两个大型数据集提供了尝试这些新算法的机会：一个是来自酵母的800000个核糖体图像的集合3（尽管在本研究中只使用了一小部分），以及来自最近研究的钙释放通道的图像集合4，在存在和不存在配体的情况下，每个图像都有400000个。[5]在每种情况下，从映射中获得的自由能景观都揭示了有关功能途径的详细信息。其他研究，与其他类型的分子，正在进行中的几个合作。
We have evidence from a number of cryo-EM studies that molecules in solution exist in a continuous distribution of conformational states, far larger in number than the discrete ones identified by the standard methods of maximum likelihood classification such as Relion. 1 This finding, if it holds up, is particularly interesting when we wish to study a processive molecular machine that either actively “runs” with the functional ligands and energy quota (GTP and ATP) supplied or “idles” in the thermal equilibrium in the absence of ligands, because it promises the chance to uncover free-energy landscapes and functional pathways experimentally, without any model assumptions.Jointly, in collaboration with the group of Abbas Ourmazd at the University of Wisconsin Milwaukee, my group has developed a method for the continuous mapping of states from large number of cryo-EM single-particle snapshots over the past seven years. 2 Two large data sets presented the opportunity to try out these new algorithms: one was a collection of 800000 ribosome images from yeast 3 (though only a fraction was used in this study), and a collection of images for the calcium release channel from a recent study, 4 with∼ 400000 each in the presence and absence of ligands. 5 In each case, the free-energy landscapes obtained from the mapping revealed detailed information about functional pathways. Other studies, with other types of molecules, are in progress in several collaborations.
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DOI：
10.1016/j.ymeth.2016.02.007
发表时间：
2016-05-01
期刊：
Methods (San Diego, Calif.)
影响因子：
--
作者：
Frank J;Ourmazd A
通讯作者：
Ourmazd A
DOI：
10.1073/pnas.1419276111
发表时间：
2014-12-09
影响因子：
11.1
作者：
Dashti, Ali;Schwander, Peter;Ourmazd, Abbas
通讯作者：
Ourmazd, Abbas
影响因子：
5.6
作者：
Scheres, Sjors H. W.
通讯作者：
Scheres, Sjors H. W.
影响因子：
64.5
作者：
des Georges, Amedee;Clarke, Oliver B.;Zalk, Ran;Yuan, Qi;Condon, Kendall J.;Grassucci, Robert A.;Hendrickson, Wayne A.;Marks, Andrew R.;Frank, Joachim
通讯作者：
Frank, Joachim