Atomic refinement with correlated solid-state NMR restraints
Atomic refinement with correlated solid-state NMR restraints
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DOI：
10.1016/s1090-7807(03)00147-2
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发表时间：
2003-08-01
影响因子：
2.2
通讯作者：
Chapman, MS
中科院分区：
文献类型：
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作者：
Bertram, R;Asbury, T;Chapman, MS
固体核磁共振提供的取向数据可以提供大量膜蛋白的结构信息。然而，所提供的信息的质量由于偶极耦合张量测量中的符号简并而有所降低。这反映在原子精炼中使用的偶极耦合惩罚函数中，当偶极符号简并存在时，它不太能够适当地约束原子。在本报告中，我们使用各种程序生成模拟的固态核磁共振数据，包括从α -螺旋和β -片膜蛋白的晶体结构进行反向计算。我们证明，如果各向异性偶极耦合测量与各向异性化学位移测量相关联，则可以解决大部分的偶极符号简并，并且如果三种数据类型相关，则可以解决所有的符号简并。两种测试膜蛋白的原子精化证明了相关数据的优势。当使用相关的偶极耦合和化学位移进行细化时，与数据不相关时相比，扰动结构收敛到具有更大比例正确偶极符号的构象。此外，当使用相关数据进行精化时，最终的结构更接近原始的无扰动结构。因此，使用相关数据进行细化可以改进原子结构。用于关联偶极耦合和化学位移数据以及建立能量函数及其衍生物以进行细化的软件CNS-SS02可在我们的网站上获得。(C) 2003 Elsevier Science（美国）版权所有。
The orientation data provided by solid-state NMR can provide a great deal of structural information about membrane proteins. The quality of the information provided is, however, somewhat degraded by sign degeneracies in measurements of the dipolar coupling tensor. This is reflected in the dipolar coupling penalty function used in atomic refinement, which is less capable of properly restraining atoms when dipolar sign degeneracies are present. In this report we generate simulated solid-state NMR data using a variety of procedures, including back-calculation from crystal structures of alpha-helical and beta-sheet membrane proteins. We demonstrate that a large fraction of the dipolar sign degeneracies are resolved if anisotropic dipolar coupling measurements are correlated with anisotropic chemical shift measurements, and that all sign degeneracies can be resolved if three data types are correlated. The advantages of correlating data are demonstrated with atomic refinement of two test membrane proteins. When refinement is performed using correlated dipolar couplings and chemical shifts, perturbed structures converge to conformations with a larger fraction of correct dipolar signs than when data are uncorrelated. In addition, the final structures are closer to the original unperturbed structures when correlated data are used in the refinement. Thus, refinement with correlated data leads to improved atomic structures. The software used to correlate dipolar coupling and chemical shift data and to set up energy functions and their derivatives for refinement, CNS-SS02, is available at our web site. (C) 2003 Elsevier Science (USA). All rights reserved.