Validation of protein backbone structures calculated from NMR angular restraints using Rosetta
Validation of protein backbone structures calculated from NMR angular restraints using Rosetta
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使用 Rosetta 验证根据 NMR 角约束计算的蛋白质主链结构
DOI：
10.1007/s10858-019-00251-7
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发表时间：
2019
影响因子：
2.7
通讯作者：
Nevzorov, Alexander A.
中科院分区：
文献类型：
--
作者：
Lapin, Joel;Nevzorov, Alexander A.
定向膜蛋白的多维固态核磁共振光谱可以通过测量偶极偶联和化学位移各向异性来推断主链扭转角，从而推断整个蛋白质折叠，这取决于每个肽面相对于外部磁场的取向。然而，多肽平面取向可以与给定的一组角度约束相一致。在获得和解释这些限制时，实验的不确定性进一步加剧了这种模糊性。先前开发的使用角度约束的结构计算算法通常涉及沿主干的顺序遍历，以找到与实验数据一致的连续肽面方向之间的扭转角。该方法在解释峰值位置时对实验不确定性很敏感，低至±10 Hz，通常会为计算结构产生很高的结构rmsd。在这里，我们提出了一个显着改进的版本的算法，其中包括拟合几个肽平面一次，以防止沿主干传播误差。此外，还设计了一种协议，用于使用Rosetta评分函数过滤结构解决方案，以找到既适合谱又满足生物信息学限制的结构。新算法的鲁棒性已经通过两种蛋白质的已知结构产生的合成角约束进行了测试：一种是可溶性蛋白2gb1（56个残基），选择它的多种二级结构元素，即α -螺旋和两个β -片，另一种是膜蛋白4a2n，其中使用了前两个跨膜螺旋（共有64个残基）。通过改变拟合平面的数量、实验误差和核磁共振维度的数量，进行了广泛的模拟。研究发现，与拟合单个扭角对相比，同时拟合两个肽面总是使计算结构的分布向较低的结构RMSD值偏移。对于每种蛋白质，无论模拟参数如何，Rosetta都能够区分出最合理的结构，相对于原始结构，结构rmsd通常低于2 Å。本研究建立了一个使用固态核磁共振角约束和生物信息学相结合的de-novo蛋白质结构预测框架。
Multidimensional solid-state NMR spectra of oriented membrane proteins can be used to infer the backbone torsion angles and hence the overall protein fold by measuring dipolar couplings and chemical shift anisotropies, which depend on the orientation of each peptide plane with respect to the external magnetic field. However, multiple peptide plane orientations can be consistent with a given set of angular restraints. This ambiguity is further exacerbated by experimental uncertainty in obtaining and interpreting such restraints. The previously developed algorithms for structure calculations using angular restraints typically involve a sequential walkthrough along the backbone to find the torsion angles between the consecutive peptide plane orientations that are consistent with the experimental data. This method is sensitive to experimental uncertainty in interpreting the peak positions of as low as ± 10 Hz, often yielding high structural RMSDs for the calculated structures. Here we present a significantly improved version of the algorithm which includes the fitting of several peptide planes at once in order to prevent propagation of error along the backbone. In addition, a protocol has been devised for filtering the structural solutions using Rosetta scoring functions in order to find the structures that both fit the spectrum and satisfy bioinformatics restraints. The robustness of the new algorithm has been tested using synthetic angular restraints generated from the known structures for two proteins: a soluble protein 2gb1 (56 residues), chosen for its diverse secondary structure elements, i.e. an alpha-helix and two beta-sheets, and a membrane protein 4a2n, from which the first two transmembrane helices (having a total of 64 residues) have been used. Extensive simulations have been performed by varying the number of fitted planes, experimental error, and the number of NMR dimensions. It has been found that simultaneously fitting two peptide planes always shifted the distribution of the calculated structures toward lower structural RMSD values as compared to fitting a single torsion-angle pair. For each protein, irrespective of the simulation parameters, Rosetta was able to distinguish the most plausible structures, often having structural RMSDs lower than 2 Å with respect to the original structure. This study establishes a framework for de-novo protein structure prediction using a combination of solid-state NMR angular restraints and bioinformatics.
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DOI：
10.1016/j.pnmrs.2010.04.005
发表时间：
2010-08
影响因子：
6.1
作者：
Saito, Hazime;Ando, Isao;Ramamoorthy, Ayyalusamy
通讯作者：
Ramamoorthy, Ayyalusamy
影响因子：
5.5
作者：
O'Meara, Matthew J.;Leaver-Fay, Andrew;Tyka, Michael D.;Stein, Amelie;Houlihan, Kevin;DiMaio, Frank;Bradley, Philip;Kortemme, Tanja;Baker, David;Snoeyink, Jack;Kuhlman, Brian
通讯作者：
Kuhlman, Brian
影响因子：
4.6
作者：
Yamamoto, Kazutoshi;Duerr, Ulrich H. N.;Xu, Jiadi;Im, Sang-Choul;Waskell, Lucy;Ramamoorthy, Ayyalusamy
通讯作者：
Ramamoorthy, Ayyalusamy
影响因子：
16.6
作者：
Gayen, Anindita;Banigan, James R.;Traaseth, Nathaniel J.
通讯作者：
Traaseth, Nathaniel J.
定向蛋白质样品的“无位移”固态核磁共振结构测定。
DOI：
--
发表时间：
2011
期刊：
Journal of magnetic resonance (San Diego, Calif. 1997 : Print)
影响因子：
--
作者：
Yuanyuan Yin;A. Nevzorov
通讯作者：
A. Nevzorov