高分辨率固态 NMR 结构的 17.6 kDa 蛋白。
High-resolution solid-state NMR structure of a 17.6 kDa protein.
机构信息
Magnetic Resonance Center, CERM, University of Florence, Via L. Sacconi, 6-50019 Sesto Fiorentino, Italy.
出版信息
J Am Chem Soc. 2010 Jan 27;132(3):1032-40. doi: 10.1021/ja906426p.
Abstract
The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.
摘要
提出了一种利用顺磁金属离子在微结晶蛋白样品中产生的赝接触位移的策略，以获得固态 NMR 谱中明确的信号分配，从而能够提取距离用于蛋白质结构计算。使用该策略，从钴（II）取代的基质金属蛋白酶 12（159 个氨基酸，17.6 kDa）的催化结构域的 PDSD、DARR、CHHC 和最近引入的 PAR 和 PAIN-CP 固态实验中，可以获得 777 个明确的（281 个序列，217 个中程和 279 个远程）距离约束。得到的结构是一个高分辨率的结构，主链 rmsd 为 1.0 +/- 0.2 A，与 X 射线结构（与 X 射线的 rmsd 为 1.3 A）非常吻合。该策略可以通过使用顺磁标记物推广到非金属蛋白酶，代表了使用固态 NMR 进行蛋白质结构测定的重要一步。
相似文献
1
High-resolution solid-state NMR structure of a 17.6 kDa protein.高分辨率固态 NMR 结构的 17.6 kDa 蛋白。
J Am Chem Soc. 2010 Jan 27;132(3):1032-40. doi: 10.1021/ja906426p.
2
Paramagnetic shifts in solid-state NMR of proteins to elicit structural information.利用蛋白质固态核磁共振中的顺磁位移来获取结构信息。
Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17284-9. doi: 10.1073/pnas.0708460105. Epub 2008 Nov 6.
3
Magic angle spinning NMR structure determination of proteins from pseudocontact shifts.利用魔角旋转 NMR 从赝接触位移确定蛋白质结构。
J Am Chem Soc. 2013 Jun 5;135(22):8294-303. doi: 10.1021/ja4021149. Epub 2013 May 24.
4
Ultrafast MAS solid-state NMR permits extensive 13C and 1H detection in paramagnetic metalloproteins.超快 MAS 固态 NMR 允许在顺磁金属蛋白中广泛检测 13C 和 1H。
J Am Chem Soc. 2010 Apr 28;132(16):5558-9. doi: 10.1021/ja100398q.
5
3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints.基于高度模糊的固态核磁共振约束确定促肾上腺皮质激素释放激素（Crh）蛋白的三维结构
J Am Chem Soc. 2008 Mar 19;130(11):3579-89. doi: 10.1021/ja078014t. Epub 2008 Feb 20.
6
Structure calculation from unambiguous long-range amide and methyl 1H-1H distance restraints for a microcrystalline protein with MAS solid-state NMR spectroscopy.利用 MAS 固态 NMR 光谱法，根据明确的长程酰胺和甲基 1H-1H 距离约束进行微晶蛋白的结构计算。
J Am Chem Soc. 2011 Apr 20;133(15):5905-12. doi: 10.1021/ja110222h. Epub 2011 Mar 24.
7
Paramagnetic ions provide structural restraints in solid-state NMR of proteins.顺磁性离子在蛋白质的固态核磁共振中提供结构限制。
J Am Chem Soc. 2007 Feb 28;129(8):2218-9. doi: 10.1021/ja068105a. Epub 2007 Feb 1.
8
Protein structure determination with paramagnetic solid-state NMR spectroscopy.利用顺磁固态 NMR 光谱学测定蛋白质结构。
Acc Chem Res. 2013 Sep 17;46(9):2117-26. doi: 10.1021/ar300360q. Epub 2013 Mar 6.
9
The catalytic domain of MMP-1 studied through tagged lanthanides.通过标记镧系元素研究 MMP-1 的催化结构域。
FEBS Lett. 2012 Mar 9;586(5):557-67. doi: 10.1016/j.febslet.2011.09.020. Epub 2011 Sep 19.
10
Methyl proton contacts obtained using heteronuclear through-bond transfers in solid-state NMR spectroscopy.在固态核磁共振光谱中使用异核通过键转移获得的甲基质子接触。
J Am Chem Soc. 2008 Aug 13;130(32):10625-32. doi: 10.1021/ja801464g. Epub 2008 Jul 16.
引用本文的文献
1
Dipolar Recoupling in Rotating Solids.旋转固体中的偶极重耦合
Chem Rev. 2024 Nov 27;124(22):12844-12917. doi: 10.1021/acs.chemrev.4c00373. Epub 2024 Nov 6.
2
Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy.通过魔角旋转固体核磁共振光谱研究的核酸-蛋白质界面
J Struct Biol X. 2022 Aug 18;6:100072. doi: 10.1016/j.yjsbx.2022.100072. eCollection 2022.
3
Overhauser Dynamic Nuclear Polarization with Selectively Deuterated BDPA Radicals.超核极化与选择性氘化 BDPA 自由基。
J Am Chem Soc. 2021 Dec 8;143(48):20281-20290. doi: 10.1021/jacs.1c09406. Epub 2021 Nov 23.
4
Strategies for RNA Resonance Assignment by C/N- and H-Detected Solid-State NMR Spectroscopy.通过碳/氮和氢检测的固态核磁共振光谱进行RNA共振归属的策略
Front Mol Biosci. 2021 Oct 20;8:743181. doi: 10.3389/fmolb.2021.743181. eCollection 2021.
5
Solid-state NMR spectroscopy.固态核磁共振光谱学
Nat Rev Methods Primers. 2021;1. doi: 10.1038/s43586-020-00002-1. Epub 2021 Jan 14.
6
Adiabatic Solid Effect.绝热固体效应
J Phys Chem Lett. 2020 May 7;11(9):3416-3421. doi: 10.1021/acs.jpclett.0c00654. Epub 2020 Apr 20.
7
Use of paramagnetic systems to speed-up NMR data acquisition and for structural and dynamic studies.使用顺磁体系加速 NMR 数据采集及结构和动态研究。
Solid State Nucl Magn Reson. 2019 Oct;102:36-46. doi: 10.1016/j.ssnmr.2019.07.002. Epub 2019 Jul 12.
8
Structural Studies of Amyloid Fibrils by Paramagnetic Solid-State Nuclear Magnetic Resonance Spectroscopy.利用顺磁固态核磁共振波谱学研究淀粉样纤维的结构。
J Am Chem Soc. 2018 Oct 17;140(41):13161-13166. doi: 10.1021/jacs.8b06758. Epub 2018 Oct 9.
9
Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency.在 100 kHz MAS 频率下通过质子检测 NMR 光谱研究完整的细菌肽聚糖。
J Struct Biol. 2019 Apr 1;206(1):66-72. doi: 10.1016/j.jsb.2018.07.009. Epub 2018 Jul 19.
10
NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology.1吉赫兹及以上频率下大分子组装体与机器的核磁共振：分子结构生物学的新变革机遇
Methods Mol Biol. 2018;1688:1-35. doi: 10.1007/978-1-4939-7386-6_1.
本文引用的文献
1
Transverse-dephasing optimized homonuclear j-decoupling in solid-state NMR spectroscopy of uniformly 13C-labeled proteins.在均匀13C标记蛋白质的固态核磁共振波谱中，横向去相优化的同核J解耦
J Am Chem Soc. 2009 Aug 12;131(31):10816-7. doi: 10.1021/ja903542h.
2
Conformational heterogeneity of the M2 proton channel and a structural model for channel activation.M2质子通道的构象异质性及通道激活的结构模型。
Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13311-6. doi: 10.1073/pnas.0906553106. Epub 2009 Jul 24.
3
Proton assisted recoupling at high spinning frequencies.高自旋频率下的质子辅助再耦合
J Phys Chem B. 2009 Jul 9;113(27):9062-9. doi: 10.1021/jp810280t.
4
Paramagnetic ions enable tuning of nuclear relaxation rates and provide long-range structural restraints in solid-state NMR of proteins.顺磁性离子能够调节核弛豫速率，并在蛋白质的固态核磁共振中提供长程结构限制。
J Am Chem Soc. 2009 Jun 17;131(23):8108-20. doi: 10.1021/ja900224z.
5
Seeded growth of beta-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure.源自阿尔茨海默病大脑的原纤维引发的β-淀粉样蛋白原纤维的接种生长产生了独特的原纤维结构。
Proc Natl Acad Sci U S A. 2009 May 5;106(18):7443-8. doi: 10.1073/pnas.0812033106. Epub 2009 Apr 17.
6
(15)N-(15)N proton assisted recoupling in magic angle spinning NMR.魔角旋转核磁共振中（15）N - （15）N质子辅助再耦合
J Am Chem Soc. 2009 Apr 29;131(16):5769-76. doi: 10.1021/ja806578y.
7
Nanomole-scale protein solid-state NMR by breaking intrinsic 1HT1 boundaries.通过突破固有1H T1界限实现纳摩尔级蛋白质固态核磁共振。
Nat Methods. 2009 Mar;6(3):215-8. doi: 10.1038/nmeth.1300. Epub 2009 Feb 8.
8
Proton assisted recoupling and protein structure determination.质子辅助重耦合与蛋白质结构测定。
J Chem Phys. 2008 Dec 28;129(24):245101. doi: 10.1063/1.3036928.
9
alphaB-crystallin: a hybrid solid-state/solution-state NMR investigation reveals structural aspects of the heterogeneous oligomer.αB-晶状体蛋白：一项混合固态/溶液态核磁共振研究揭示了异质寡聚体的结构特征。
J Mol Biol. 2009 Feb 6;385(5):1481-97. doi: 10.1016/j.jmb.2008.10.097. Epub 2008 Nov 14.
10
Fast acquisition of multi-dimensional spectra in solid-state NMR enabled by ultra-fast MAS.通过超快魔角旋转实现固态核磁共振中多维谱的快速采集。
J Magn Reson. 2009 Feb;196(2):133-41. doi: 10.1016/j.jmr.2008.10.019. Epub 2008 Nov 7.
Zotero 插件