• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

用于通过核磁共振确定大分子结构的结构精修新方法。

New methods of structure refinement for macromolecular structure determination by NMR.

作者信息

Clore G M, Gronenborn A M

机构信息

Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.

出版信息

Proc Natl Acad Sci U S A. 1998 May 26;95(11):5891-8. doi: 10.1073/pnas.95.11.5891.

DOI:10.1073/pnas.95.11.5891
PMID:9600889
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC34492/
Abstract

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

摘要

多维核磁共振方法学的最新进展使得超过250个残基的蛋白质溶液结构得以解析。在本文中,我们讨论了几种结构优化方法,这些方法有望提高通过核磁共振确定的大分子结构的准确性。这些方法包括使用构象数据库势以及直接根据三键耦合常数、二级13C化学位移、1H化学位移、T1/T2比值和残余偶极耦合进行优化。后两种测量提供了其他溶液核磁共振参数无法获得的远程限制。

相似文献

1
New methods of structure refinement for macromolecular structure determination by NMR.用于通过核磁共振确定大分子结构的结构精修新方法。
Proc Natl Acad Sci U S A. 1998 May 26;95(11):5891-8. doi: 10.1073/pnas.95.11.5891.
2
Determining the structures of large proteins and protein complexes by NMR.通过核磁共振确定大型蛋白质和蛋白质复合物的结构。
Trends Biotechnol. 1998 Jan;16(1):22-34. doi: 10.1016/S0167-7799(97)01135-9.
3
Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.借助源自结构数据库的构象数据库势来提高核磁共振(NMR)和晶体学蛋白质结构的质量。
Protein Sci. 1996 Jun;5(6):1067-80. doi: 10.1002/pro.5560050609.
4
NMR structure determination of proteins and protein complexes larger than 20 kDa.大于20 kDa的蛋白质和蛋白质复合物的核磁共振结构测定。
Curr Opin Chem Biol. 1998 Oct;2(5):564-70. doi: 10.1016/s1367-5931(98)80084-7.
5
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.REDCRAFT:一个利用剩余偶极耦合核磁共振数据来确定溶液中全氘代蛋白质结构的计算平台。
PLoS Comput Biol. 2021 Feb 1;17(2):e1008060. doi: 10.1371/journal.pcbi.1008060. eCollection 2021 Feb.
6
Direct refinement against proton-proton dipolar couplings in NMR structure determination of macromolecules.在大分子的核磁共振结构测定中直接根据质子-质子偶极耦合进行精修。
J Magn Reson. 2000 Feb;142(2):393-6. doi: 10.1006/jmre.1999.1985.
7
Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.通过描述碱基-碱基位置相互作用的数据库平均力势来提高DNA核磁共振结构的准确性。
J Am Chem Soc. 2001 May 2;123(17):3903-18. doi: 10.1021/ja010033u.
8
Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings.利用一键和二键剩余偶极耦合对d(GCGAAGC)发夹结构进行优化。
J Biomol NMR. 2002 Sep;24(1):1-14. doi: 10.1023/a:1020632900961.
9
Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein.利用剩余偶极耦合确定低核Overhauser效应密度蛋白质的全局折叠:应用于370个残基的麦芽糖糊精结合蛋白
J Mol Biol. 2000 Jun 30;300(1):197-212. doi: 10.1006/jmbi.2000.3842.
10
NMR structures of proteins and protein complexes beyond 20,000 M(r).分子量超过20,000的蛋白质及蛋白质复合物的核磁共振结构
Nat Struct Biol. 1997 Oct;4 Suppl:849-53.

引用本文的文献

1
NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease.NMR 光谱学、激发态与细胞生物学问题的相关性——亨廷顿病的研究:亨廷顿蛋白的短暂预核形成四聚体及其对亨廷顿病的启示。
J Cell Sci. 2022 Jun 15;135(12). doi: 10.1242/jcs.258695.
2
Meet the IUPAB councilor - Angela M. Gronenborn.认识一下国际生物物理联合会理事会成员——安吉拉·M·格罗嫩伯恩。
Biophys Rev. 2021 Nov 19;13(6):835-838. doi: 10.1007/s12551-021-00886-7. eCollection 2021 Dec.
3
NMR resonance assignment and structure prediction of the C-terminal domain of the microtubule end-binding protein 3.微管末端结合蛋白 3 的 C 末端结构域的 NMR 共振分配和结构预测。
PLoS One. 2020 May 18;15(5):e0232338. doi: 10.1371/journal.pone.0232338. eCollection 2020.
4
Assessing Structural Preferences of Unstructured Protein Regions by NMR.利用 NMR 评估无规蛋白区域的结构偏好。
Biophys J. 2019 Nov 19;117(10):1948-1953. doi: 10.1016/j.bpj.2019.10.008. Epub 2019 Oct 14.
5
Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'.魔角旋转 NMR 光谱法测定的蛋白质结构的准确性和精密度:有些“需要朋友的一点帮助”。
J Biomol NMR. 2019 Jul;73(6-7):333-346. doi: 10.1007/s10858-019-00233-9. Epub 2019 Mar 7.
6
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.高质量核磁共振结构:一种用于Xplor-NIH的含隐式水和膜溶剂化的新力场。
J Biomol NMR. 2017 Jan;67(1):35-49. doi: 10.1007/s10858-016-0082-5. Epub 2016 Dec 29.
7
Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.结合核磁共振剩余偶极耦合和溶液X射线散射的复杂大分子系统构象集合结构表征的混合方法
Chem Rev. 2016 Jun 8;116(11):6305-22. doi: 10.1021/acs.chemrev.5b00592. Epub 2016 Jan 7.
8
Practical Aspects of Paramagnetic Relaxation Enhancement in Biological Macromolecules.生物大分子中顺磁弛豫增强的实际应用
Methods Enzymol. 2015;564:485-97. doi: 10.1016/bs.mie.2015.06.032. Epub 2015 Jul 2.
9
Visualizing transient dark states by NMR spectroscopy.通过核磁共振光谱法可视化瞬态暗态。
Q Rev Biophys. 2015 Feb;48(1):35-116. doi: 10.1017/S0033583514000122.
10
Protein NMR structures refined without NOE data.无NOE数据的蛋白质核磁共振结构精制。
PLoS One. 2014 Oct 3;9(10):e108888. doi: 10.1371/journal.pone.0108888. eCollection 2014.

本文引用的文献

1
Model building and refinement practice.模型构建与优化实践。
Methods Enzymol. 1997;277:208-30. doi: 10.1016/s0076-6879(97)77013-7.
2
Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude.在存在未知大小菱形度的情况下,针对剩余偶极耦合进行直接结构精修。
J Magn Reson. 1998 Mar;131(1):159-62. doi: 10.1006/jmre.1997.1345.
3
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.扭转角分子动力学作为核磁共振结构计算的一种新型高效工具。
J Magn Reson. 1997 Jan;124(1):154-64. doi: 10.1006/jmre.1996.1027.
4
Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium.在稀液晶介质中通过核磁共振直接测量生物分子中的距离和角度。
Science. 1997 Nov 7;278(5340):1111-4. doi: 10.1126/science.278.5340.1111.
5
Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution.偶极1H-15N和1H-13C耦合在溶液中磁性取向大分子结构测定中的应用。
Nat Struct Biol. 1997 Sep;4(9):732-8. doi: 10.1038/nsb0997-732.
6
The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.HMG-I(Y)-DNA复合物的溶液结构定义了一种新的结构型小沟结合基序。
Nat Struct Biol. 1997 Aug;4(8):657-65. doi: 10.1038/nsb0897-657.
7
Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids.用于优化蛋白质和核酸的核磁共振(NMR)及X射线结构的构象数据库势场的改进与扩展。
J Magn Reson. 1997 Mar;125(1):171-7. doi: 10.1006/jmre.1997.1116.
8
Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.根据异核弛豫时间对旋转扩散各向异性的依赖性来定义核磁共振结构测定中的长程有序。
Nat Struct Biol. 1997 Jun;4(6):443-9. doi: 10.1038/nsb0697-443.
9
The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.嗜碱芽孢杆菌丝氨酸蛋白酶PB92的溶液结构呈现出一个具有灵活底物结合位点的刚性折叠。
Structure. 1997 Apr 15;5(4):521-32. doi: 10.1016/s0969-2126(97)00208-6.
10
Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR.利用多维核磁共振技术解析大肠杆菌磷酸烯醇式丙酮酸:糖磷酸转移酶系统中酶I 30 kDa N端结构域的溶液结构
Biochemistry. 1997 Mar 4;36(9):2517-30. doi: 10.1021/bi962924y.