• 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

扭转角用于绘制和可视化蛋白质的构象空间。

Torsion angles to map and visualize the conformational space of a protein.

机构信息

Division of Life Sciences, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.

Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.

出版信息

Protein Sci. 2023 Apr;32(4):e4608. doi: 10.1002/pro.4608.

DOI:10.1002/pro.4608
Abstract

Present understanding of protein structure dynamics trails behind that of static structures. A torsion-angle-based approach, called the representation of protein entities, derives an interpretable conformational space that correlates with data collection temperature, resolution, and reaction coordinate. For more complex systems, atomic coordinates fail to separate functional conformational states, which are still preserved by torsion angle-derived space. This indicates that torsion angles are often a more sensitive and biologically relevant descriptor for protein conformational dynamics than atomic coordinates.

摘要

目前,人们对蛋白质结构动力学的理解落后于对静态结构的理解。一种基于扭转角的方法,称为蛋白质实体表示法,推导出一个可解释的构象空间,该空间与数据采集温度、分辨率和反应坐标相关。对于更复杂的系统,原子坐标无法分离功能构象状态,而这些状态仍然由扭转角衍生空间保留。这表明,与原子坐标相比,扭转角通常是蛋白质构象动力学更敏感和更具生物学相关性的描述符。

相似文献

1
Torsion angles to map and visualize the conformational space of a protein.扭转角用于绘制和可视化蛋白质的构象空间。
Protein Sci. 2023 Apr;32(4):e4608. doi: 10.1002/pro.4608.
2
Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression.蛋白质构象变化能否用扭转角空间来表示?一种用重标极差回归的研究。
J Chem Inf Model. 2019 Nov 25;59(11):4929-4941. doi: 10.1021/acs.jcim.9b00627. Epub 2019 Oct 29.
3
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.在扭转角空间中同时表示蛋白质 NMR 结构的单结构和束结构。
J Biomol NMR. 2012 Apr;52(4):351-64. doi: 10.1007/s10858-012-9615-8. Epub 2012 Feb 22.
4
Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures.细粒度统计扭转角势在区分天然蛋白质结构方面很有效。
Curr Drug Discov Technol. 2006 Mar;3(1):75-81. doi: 10.2174/157016306776637591.
5
Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction.从 NMR 确定的结构中获得的骨架扭转角的波动及其预测。
Proteins. 2010 Dec;78(16):3353-62. doi: 10.1002/prot.22842.
6
Effective protein conformational sampling based on predicted torsion angles.基于预测扭转角的有效蛋白质构象采样
J Comput Chem. 2016 Apr 30;37(11):976-80. doi: 10.1002/jcc.24285. Epub 2015 Dec 23.
7
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.扭转角分子动力学在蛋白质构象高效采样中的应用。
J Comput Chem. 2005 Nov 30;26(15):1565-78. doi: 10.1002/jcc.20293.
8
T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles.T-Analyst:一种通过扭转角进行蛋白质构象变化高效分析的程序。
J Comput Aided Mol Des. 2010 Oct;24(10):819-27. doi: 10.1007/s10822-010-9376-y. Epub 2010 Aug 6.
9
Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.基于平均力扭转角势对蛋白质核磁共振结构进行优化时问题的来源及解决方案
J Magn Reson. 2000 Oct;146(2):249-54. doi: 10.1006/jmre.2000.2142.
10
TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences.TANGLE:一种两级支持向量回归方法,用于从蛋白质一级序列预测蛋白质主链扭转角。
PLoS One. 2012;7(2):e30361. doi: 10.1371/journal.pone.0030361. Epub 2012 Feb 2.

引用本文的文献

1
Orchestrating function: Concerted dynamics, allostery, and catalysis in protein tyrosine phosphatases.协调功能:蛋白酪氨酸磷酸酶中的协同动力学、别构效应与催化作用
Curr Opin Struct Biol. 2025 Aug 1;94:103125. doi: 10.1016/j.sbi.2025.103125.
2
Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.通过多温度、时间分辨串行晶体学探究酶动力学的调制。
Nat Commun. 2025 Jul 16;16(1):6553. doi: 10.1038/s41467-025-61631-2.
3
Advances in uncovering the mechanisms of macromolecular conformational entropy.

本文引用的文献

1
Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies.Xtrapol8 可实现晶体学研究中低占据中间态的自动阐明。
Commun Biol. 2022 Jun 29;5(1):640. doi: 10.1038/s42003-022-03575-7.
2
The protein-folding problem: Not yet solved.蛋白质折叠问题:尚未解决。
Science. 2022 Feb 4;375(6580):507. doi: 10.1126/science.abn9422. Epub 2022 Feb 3.
3
Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.室温 XFEL 晶体学揭示了光合作用 I 中两个叶绿醌附近的不对称性。
揭示大分子构象熵机制的进展。
Nat Chem Biol. 2025 May;21(5):623-634. doi: 10.1038/s41589-025-01879-3. Epub 2025 Apr 24.
4
Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens.从晶体学药物片段筛选中绘制蛋白质构象景观图。
J Chem Inf Model. 2024 Dec 9;64(23):8937-8951. doi: 10.1021/acs.jcim.4c01380. Epub 2024 Nov 12.
5
Mapping protein conformational landscapes from crystallographic drug fragment screens.从晶体学药物片段筛选中绘制蛋白质构象图谱。
bioRxiv. 2024 Jul 30:2024.07.29.605395. doi: 10.1101/2024.07.29.605395.
6
An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin.紫外线驱动的针对眼晶状体蛋白人γ-D晶状体蛋白氧化应激的挽救途径。
Commun Chem. 2024 Apr 10;7(1):81. doi: 10.1038/s42004-024-01163-w.
7
Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP.推向极端:高温与压力对 STEP 结构的独特影响。
Commun Biol. 2024 Jan 12;7(1):59. doi: 10.1038/s42003-023-05609-0.
8
Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase.推向极端:高温与压力对一种非典型磷酸酶结构的不同影响。
bioRxiv. 2023 May 3:2023.05.02.538097. doi: 10.1101/2023.05.02.538097.
Sci Rep. 2021 Nov 8;11(1):21787. doi: 10.1038/s41598-021-00236-3.
4
A method for intuitively extracting macromolecular dynamics from structural disorder.一种直观提取结构无序中大分子动力学的方法。
Nat Commun. 2021 Sep 17;12(1):5493. doi: 10.1038/s41467-021-25814-x.
5
Highly accurate protein structure prediction with AlphaFold.利用 AlphaFold 进行高精度蛋白质结构预测。
Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2. Epub 2021 Jul 15.
6
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins.漂泊者:基于键的参数化可减少过度拟合,从而改进蛋白质的精修。
Acta Crystallogr D Struct Biol. 2021 Apr 1;77(Pt 4):424-437. doi: 10.1107/S2059798321000826. Epub 2021 Mar 30.
7
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.qFit 3:用于 X 射线晶体学和单颗粒冷冻电镜密度图的蛋白质和配体多构象建模。
Protein Sci. 2021 Jan;30(1):270-285. doi: 10.1002/pro.4001. Epub 2020 Nov 30.
8
Structural plasticity of SARS-CoV-2 3CL M active site cavity revealed by room temperature X-ray crystallography.室温 X 射线晶体学揭示 SARS-CoV-2 3CL M 活性位点腔的结构可塑性。
Nat Commun. 2020 Jun 24;11(1):3202. doi: 10.1038/s41467-020-16954-7.
9
Diffuse X-ray scattering from correlated motions in a protein crystal.蛋白质晶体中相关运动的漫散射 X 射线。
Nat Commun. 2020 Mar 9;11(1):1271. doi: 10.1038/s41467-020-14933-6.
10
Molecular Dynamics Simulations of Macromolecular Crystals.大分子晶体的分子动力学模拟
Wiley Interdiscip Rev Comput Mol Sci. 2019 Jul-Aug;9(4). doi: 10.1002/wcms.1402. Epub 2018 Nov 16.