通过核磁共振化学位移确定蛋白质结构
Protein structure determination from NMR chemical shifts.
作者信息
Cavalli Andrea, Salvatella Xavier, Dobson Christopher M, Vendruscolo Michele
机构信息
Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom.
出版信息
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20. doi: 10.1073/pnas.0610313104. Epub 2007 May 29.
Abstract
NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.
摘要
核磁共振光谱在确定蛋白质和其他生物大分子的结构及动力学方面发挥着重要作用。化学位移是最易于且准确测量的核磁共振参数，它们能高度特异性地反映蛋白质天然态和非天然态的构象。我们以11个代表主要结构类别的蛋白质为例，这些蛋白质含有多达123个残基，结果表明可以将化学位移作为结构约束，结合传统的分子力学力场，以2埃或更高的分辨率确定蛋白质的构象。这一策略应具有广泛的适用性，并且经过进一步发展，将能够进行定量结构分析，以解决一系列当前结构技术无法解决的复杂生物学问题。
相似文献
1
Protein structure determination from NMR chemical shifts.通过核磁共振化学位移确定蛋白质结构
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20. doi: 10.1073/pnas.0610313104. Epub 2007 May 29.
2
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.利用核磁共振化学位移作为蛋白质分子动力学模拟的结构约束条件。
Structure. 2010 Aug 11;18(8):923-33. doi: 10.1016/j.str.2010.04.016.
3
Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology.高压 NMR 光谱学的实际应用及其在蛋白质生物物理学和结构生物学中的应用。
Methods. 2018 Sep 15;148:67-80. doi: 10.1016/j.ymeth.2018.06.012. Epub 2018 Jun 30.
4
3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.利用稀疏顺磁核磁共振数据对蛋白质进行三维计算建模
Methods Mol Biol. 2017;1526:3-21. doi: 10.1007/978-1-4939-6613-4_1.
5
Protein structure determination from pseudocontact shifts using ROSETTA.利用 ROSETTA 从赝接触位移确定蛋白质结构。
J Mol Biol. 2012 Mar 9;416(5):668-77. doi: 10.1016/j.jmb.2011.12.056. Epub 2012 Jan 18.
6
Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.使用分子片段置换和核磁共振化学位移对蛋白质进行平衡模拟。
Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13852-7. doi: 10.1073/pnas.1404948111. Epub 2014 Sep 5.
7
Refinement of NMR-determined protein structures with database derived mean-force potentials.利用数据库衍生的平均力势对核磁共振测定的蛋白质结构进行优化。
Proteins. 2007 Jul 1;68(1):232-42. doi: 10.1002/prot.21358.
8
Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles.使用伪接触位移和剩余偶极耦合作为确定蛋白质结构集合的精确核磁共振约束条件。
Biochemistry. 2015 Dec 29;54(51):7470-6. doi: 10.1021/acs.biochem.5b01138. Epub 2015 Dec 17.
9
Recent advances in computational methods for nuclear magnetic resonance data processing.近年来，在核磁共振数据处理的计算方法方面取得了进展。
Genomics Proteomics Bioinformatics. 2013 Feb;11(1):29-33. doi: 10.1016/j.gpb.2012.12.003. Epub 2013 Jan 11.
10
NMR refinement and peptide folding using the GROMACS software.使用 GROMACS 软件进行 NMR 精修和肽折叠。
J Biomol NMR. 2021 May;75(4-5):143-149. doi: 10.1007/s10858-021-00363-z. Epub 2021 Mar 28.
引用本文的文献
1
Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1].用于蛋白质模拟力场基准测试的基于结构的实验数据集 [文章 v0.1]
ArXiv. 2025 Mar 25:arXiv:2303.11056v2.
2
Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.使用反常X射线散射干涉测量法测定蛋白质中的绝对分子内距离。
Nanoscale. 2025 Feb 6;17(6):3322-3330. doi: 10.1039/d4nr03375b.
3
Mapping the FF domain folding pathway via structures of transiently populated folding intermediates.通过瞬时形成的折叠中间体的结构来绘制FF结构域的折叠途径。
Proc Natl Acad Sci U S A. 2024 Dec 10;121(50):e2416682121. doi: 10.1073/pnas.2416682121. Epub 2024 Dec 4.
4
UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.UCBShift 2.0：从骨干到侧链蛋白质化学位移预测蛋白质结构的桥梁。
J Am Chem Soc. 2024 Nov 20;146(46):31733-31745. doi: 10.1021/jacs.4c10474. Epub 2024 Nov 12.
5
Spiers Memorial Lecture: NMR crystallography.斯皮尔斯纪念讲座：核磁共振晶体学。
Faraday Discuss. 2025 Jan 8;255(0):9-45. doi: 10.1039/d4fd00151f.
6
Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation.利用残基特异性非天然氨基酸掺入工程化蛋白质和材料。
Chem Rev. 2024 Aug 14;124(15):9113-9135. doi: 10.1021/acs.chemrev.3c00855. Epub 2024 Jul 15.
7
Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks.核磁共振化学位移的准确预测：将密度泛函理论计算与三维图神经网络相结合
J Chem Theory Comput. 2024 Jun 25;20(12):5250-5258. doi: 10.1021/acs.jctc.4c00422. Epub 2024 Jun 6.
8
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.智能分辨率：将冷冻电镜与人工智能驱动的多分辨率模拟相结合，以观察严重急性呼吸综合征冠状病毒2的复制转录机制在实际运作中的情况。
Int J High Perform Comput Appl. 2022 Nov;36(5-6):603-623. doi: 10.1177/10943420221113513. Epub 2022 Aug 5.
9
Molecular basis for curvature formation in SepF polymerization.SepF 聚合过程中曲率形成的分子基础。
Proc Natl Acad Sci U S A. 2024 Feb 27;121(9):e2316922121. doi: 10.1073/pnas.2316922121. Epub 2024 Feb 21.
10
Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins.蛋白视紫红质中颜色开关的分子机制和进化稳健性。
Sci Adv. 2024 Jan 26;10(4):eadj0384. doi: 10.1126/sciadv.adj0384. Epub 2024 Jan 24.
本文引用的文献
1
NMR study of the tetrameric KcsA potassium channel in detergent micelles.在去污剂胶束中对四聚体KcsA钾通道的核磁共振研究。
Protein Sci. 2006 Apr;15(4):684-98. doi: 10.1110/ps.051954706. Epub 2006 Mar 7.
2
The impact of structural genomics: expectations and outcomes.结构基因组学的影响：期望与成果
Science. 2006 Jan 20;311(5759):347-51. doi: 10.1126/science.1121018.
3
Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins.一种小α/β蛋白的剩余偶极耦合、主链序参数与晶体学B因子的一致性：蛋白质中高概率、快速原子运动的统一图景
J Mol Biol. 2006 Feb 3;355(5):879-86. doi: 10.1016/j.jmb.2005.11.042.
4
Intrinsic dynamics of an enzyme underlies catalysis.酶的内在动力学是催化作用的基础。
Nature. 2005 Nov 3;438(7064):117-21. doi: 10.1038/nature04105.
5
Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release.超分子复合物的定量核磁共振光谱：ClpP中的动态侧孔对产物释放很重要。
Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16678-83. doi: 10.1073/pnas.0507370102. Epub 2005 Nov 1.
6
Progress in modeling of protein structures and interactions.蛋白质结构与相互作用建模的进展。
Science. 2005 Oct 28;310(5748):638-42. doi: 10.1126/science.1112160.
7
Building native protein conformation from highly approximate backbone torsion angles.从高度近似的主链扭转角构建天然蛋白质构象。
Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16227-32. doi: 10.1073/pnas.0508415102. Epub 2005 Oct 26.
8
Toward high-resolution de novo structure prediction for small proteins.迈向小蛋白质的高分辨率从头结构预测
Science. 2005 Sep 16;309(5742):1868-71. doi: 10.1126/science.1113801.
9
Intrinsically unstructured proteins and their functions.内在无序蛋白质及其功能。
Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208. doi: 10.1038/nrm1589.
10
Towards complete descriptions of the free-energy landscapes of proteins.迈向对蛋白质自由能景观的完整描述。
Philos Trans A Math Phys Eng Sci. 2005 Feb 15;363(1827):433-50; discussion 450-2. doi: 10.1098/rsta.2004.1501.
Zotero 插件