Suppr超能文献

使用实验 NMR 数据对单体 AlphaFold2 蛋白质结构模型进行盲评估。

Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.

机构信息

Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

出版信息

J Magn Reson. 2023 Jul;352:107481. doi: 10.1016/j.jmr.2023.107481. Epub 2023 May 20.

Abstract

Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been observed. Since AF2 was trained on X-ray crystal and cryoEM structures, we assessed how accurately AF2 can model small, monomeric, solution protein NMR structures which (i) were not used in the AF2 training data set, and (ii) did not have homologous structures in the Protein Data Bank at the time of AF2 training. We identified nine open-source protein NMR data sets for such "blind" targets, including chemical shift, raw NMR FID data, NOESY peak lists, and (for 1 case) N-H residual dipolar coupling data. For these nine small (70-108 residues) monomeric proteins, we generated AF2 prediction models and assessed how well these models fit to these experimental NMR data, using several well-established NMR structure validation tools. In most of these cases, the AF2 models fit the NMR data nearly as well, or sometimes better than, the corresponding NMR structure models previously deposited in the Protein Data Bank. These results provide benchmark NMR data for assessing new NMR data analysis and protein structure prediction methods. They also document the potential for using AF2 as a guiding tool in protein NMR data analysis, and more generally for hypothesis generation in structural biology research.

摘要

近年来,蛋白质结构的分子建模方面的进展正在改变结构生物学领域。由 DeepMind, Inc. 开发的人工智能系统 AlphaFold-2 (AF2),利用基于注意力的深度学习,能够以相对 X 射线晶体学和低温电子显微镜 (cryoEM) 确定的结构更高的精度预测蛋白质结构模型。将 AF2 模型与使用溶液 NMR 数据确定的结构进行比较,观察到两者既有高度相似之处,也有明显差异。由于 AF2 是基于 X 射线晶体和 cryoEM 结构进行训练的,我们评估了 AF2 对小的、单体的、溶液状态下的蛋白质 NMR 结构进行建模的准确性,这些结构 (i) 未在 AF2 训练数据集中使用,并且 (ii) 在 AF2 训练时在蛋白质数据库中没有同源结构。我们确定了九个用于此类“盲”目标的开源蛋白质 NMR 数据集,包括化学位移、原始 NMR FID 数据、NOESY 峰列表,以及(对于 1 个案例)N-H 残差偶极耦合数据。对于这九个小的(70-108 个残基)单体蛋白质,我们生成了 AF2 预测模型,并使用几个经过良好验证的 NMR 结构验证工具评估了这些模型与这些实验 NMR 数据的拟合程度。在大多数情况下,AF2 模型对 NMR 数据的拟合程度与之前在蛋白质数据库中提交的相应 NMR 结构模型几乎一样,或者有时更好。这些结果为评估新的 NMR 数据分析和蛋白质结构预测方法提供了基准 NMR 数据。它们还证明了在蛋白质 NMR 数据分析中使用 AF2 作为指导工具的潜力,更广泛地说,在结构生物学研究中的假设生成方面具有潜力。

相似文献

1
Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.
J Magn Reson. 2023 Jul;352:107481. doi: 10.1016/j.jmr.2023.107481. Epub 2023 May 20.
2
Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.
bioRxiv. 2023 Jan 22:2023.01.22.525096. doi: 10.1101/2023.01.22.525096.
3
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Front Mol Biosci. 2022 Jun 13;9:877000. doi: 10.3389/fmolb.2022.877000. eCollection 2022.
4
Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR.
bioRxiv. 2025 Feb 26:2024.06.26.600902. doi: 10.1101/2024.06.26.600902.
5
AlphaFold2 and its applications in the fields of biology and medicine.
Signal Transduct Target Ther. 2023 Mar 14;8(1):115. doi: 10.1038/s41392-023-01381-z.
6
Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.
Int J Mol Sci. 2024 Sep 21;25(18):10139. doi: 10.3390/ijms251810139.
7
AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!
J Magn Reson. 2024 Jul;364:107725. doi: 10.1016/j.jmr.2024.107725. Epub 2024 Jun 19.
9
A structural biology community assessment of AlphaFold2 applications.
Nat Struct Mol Biol. 2022 Nov;29(11):1056-1067. doi: 10.1038/s41594-022-00849-w. Epub 2022 Nov 7.
10
A Perspective on the Prospective Use of AI in Protein Structure Prediction.
J Chem Inf Model. 2024 Jan 8;64(1):26-41. doi: 10.1021/acs.jcim.3c01361. Epub 2023 Dec 20.

引用本文的文献

1
PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes.
Nucleic Acids Res. 2025 Aug 11;53(15). doi: 10.1093/nar/gkaf774.
2
Assisting and accelerating NMR assignment with restrained structure prediction.
Commun Biol. 2025 Jul 18;8(1):1067. doi: 10.1038/s42003-025-08466-1.
3
Functional Annotation and Structural Characterization of Hypothetical Proteins in and Isolated from Honey.
ACS Omega. 2025 Feb 27;10(9):8993-9006. doi: 10.1021/acsomega.4c07105. eCollection 2025 Mar 11.
5
Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR.
Res Sq. 2025 Feb 19:rs.3.rs-5994356. doi: 10.21203/rs.3.rs-5994356/v1.
6
Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.
bioRxiv. 2025 Feb 14:2025.02.10.637534. doi: 10.1101/2025.02.10.637534.
8
The physics-AI dialogue in drug design.
RSC Med Chem. 2025 Jan 23;16(4):1499-1515. doi: 10.1039/d4md00869c. eCollection 2025 Apr 16.
10
AlphaFold two years on: Validation and impact.
Proc Natl Acad Sci U S A. 2024 Aug 20;121(34):e2315002121. doi: 10.1073/pnas.2315002121. Epub 2024 Aug 12.

本文引用的文献

1
Biophysical analysis of luciferase bioluminescence mechanisms using a non-oxidizable coelenterazine.
BBA Adv. 2022 Dec 23;3:100068. doi: 10.1016/j.bbadva.2022.100068. eCollection 2023.
2
Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA.
Nat Commun. 2022 Oct 18;13(1):6151. doi: 10.1038/s41467-022-33879-5.
3
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Front Mol Biosci. 2022 Jun 13;9:877000. doi: 10.3389/fmolb.2022.877000. eCollection 2022.
4
ColabFold: making protein folding accessible to all.
Nat Methods. 2022 Jun;19(6):679-682. doi: 10.1038/s41592-022-01488-1. Epub 2022 May 30.
6
The accuracy of protein structures in solution determined by AlphaFold and NMR.
Structure. 2022 Jul 7;30(7):925-933.e2. doi: 10.1016/j.str.2022.04.005. Epub 2022 May 9.
7
Multi-state modeling of G-protein coupled receptors at experimental accuracy.
Proteins. 2022 Nov;90(11):1873-1885. doi: 10.1002/prot.26382. Epub 2022 May 16.
9
Protein structure predictions to atomic accuracy with AlphaFold.
Nat Methods. 2022 Jan;19(1):11-12. doi: 10.1038/s41592-021-01362-6.
10
The impact of AlphaFold2 one year on.
Nat Methods. 2022 Jan;19(1):15-20. doi: 10.1038/s41592-021-01365-3.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验