Suppr超能文献

细胞组装的综合建模。

Integrative modelling of cellular assemblies.

机构信息

Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.

Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States.

出版信息

Curr Opin Struct Biol. 2017 Oct;46:102-109. doi: 10.1016/j.sbi.2017.07.001. Epub 2017 Jul 20.

Abstract

A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively. We highlight general concepts in integrative modelling and discuss the need for careful formulation and merging of different types of information.

摘要

可采用多种实验技术来了解细胞组装活动背后的精确分子机制。单一实验技术的固有局限性通常需要整合来自互补方法的数据,以充分了解组装结构和功能。在这里,我们综述了用于细胞组装(包括蛋白质复合物和基因组组装)综合建模的流行计算方法。我们提供了不同实验技术分别为这些组装体生成的综合模型的最新实例,特别是包括来自 3 维电子显微镜(3D-EM)和染色体构象捕获实验的数据。我们强调了综合建模中的一般概念,并讨论了仔细构建和合并不同类型信息的必要性。

相似文献

1
Integrative modelling of cellular assemblies.
Curr Opin Struct Biol. 2017 Oct;46:102-109. doi: 10.1016/j.sbi.2017.07.001. Epub 2017 Jul 20.
2
Integrative Mass Spectrometry-Based Approaches for Modeling Macromolecular Assemblies.
Methods Mol Biol. 2021;2247:221-241. doi: 10.1007/978-1-0716-1126-5_12.
3
Modelling structures in cryo-EM maps.
Curr Opin Struct Biol. 2019 Oct;58:105-114. doi: 10.1016/j.sbi.2019.05.024. Epub 2019 Aug 5.
4
Integrative Structure Modeling: Overview and Assessment.
Annu Rev Biochem. 2019 Jun 20;88:113-135. doi: 10.1146/annurev-biochem-013118-111429. Epub 2019 Mar 4.
5
Role of integrative structural biology in understanding transcriptional initiation.
Methods. 2019 Apr 15;159-160:4-22. doi: 10.1016/j.ymeth.2019.03.009. Epub 2019 Mar 16.
6
ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.
PLoS One. 2012;7(12):e49733. doi: 10.1371/journal.pone.0049733. Epub 2012 Dec 14.
7
Single-particle cryo-electron microscopy of macromolecular complexes.
Microscopy (Oxf). 2016 Feb;65(1):9-22. doi: 10.1093/jmicro/dfv366. Epub 2015 Nov 25.
8
Finding the right fit: chiseling structures out of cryo-electron microscopy maps.
Curr Opin Struct Biol. 2014 Apr;25:118-25. doi: 10.1016/j.sbi.2014.04.001. Epub 2014 May 9.
9
Conformational States of macromolecular assemblies explored by integrative structure calculation.
Structure. 2013 Sep 3;21(9):1500-8. doi: 10.1016/j.str.2013.08.006.
10
Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.
Biophys J. 2016 Feb 23;110(4):785-97. doi: 10.1016/j.bpj.2015.12.038. Epub 2016 Feb 1.

引用本文的文献

1
Challenges of Protein-Protein Docking of the Membrane Proteins.
Methods Mol Biol. 2024;2780:203-255. doi: 10.1007/978-1-0716-3985-6_12.
2
Molecular insights into LINC complex architecture through the crystal structure of a luminal trimeric coiled-coil domain of SUN1.
Front Cell Dev Biol. 2023 Jun 21;11:1144277. doi: 10.3389/fcell.2023.1144277. eCollection 2023.
3
New system for archiving integrative structures.
Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1486-1496. doi: 10.1107/S2059798321010871. Epub 2021 Nov 29.
4
Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.
Front Chem. 2021 Mar 11;9:603639. doi: 10.3389/fchem.2021.603639. eCollection 2021.
6
Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.
Methods Mol Biol. 2021;2215:189-223. doi: 10.1007/978-1-0716-0966-8_9.
7
State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.
Prog Biophys Mol Biol. 2021 Mar;160:104-120. doi: 10.1016/j.pbiomolbio.2020.08.006. Epub 2020 Aug 28.
8
Archiving and disseminating integrative structure models.
J Biomol NMR. 2019 Jul;73(6-7):385-398. doi: 10.1007/s10858-019-00264-2. Epub 2019 Jul 5.
9
Computational approaches to macromolecular interactions in the cell.
Curr Opin Struct Biol. 2019 Apr;55:59-65. doi: 10.1016/j.sbi.2019.03.012. Epub 2019 Apr 15.
10
Advances in coarse-grained modeling of macromolecular complexes.
Curr Opin Struct Biol. 2018 Oct;52:119-126. doi: 10.1016/j.sbi.2018.11.005. Epub 2018 Nov 30.

本文引用的文献

1
3D structures of individual mammalian genomes studied by single-cell Hi-C.
Nature. 2017 Apr 6;544(7648):59-64. doi: 10.1038/nature21429. Epub 2017 Mar 13.
2
Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.
Nat Commun. 2017 Mar 8;8:14665. doi: 10.1038/ncomms14665.
3
Comprehensive characterization of neutrophil genome topology.
Genes Dev. 2017 Jan 15;31(2):141-153. doi: 10.1101/gad.293910.116. Epub 2017 Feb 6.
4
Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1560-1565. doi: 10.1073/pnas.1615310114. Epub 2017 Jan 31.
5
Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.
Genome Biol. 2017 Jan 30;18(1):21. doi: 10.1186/s13059-016-1146-2.
6
Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data.
PLoS Comput Biol. 2016 Dec 27;12(12):e1005292. doi: 10.1371/journal.pcbi.1005292. eCollection 2016 Dec.
7
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo.
Cell Rep. 2016 Nov 15;17(8):2125-2136. doi: 10.1016/j.celrep.2016.10.060.
8
The diverse and expanding role of mass spectrometry in structural and molecular biology.
EMBO J. 2016 Dec 15;35(24):2634-2657. doi: 10.15252/embj.201694818. Epub 2016 Oct 26.
9
Structure of the bacterial plant-ferredoxin receptor FusA.
Nat Commun. 2016 Oct 31;7:13308. doi: 10.1038/ncomms13308.

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