Literature DB >> 28735107

Integrative modelling of cellular assemblies.

Agnel Praveen Joseph1, Guido Polles2, Frank Alber3, Maya Topf4.   

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.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28735107      PMCID: PMC5683902          DOI: 10.1016/j.sbi.2017.07.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  77 in total

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Authors:  Jill Trewhella
Journal:  Curr Opin Struct Biol       Date:  2016-05-30       Impact factor: 6.809

2.  Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

Authors:  Harianto Tjong; Wenyuan Li; Reza Kalhor; Chao Dai; Shengli Hao; Ke Gong; Yonggang Zhou; Haochen Li; Xianghong Jasmine Zhou; Mark A Le Gros; Carolyn A Larabell; Lin Chen; Frank Alber
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-07       Impact factor: 11.205

Review 3.  Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?

Authors:  Martin Beck; Wolfgang Baumeister
Journal:  Trends Cell Biol       Date:  2016-09-23       Impact factor: 20.808

4.  PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

Authors:  Guray Kuzu; Ozlem Keskin; Ruth Nussinov; Attila Gursoy
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-09-20       Impact factor: 7.652

5.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

6.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

Review 7.  Use of electron paramagnetic resonance to solve biochemical problems.

Authors:  Indra D Sahu; Robert M McCarrick; Gary A Lorigan
Journal:  Biochemistry       Date:  2013-08-20       Impact factor: 3.162

8.  Formation of Chromosomal Domains by Loop Extrusion.

Authors:  Geoffrey Fudenberg; Maxim Imakaev; Carolyn Lu; Anton Goloborodko; Nezar Abdennur; Leonid A Mirny
Journal:  Cell Rep       Date:  2016-05-19       Impact factor: 9.423

9.  Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.

Authors:  Chao Dai; Wenyuan Li; Harianto Tjong; Shengli Hao; Yonggang Zhou; Qingjiao Li; Lin Chen; Bing Zhu; Frank Alber; Xianghong Jasmine Zhou
Journal:  Nat Commun       Date:  2016-05-31       Impact factor: 14.919

10.  TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

Authors:  Irene Farabella; Daven Vasishtan; Agnel Praveen Joseph; Arun Prasad Pandurangan; Harpal Sahota; Maya Topf
Journal:  J Appl Crystallogr       Date:  2015-06-27       Impact factor: 3.304

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  9 in total

Review 1.  Advances in coarse-grained modeling of macromolecular complexes.

Authors:  Alexander J Pak; Gregory A Voth
Journal:  Curr Opin Struct Biol       Date:  2018-11-30       Impact factor: 6.809

Review 2.  Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.

Authors:  Tristan Cragnolini; Aaron Sweeney; Maya Topf
Journal:  Methods Mol Biol       Date:  2021

Review 3.  Computational approaches to macromolecular interactions in the cell.

Authors:  Ilya A Vakser; Eric J Deeds
Journal:  Curr Opin Struct Biol       Date:  2019-04-15       Impact factor: 6.809

4.  On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies.

Authors:  Matteo T Degiacomi
Journal:  J Am Soc Mass Spectrom       Date:  2018-05-07       Impact factor: 3.109

5.  Archiving and disseminating integrative structure models.

Authors:  Brinda Vallat; Benjamin Webb; John Westbrook; Andrej Sali; Helen M Berman
Journal:  J Biomol NMR       Date:  2019-07-05       Impact factor: 2.835

6.  State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

Authors:  Yan Zhang; James Krieger; Karolina Mikulska-Ruminska; Burak Kaynak; Carlos Oscar S Sorzano; José-María Carazo; Jianhua Xing; Ivet Bahar
Journal:  Prog Biophys Mol Biol       Date:  2020-08-28       Impact factor: 3.667

7.  Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings.

Authors:  Caitlyn L McCafferty; David W Taylor; Edward M Marcotte
Journal:  Protein Sci       Date:  2021-04-09       Impact factor: 6.725

8.  New system for archiving integrative structures.

Authors:  Brinda Vallat; Benjamin Webb; Maryam Fayazi; Serban Voinea; Hongsuda Tangmunarunkit; Sai J Ganesan; Catherine L Lawson; John D Westbrook; Carl Kesselman; Andrej Sali; Helen M Berman
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-11-29       Impact factor: 7.652

Review 9.  Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.

Authors:  Rebecca Beveridge; Antonio N Calabrese
Journal:  Front Chem       Date:  2021-03-11       Impact factor: 5.221

  9 in total

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