Literature DB >> 29107896

CryoEM-based hybrid modeling approaches for structure determination.

C Keith Cassidy1, Benjamin A Himes2, Zaida Luthey-Schulten3, Peijun Zhang4.   

Abstract

Recent advances in cryo-electron microscopy (cryoEM) have dramatically improved the resolutions at which vitrified biological specimens can be studied, revealing new structural and mechanistic insights over a broad range of spatial scales. Bolstered by these advances, much effort has been directed toward the development of hybrid modeling methodologies for the construction and refinement of high-fidelity atomistic models from cryoEM data. In this brief review, we will survey the key elements of cryoEM-based hybrid modeling, providing an overview of available computational tools and strategies as well as several recent applications.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29107896      PMCID: PMC5934336          DOI: 10.1016/j.mib.2017.10.002

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  121 in total

1.  Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

Authors:  Juan Esquivel-Rodríguez; Daisuke Kihara
Journal:  J Phys Chem B       Date:  2012-03-30       Impact factor: 2.991

2.  NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.

Authors:  Karsten Suhre; Jorge Navaza; Yves Henri Sanejouand
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-08-19

3.  Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

Authors:  Gerrit Langer; Serge X Cohen; Victor S Lamzin; Anastassis Perrakis
Journal:  Nat Protoc       Date:  2008       Impact factor: 13.491

4.  Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.

Authors:  Elizabeth Villa; Jayati Sengupta; Leonardo G Trabuco; Jamie LeBarron; William T Baxter; Tanvir R Shaikh; Robert A Grassucci; Poul Nissen; Måns Ehrenberg; Klaus Schulten; Joachim Frank
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-02       Impact factor: 11.205

5.  iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.

Authors:  José Ramón Lopéz-Blanco; Pablo Chacón
Journal:  J Struct Biol       Date:  2013-08-30       Impact factor: 2.867

6.  Protein structure modeling with MODELLER.

Authors:  Benjamin Webb; Andrej Sali
Journal:  Methods Mol Biol       Date:  2014

7.  The joys and perils of flexible fitting.

Authors:  Niels Volkmann
Journal:  Adv Exp Med Biol       Date:  2014       Impact factor: 2.622

8.  Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.

Authors:  Alan Merk; Alberto Bartesaghi; Soojay Banerjee; Veronica Falconieri; Prashant Rao; Mindy I Davis; Rajan Pragani; Matthew B Boxer; Lesley A Earl; Jacqueline L S Milne; Sriram Subramaniam
Journal:  Cell       Date:  2016-05-26       Impact factor: 41.582

9.  The Protein Data Bank archive as an open data resource.

Authors:  Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
Journal:  J Comput Aided Mol Des       Date:  2014-07-26       Impact factor: 3.686

10.  High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

Authors:  Shaoxia Chen; Greg McMullan; Abdul R Faruqi; Garib N Murshudov; Judith M Short; Sjors H W Scheres; Richard Henderson
Journal:  Ultramicroscopy       Date:  2013-06-21       Impact factor: 2.689

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  7 in total

1.  CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles.

Authors:  Sylvain Träger; Giorgio Tamò; Deniz Aydin; Giulia Fonti; Martina Audagnotto; Matteo Dal Peraro
Journal:  Bioinformatics       Date:  2021-05-17       Impact factor: 6.937

2.  FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

Authors:  Johanna Ks Tiemann; Alexander S Rose; Jochen Ismer; Mitra D Darvish; Tarek Hilal; Christian Mt Spahn; Peter W Hildebrand
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

3.  In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States.

Authors:  Wen Yang; C Keith Cassidy; Peter Ames; Christoph A Diebolder; Klaus Schulten; Zaida Luthey-Schulten; John S Parkinson; Ariane Briegel
Journal:  mBio       Date:  2019-07-02       Impact factor: 7.867

Review 4.  Monomeric Intermediates Formed by Vesiculovirus Glycoprotein during Its Low-pH-induced Structural Transition.

Authors:  Abbas Abou-Hamdan; Laura Belot; Aurélie Albertini; Yves Gaudin
Journal:  J Mol Biol       Date:  2018-04-18       Impact factor: 5.469

Review 5.  Advances in cryo-electron tomography and subtomogram averaging and classification.

Authors:  Peijun Zhang
Journal:  Curr Opin Struct Biol       Date:  2019-07-05       Impact factor: 6.809

6.  Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain.

Authors:  Alister Burt; C Keith Cassidy; Peter Ames; Maria Bacia-Verloop; Megghane Baulard; Karine Huard; Zaida Luthey-Schulten; Ambroise Desfosses; Phillip J Stansfeld; William Margolin; John S Parkinson; Irina Gutsche
Journal:  Nat Commun       Date:  2020-02-06       Impact factor: 14.919

7.  Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations.

Authors:  C Keith Cassidy; Benjamin A Himes; Dapeng Sun; Jun Ma; Gongpu Zhao; John S Parkinson; Phillip J Stansfeld; Zaida Luthey-Schulten; Peijun Zhang
Journal:  Commun Biol       Date:  2020-01-10
  7 in total

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