Literature DB >> 27673321

While the revolution will not be crystallized, biochemistry reigns supreme.

Yoshimasa Takizawa1,2, Elad Binshtein1,2, Amanda L Erwin1,2, Tasia M Pyburn1,2, Kathleen F Mittendorf3, Melanie D Ohi1,2.   

Abstract

Single-particle cryo-electron microscopy (EM) is currently gaining attention for the ability to calculate structures that reach sub-5 Å resolutions; however, the technique is more than just an alternative approach to X-ray crystallography. Molecular machines work via dynamic conformational changes, making structural flexibility the hallmark of function. While the dynamic regions in molecules are essential, they are also the most challenging to structurally characterize. Single-particle EM has the distinct advantage of being able to directly visualize purified molecules without the formation of ordered arrays of molecules locked into identical conformations. Additionally, structures determined using single-particle EM can span resolution ranges from very low- to atomic-levels (>30-1.8 Å), sometimes even in the same structure. The ability to accommodate various resolutions gives single-particle EM the unique capacity to structurally characterize dynamic regions of biological molecules, thereby contributing essential structural information needed for the development of molecular models that explain function. Further, many important molecular machines are intrinsically dynamic and compositionally heterogeneous. Structures of these complexes may never reach sub-5 Å resolutions due to this flexibility required for function. Thus, the biochemical quality of the sample, as well as, the calculation and interpretation of low- to mid-resolution cryo-EM structures (30-8 Å) remains critical for generating insights into the architecture of many challenging biological samples that cannot be visualized using alternative techniques.
© 2016 The Protein Society.

Keywords:  biochemistry; cryo-electron microscopy; negative stain; spliceosomes

Mesh:

Year:  2016        PMID: 27673321      PMCID: PMC5192976          DOI: 10.1002/pro.3054

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  125 in total

1.  Possibilities of subunit localization with fluorescent protein tags and electron microscopy examplified by a cyanobacterial NDH-1 study.

Authors:  Mariam Birungi; Mihaela Folea; Natalia Battchikova; Min Xu; Hualing Mi; Teruo Ogawa; Eva-Mari Aro; Egbert J Boekema
Journal:  Biochim Biophys Acta       Date:  2010-06-12

2.  The revolution will not be crystallized: a new method sweeps through structural biology.

Authors:  Ewen Callaway
Journal:  Nature       Date:  2015-09-10       Impact factor: 49.962

3.  FREALIGN: high-resolution refinement of single particle structures.

Authors:  Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2006-06-02       Impact factor: 2.867

4.  Structure of integrin alpha5beta1 in complex with fibronectin.

Authors:  Junichi Takagi; Konstantin Strokovich; Timothy A Springer; Thomas Walz
Journal:  EMBO J       Date:  2003-09-15       Impact factor: 11.598

5.  Molecular architecture of the human U4/U6.U5 tri-snRNP.

Authors:  Dmitry E Agafonov; Berthold Kastner; Olexandr Dybkov; Romina V Hofele; Wen-Ti Liu; Henning Urlaub; Reinhard Lührmann; Holger Stark
Journal:  Science       Date:  2016-02-18       Impact factor: 47.728

6.  Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.

Authors:  Doreen Matthies; Olivier Dalmas; Mario J Borgnia; Pawel K Dominik; Alan Merk; Prashant Rao; Bharat G Reddy; Shahidul Islam; Alberto Bartesaghi; Eduardo Perozo; Sriram Subramaniam
Journal:  Cell       Date:  2016-02-11       Impact factor: 41.582

7.  Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.

Authors:  Qiu Wang; Tsutomu Matsui; Tatiana Domitrovic; Yili Zheng; Peter C Doerschuk; John E Johnson
Journal:  J Struct Biol       Date:  2012-12-12       Impact factor: 2.867

Review 8.  Overview and future of single particle electron cryomicroscopy.

Authors:  Richard Henderson
Journal:  Arch Biochem Biophys       Date:  2015-03-18       Impact factor: 4.013

9.  Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.

Authors:  Zhen Yan; Xiaochen Bai; Chuangye Yan; Jianping Wu; Zhangqiang Li; Tian Xie; Wei Peng; Changcheng Yin; Xueming Li; Sjors H W Scheres; Yigong Shi; Nieng Yan
Journal:  Nature       Date:  2014-12-15       Impact factor: 49.962

10.  Localization and orientation of the gamma-tubulin small complex components using protein tags as labels for single particle EM.

Authors:  Rebeca M Choy; Justin M Kollman; Alex Zelter; Trisha N Davis; David A Agard
Journal:  J Struct Biol       Date:  2009-08-31       Impact factor: 2.867

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  11 in total

1.  Dissection of affinity captured LINE-1 macromolecular complexes.

Authors:  Martin S Taylor; Ilya Altukhov; Kelly R Molloy; Paolo Mita; Hua Jiang; Emily M Adney; Aleksandra Wudzinska; Sana Badri; Dmitry Ischenko; George Eng; Kathleen H Burns; David Fenyö; Brian T Chait; Dmitry Alexeev; Michael P Rout; Jef D Boeke; John LaCava
Journal:  Elife       Date:  2018-01-08       Impact factor: 8.140

Review 2.  Challenges and opportunities in cryo-EM single-particle analysis.

Authors:  Dmitry Lyumkis
Journal:  J Biol Chem       Date:  2019-02-25       Impact factor: 5.157

Review 3.  Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase.

Authors:  James Shorter; Daniel R Southworth
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-08-01       Impact factor: 10.005

Review 4.  Dawning of a new era in TRP channel structural biology by cryo-electron microscopy.

Authors:  M Gregor Madej; Christine M Ziegler
Journal:  Pflugers Arch       Date:  2018-01-17       Impact factor: 3.657

5.  Structural and functional analyses of the spliceosome requires a multi-disciplinary approach.

Authors:  Melanie D Ohi
Journal:  Methods       Date:  2017-08-01       Impact factor: 3.608

Review 6.  Cryo-EM: beyond the microscope.

Authors:  Lesley A Earl; Veronica Falconieri; Jacqueline Ls Milne; Sriram Subramaniam
Journal:  Curr Opin Struct Biol       Date:  2017-06-21       Impact factor: 6.809

7.  Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.

Authors:  Paul Dominic B Olinares; Jin Young Kang; Eliza Llewellyn; Courtney Chiu; James Chen; Brandon Malone; Ruth M Saecker; Elizabeth A Campbell; Seth A Darst; Brian T Chait
Journal:  Structure       Date:  2020-11-19       Impact factor: 5.006

Review 8.  Role of integrative structural biology in understanding transcriptional initiation.

Authors:  Michael J Trnka; Riccardo Pellarin; Philip J Robinson
Journal:  Methods       Date:  2019-03-16       Impact factor: 3.608

9.  The central role of the tail in switching off 10S myosin II activity.

Authors:  Shixin Yang; Kyoung Hwan Lee; John L Woodhead; Osamu Sato; Mitsuo Ikebe; Roger Craig
Journal:  J Gen Physiol       Date:  2019-08-06       Impact factor: 4.086

10.  Methods for merging data sets in electron cryo-microscopy.

Authors:  Max E Wilkinson; Ananthanarayanan Kumar; Ana Casañal
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-08-23       Impact factor: 7.652

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