Literature DB >> 32735770

Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED.

Lan Zhu1, Guanhong Bu2, Liang Jing1, Dan Shi3, Ming-Yue Lee1, Tamir Gonen4, Wei Liu5, Brent L Nannenga6.   

Abstract

The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  GPCR; Proteinase K; additive phase conversion; cholesterol; cryo-electron microscopy (cryo-EM); lipase hydrolysis; lipidic cubic phase (LCP); membrane protein; microcrystal electron diffraction (MicroED); microcrystallography

Year:  2020        PMID: 32735770      PMCID: PMC7544639          DOI: 10.1016/j.str.2020.07.006

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  72 in total

1.  The cubicon method for concentrating membrane proteins in the cubic mesophase.

Authors:  Pikyee Ma; Dietmar Weichert; Luba A Aleksandrov; Timothy J Jensen; John R Riordan; Xiangyu Liu; Brian K Kobilka; Martin Caffrey
Journal:  Nat Protoc       Date:  2017-08-03       Impact factor: 13.491

Review 2.  Overview of Biochemical Assays in Lipidic Cubic Phase.

Authors:  Zhu Lan; Ming-Yue Lee; Eugene Chun; Bin Liu; Wei Liu
Journal:  Trends Biochem Sci       Date:  2018-09-19       Impact factor: 13.807

3.  The phase diagram of the monoolein/water system: metastability and equilibrium aspects.

Authors:  H Qiu; M Caffrey
Journal:  Biomaterials       Date:  2000-02       Impact factor: 12.479

Review 4.  Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Authors:  Benjamin Stauch; Vadim Cherezov
Journal:  Annu Rev Biophys       Date:  2018-03-15       Impact factor: 12.981

5.  Structural basis for allosteric regulation of GPCRs by sodium ions.

Authors:  Wei Liu; Eugene Chun; Aaron A Thompson; Pavel Chubukov; Fei Xu; Vsevolod Katritch; Gye Won Han; Christopher B Roth; Laura H Heitman; Adriaan P IJzerman; Vadim Cherezov; Raymond C Stevens
Journal:  Science       Date:  2012-07-13       Impact factor: 47.728

6.  Two polymorphic cholesterol monohydrate crystal structures form in macrophage culture models of atherosclerosis.

Authors:  Neta Varsano; Fabio Beghi; Nadav Elad; Eva Pereiro; Tali Dadosh; Iddo Pinkas; Ana J Perez-Berna; Xueting Jin; Howard S Kruth; Leslie Leiserowitz; Lia Addadi
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-02       Impact factor: 11.205

7.  A fast, simple and robust protocol for growing crystals in the lipidic cubic phase.

Authors:  Margaret Aherne; Joseph A Lyons; Martin Caffrey
Journal:  J Appl Crystallogr       Date:  2012-10-10       Impact factor: 3.304

8.  Recent developments in the CCP-EM software suite.

Authors:  Tom Burnley; Colin M Palmer; Martyn Winn
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-05-31       Impact factor: 7.652

9.  Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.

Authors:  M Jason de la Cruz; Johan Hattne; Dan Shi; Paul Seidler; Jose Rodriguez; Francis E Reyes; Michael R Sawaya; Duilio Cascio; Simon C Weiss; Sun Kyung Kim; Cynthia S Hinck; Andrew P Hinck; Guillermo Calero; David Eisenberg; Tamir Gonen
Journal:  Nat Methods       Date:  2017-02-13       Impact factor: 28.547

10.  Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.

Authors:  Meriem El Ghachi; Nicole Howe; Chia-Ying Huang; Vincent Olieric; Rangana Warshamanage; Thierry Touzé; Dietmar Weichert; Phillip J Stansfeld; Meitian Wang; Fred Kerff; Martin Caffrey
Journal:  Nat Commun       Date:  2018-03-14       Impact factor: 14.919

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  8 in total

1.  MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP.

Authors:  Michael W Martynowycz; Anna Shiriaeva; Xuanrui Ge; Johan Hattne; Brent L Nannenga; Vadim Cherezov; Tamir Gonen
Journal:  Proc Natl Acad Sci U S A       Date:  2021-09-07       Impact factor: 11.205

Review 2.  Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM.

Authors:  Sarah J Piper; Rachel M Johnson; Denise Wootten; Patrick M Sexton
Journal:  Chem Rev       Date:  2022-07-18       Impact factor: 72.087

Review 3.  Electron Diffraction of 3D Molecular Crystals.

Authors:  Ambarneil Saha; Shervin S Nia; José A Rodríguez
Journal:  Chem Rev       Date:  2022-08-15       Impact factor: 72.087

4.  Rapid Structural Analysis of a Synthetic Non-canonical Amino Acid by Microcrystal Electron Diffraction.

Authors:  Patrick R Gleason; Brent L Nannenga; Jeremy H Mills
Journal:  Front Mol Biosci       Date:  2021-01-08

Review 5.  Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics.

Authors:  Johannes Thoma; Björn M Burmann
Journal:  Int J Mol Sci       Date:  2020-12-23       Impact factor: 5.923

6.  MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography.

Authors:  Max T B Clabbers; Susannah Holmes; Timothy W Muusse; Parimala R Vajjhala; Sara J Thygesen; Alpeshkumar K Malde; Dominic J B Hunter; Tristan I Croll; Leonie Flueckiger; Jeffrey D Nanson; Md Habibur Rahaman; Andrew Aquila; Mark S Hunter; Mengning Liang; Chun Hong Yoon; Jingjing Zhao; Nadia A Zatsepin; Brian Abbey; Emma Sierecki; Yann Gambin; Katryn J Stacey; Connie Darmanin; Bostjan Kobe; Hongyi Xu; Thomas Ve
Journal:  Nat Commun       Date:  2021-05-10       Impact factor: 14.919

Review 7.  MicroED: conception, practice and future opportunities.

Authors:  Max T B Clabbers; Anna Shiriaeva; Tamir Gonen
Journal:  IUCrJ       Date:  2022-01-18       Impact factor: 4.769

8.  Studying membrane proteins with MicroED.

Authors:  Marc J Gallenito; Tamir Gonen
Journal:  Biochem Soc Trans       Date:  2022-02-28       Impact factor: 4.919

  8 in total

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