Literature DB >> 27139624

Transmission electron microscopy for the evaluation and optimization of crystal growth.

Hilary P Stevenson1, Guowu Lin1, Christopher O Barnes1, Ieva Sutkeviciute2, Troy Krzysiak1, Simon C Weiss1, Shelley Reynolds1, Ying Wu1, Veeranagu Nagarajan3, Alexander M Makhov1, Robert Lawrence4, Emily Lamm1, Lisa Clark1, Timothy J Gardella5, Brenda G Hogue4, Craig M Ogata6, Jinwoo Ahn1, Angela M Gronenborn1, James F Conway1, Jean Pierre Vilardaga2, Aina E Cohen7, Guillermo Calero1.   

Abstract

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

Entities:  

Keywords:  X-ray free-electron lasers; XFELs; crystal optimization; micro-electron diffraction; nanocrystallography; structural biology; transmission electron microscopy

Mesh:

Substances:

Year:  2016        PMID: 27139624      PMCID: PMC4854312          DOI: 10.1107/S2059798316001546

Source DB:  PubMed          Journal:  Acta Crystallogr D Struct Biol        ISSN: 2059-7983            Impact factor:   7.652


  41 in total

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Journal:  Methods Biochem Anal       Date:  1976

Review 2.  Post-crystallization treatments for improving diffraction quality of protein crystals.

Authors:  Begoña Heras; Jennifer L Martin
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-08-16

Review 3.  Nanobody stabilization of G protein-coupled receptor conformational states.

Authors:  Jan Steyaert; Brian K Kobilka
Journal:  Curr Opin Struct Biol       Date:  2011-07-21       Impact factor: 6.809

4.  A general path for large-scale solubilization of cellular proteins: from membrane receptors to multiprotein complexes.

Authors:  Filippo Pullara; Jennifer Guerrero-Santoro; Monica Calero; Qiangmin Zhang; Ye Peng; Henrik Spåhr; Guy L Kornberg; Antonella Cusimano; Hilary P Stevenson; Hugo Santamaria-Suarez; Shelley L Reynolds; Ian S Brown; Satdarshan P S Monga; Bennett Van Houten; Vesna Rapić-Otrin; Guillermo Calero; Arthur S Levine
Journal:  Protein Expr Purif       Date:  2012-11-05       Impact factor: 1.650

5.  Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent.

Authors:  M Blaber; W A Baase; N Gassner; B W Matthews
Journal:  J Mol Biol       Date:  1995-02-17       Impact factor: 5.469

6.  G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody.

Authors:  Tomoya Hino; Takatoshi Arakawa; Hiroko Iwanari; Takami Yurugi-Kobayashi; Chiyo Ikeda-Suno; Yoshiko Nakada-Nakura; Osamu Kusano-Arai; Simone Weyand; Tatsuro Shimamura; Norimichi Nomura; Alexander D Cameron; Takuya Kobayashi; Takao Hamakubo; So Iwata; Takeshi Murata
Journal:  Nature       Date:  2012-01-29       Impact factor: 49.962

7.  Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures.

Authors:  Mohamed Ibrahim; Ruchira Chatterjee; Julia Hellmich; Rosalie Tran; Martin Bommer; Vittal K Yachandra; Junko Yano; Jan Kern; Athina Zouni
Journal:  Struct Dyn       Date:  2015       Impact factor: 2.920

8.  NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity.

Authors:  In-Ja L Byeon; Jinwoo Ahn; Mithun Mitra; Chang-Hyeock Byeon; Kamil Hercík; Jozef Hritz; Lisa M Charlton; Judith G Levin; Angela M Gronenborn
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

9.  Some practical guidelines for UV imaging in the protein crystallization laboratory.

Authors:  Sebastien Desbois; Shane A Seabrook; Janet Newman
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-01-26

10.  Identifying, studying and making good use of macromolecular crystals.

Authors:  Guillermo Calero; Aina E Cohen; Joseph R Luft; Janet Newman; Edward H Snell
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-07-25       Impact factor: 1.056

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  11 in total

1.  MicroED Sample Preparation and Data Collection For Protein Crystals.

Authors:  Guanhong Bu; Brent L Nannenga
Journal:  Methods Mol Biol       Date:  2021

2.  Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals.

Authors:  Guowu Lin; Simon C Weiss; Sandra Vergara; Carlos Camacho; Guillermo Calero
Journal:  Methods       Date:  2019-04-25       Impact factor: 3.608

Review 3.  The cryo-EM method microcrystal electron diffraction (MicroED).

Authors:  Brent L Nannenga; Tamir Gonen
Journal:  Nat Methods       Date:  2019-04-29       Impact factor: 28.547

Review 4.  The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals.

Authors:  Nadia A Zatsepin; Chufeng Li; Paige Colasurd; Brent L Nannenga
Journal:  Curr Opin Struct Biol       Date:  2019-07-22       Impact factor: 6.809

Review 5.  Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography.

Authors:  Christopher O Barnes; Elena G Kovaleva; Xiaofeng Fu; Hilary P Stevenson; Aaron S Brewster; Daniel P DePonte; Elizabeth L Baxter; Aina E Cohen; Guillermo Calero
Journal:  Arch Biochem Biophys       Date:  2016-03-02       Impact factor: 4.013

6.  MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

Authors:  Sandra Vergara; Dylan A Lukes; Michael W Martynowycz; Ulises Santiago; Germán Plascencia-Villa; Simon C Weiss; M Jason de la Cruz; David M Black; Marcos M Alvarez; Xochitl López-Lozano; Christopher O Barnes; Guowu Lin; Hans-Christian Weissker; Robert L Whetten; Tamir Gonen; Miguel Jose Yacaman; Guillermo Calero
Journal:  J Phys Chem Lett       Date:  2017-10-31       Impact factor: 6.475

7.  Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

Authors:  M T B Clabbers; E van Genderen; W Wan; E L Wiegers; T Gruene; J P Abrahams
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-08-15       Impact factor: 7.652

8.  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

9.  The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.

Authors:  Christopher O Barnes; Ying Wu; Jinhu Song; Guowu Lin; Elizabeth L Baxter; Aaron S Brewster; V Nagarajan; Andrew Holmes; S Michael Soltis; Nicholas K Sauter; Jinwoo Ahn; Aina E Cohen; Guillermo Calero
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-24       Impact factor: 11.205

10.  MicroED: a versatile cryoEM method for structure determination.

Authors:  Brent L Nannenga; Tamir Gonen
Journal:  Emerg Top Life Sci       Date:  2018-02-06
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