Literature DB >> 24872454

Use of transmission electron microscopy to identify nanocrystals of challenging protein targets.

Hilary P Stevenson1, Alexander M Makhov1, Monica Calero1, Andrea L Edwards2, Oliver B Zeldin3, Irimpan I Mathews4, Guowu Lin1, Christopher O Barnes1, Hugo Santamaria1, Ted M Ross5, S Michael Soltis4, Chaitan Khosla2, V Nagarajan6, James F Conway1, Aina E Cohen7, Guillermo Calero8.   

Abstract

The current practice for identifying crystal hits for X-ray crystallography relies on optical microscopy techniques that are limited to detecting crystals no smaller than 5 μm. Because of these limitations, nanometer-sized protein crystals cannot be distinguished from common amorphous precipitates, and therefore go unnoticed during screening. These crystals would be ideal candidates for further optimization or for femtosecond X-ray protein nanocrystallography. The latter technique offers the possibility to solve high-resolution structures using submicron crystals. Transmission electron microscopy (TEM) was used to visualize nanocrystals (NCs) found in crystallization drops that would classically not be considered as "hits." We found that protein NCs were readily detected in all samples tested, including multiprotein complexes and membrane proteins. NC quality was evaluated by TEM visualization of lattices, and diffraction quality was validated by experiments in an X-ray free electron laser.

Entities:  

Keywords:  crystal characterization; crystal optimization; femtosecond diffraction; nanocrystal detection; structural biology

Mesh:

Substances:

Year:  2014        PMID: 24872454      PMCID: PMC4060711          DOI: 10.1073/pnas.1400240111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  24 in total

1.  In vivo protein crystallization opens new routes in structural biology.

Authors:  Rudolf Koopmann; Karolina Cupelli; Lars Redecke; Karol Nass; Daniel P Deponte; Thomas A White; Francesco Stellato; Dirk Rehders; Mengning Liang; Jakob Andreasson; Andrew Aquila; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; Sébastien Boutet; John D Bozek; Carl Caleman; Nicola Coppola; Jan Davidsson; R Bruce Doak; Tomas Ekeberg; Sascha W Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Heinz Graafsma; Lars Gumprecht; Janos Hajdu; Christina Y Hampton; Andreas Hartmann; Robert Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; Mark S Hunter; Stephan Kassemeyer; Richard A Kirian; Lukas Lomb; Filipe R N C Maia; Nils Kimmel; Andrew V Martin; Marc Messerschmidt; Christian Reich; Daniel Rolles; Benedikt Rudek; Artem Rudenko; Ilme Schlichting; Joachim Schulz; M Marvin Seibert; Robert L Shoeman; Raymond G Sierra; Heike Soltau; Stephan Stern; Lothar Strüder; Nicusor Timneanu; Joachim Ullrich; Xiaoyu Wang; Georg Weidenspointner; Uwe Weierstall; Garth J Williams; Cornelia B Wunderer; Petra Fromme; John C H Spence; Thilo Stehle; Henry N Chapman; Christian Betzel; Michael Duszenko
Journal:  Nat Methods       Date:  2012-01-29       Impact factor: 28.547

2.  Characterization of precrystallization aggregation of canavalin by dynamic light scattering.

Authors:  W Kadima; A McPherson; M F Dunn; F A Jurnak
Journal:  Biophys J       Date:  1990-01       Impact factor: 4.033

3.  Imaging protein three-dimensional nanocrystals with cryo-EM.

Authors:  Igor Nederlof; Yao Wang Li; Marin van Heel; Jan Pieter Abrahams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-04-19

4.  Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Authors:  Jan Kern; Roberto Alonso-Mori; Rosalie Tran; Johan Hattne; Richard J Gildea; Nathaniel Echols; Carina Glöckner; Julia Hellmich; Hartawan Laksmono; Raymond G Sierra; Benedikt Lassalle-Kaiser; Sergey Koroidov; Alyssa Lampe; Guangye Han; Sheraz Gul; Dörte Difiore; Despina Milathianaki; Alan R Fry; Alan Miahnahri; Donald W Schafer; Marc Messerschmidt; M Marvin Seibert; Jason E Koglin; Dimosthenis Sokaras; Tsu-Chien Weng; Jonas Sellberg; Matthew J Latimer; Ralf W Grosse-Kunstleve; Petrus H Zwart; William E White; Pieter Glatzel; Paul D Adams; Michael J Bogan; Garth J Williams; Sébastien Boutet; Johannes Messinger; Athina Zouni; Nicholas K Sauter; Vittal K Yachandra; Uwe Bergmann; Junko Yano
Journal:  Science       Date:  2013-02-14       Impact factor: 47.728

5.  High-resolution protein structure determination by serial femtosecond crystallography.

Authors:  Sébastien Boutet; Lukas Lomb; Garth J Williams; Thomas R M Barends; Andrew Aquila; R Bruce Doak; Uwe Weierstall; Daniel P DePonte; Jan Steinbrener; Robert L Shoeman; Marc Messerschmidt; Anton Barty; Thomas A White; Stephan Kassemeyer; Richard A Kirian; M Marvin Seibert; Paul A Montanez; Chris Kenney; Ryan Herbst; Philip Hart; Jack Pines; Gunther Haller; Sol M Gruner; Hugh T Philipp; Mark W Tate; Marianne Hromalik; Lucas J Koerner; Niels van Bakel; John Morse; Wilfred Ghonsalves; David Arnlund; Michael J Bogan; Carl Caleman; Raimund Fromme; Christina Y Hampton; Mark S Hunter; Linda C Johansson; Gergely Katona; Christopher Kupitz; Mengning Liang; Andrew V Martin; Karol Nass; Lars Redecke; Francesco Stellato; Nicusor Timneanu; Dingjie Wang; Nadia A Zatsepin; Donald Schafer; James Defever; Richard Neutze; Petra Fromme; John C H Spence; Henry N Chapman; Ilme Schlichting
Journal:  Science       Date:  2012-05-31       Impact factor: 47.728

6.  Cloning, expression and two-step purification of recombinant His-tag enhanced green fluorescent protein over-expressed in Escherichia coli.

Authors:  W Dieryck; A M Noubhani; D Coulon; X Santarelli
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2003-03-25       Impact factor: 3.205

7.  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

8.  Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.

Authors:  Lars Redecke; Karol Nass; Daniel P DePonte; Thomas A White; Dirk Rehders; Anton Barty; Francesco Stellato; Mengning Liang; Thomas R M Barends; Sébastien Boutet; Garth J Williams; Marc Messerschmidt; M Marvin Seibert; Andrew Aquila; David Arnlund; Sasa Bajt; Torsten Barth; Michael J Bogan; Carl Caleman; Tzu-Chiao Chao; R Bruce Doak; Holger Fleckenstein; Matthias Frank; Raimund Fromme; Lorenzo Galli; Ingo Grotjohann; Mark S Hunter; Linda C Johansson; Stephan Kassemeyer; Gergely Katona; Richard A Kirian; Rudolf Koopmann; Chris Kupitz; Lukas Lomb; Andrew V Martin; Stefan Mogk; Richard Neutze; Robert L Shoeman; Jan Steinbrener; Nicusor Timneanu; Dingjie Wang; Uwe Weierstall; Nadia A Zatsepin; John C H Spence; Petra Fromme; Ilme Schlichting; Michael Duszenko; Christian Betzel; Henry N Chapman
Journal:  Science       Date:  2012-11-29       Impact factor: 47.728

9.  Three-dimensional electron crystallography of protein microcrystals.

Authors:  Dan Shi; Brent L Nannenga; Matthew G Iadanza; Tamir Gonen
Journal:  Elife       Date:  2013-11-19       Impact factor: 8.140

10.  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
View more
  23 in total

1.  Goniometer-based femtosecond crystallography with X-ray free electron lasers.

Authors:  Aina E Cohen; S Michael Soltis; Ana González; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Elizabeth L Baxter; Winnie Brehmer; Aaron S Brewster; Axel T Brunger; Guillermo Calero; Joseph F Chang; Matthieu Chollet; Paul Ehrensberger; Thomas L Eriksson; Yiping Feng; Johan Hattne; Britt Hedman; Michael Hollenbeck; James M Holton; Stephen Keable; Brian K Kobilka; Elena G Kovaleva; Andrew C Kruse; Henrik T Lemke; Guowu Lin; Artem Y Lyubimov; Aashish Manglik; Irimpan I Mathews; Scott E McPhillips; Silke Nelson; John W Peters; Nicholas K Sauter; Clyde A Smith; Jinhu Song; Hilary P Stevenson; Yingssu Tsai; Monarin Uervirojnangkoorn; Vladimir Vinetsky; Soichi Wakatsuki; William I Weis; Oleg A Zadvornyy; Oliver B Zeldin; Diling Zhu; Keith O Hodgson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-31       Impact factor: 11.205

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

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

3.  Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector.

Authors:  H P Stevenson; D P DePonte; A M Makhov; James F Conway; O B Zeldin; S Boutet; G Calero; A E Cohen
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

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

Authors:  Hilary P Stevenson; Guowu Lin; Christopher O Barnes; Ieva Sutkeviciute; Troy Krzysiak; Simon C Weiss; Shelley Reynolds; Ying Wu; Veeranagu Nagarajan; Alexander M Makhov; Robert Lawrence; Emily Lamm; Lisa Clark; Timothy J Gardella; Brenda G Hogue; Craig M Ogata; Jinwoo Ahn; Angela M Gronenborn; James F Conway; Jean Pierre Vilardaga; Aina E Cohen; Guillermo Calero
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-04-26       Impact factor: 7.652

5.  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 6.  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 7.  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 8.  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

Review 9.  Serial femtosecond crystallography: A revolution in structural biology.

Authors:  Jose M Martin-Garcia; Chelsie E Conrad; Jesse Coe; Shatabdi Roy-Chowdhury; Petra Fromme
Journal:  Arch Biochem Biophys       Date:  2016-04-30       Impact factor: 4.013

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

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

北京卡尤迪生物科技股份有限公司 © 2022-2023.