Literature DB >> 33312102

Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures.

Tzanko Doukov1, Daniel Herschlag2,3,4, Filip Yabukarski2.   

Abstract

Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage. © International Union of Crystallography 2020.

Entities:  

Keywords:  X-ray crystallography; data collection methods; physiological temperature; protein crystals; room temperature

Year:  2020        PMID: 33312102      PMCID: PMC7710493          DOI: 10.1107/S1600576720013503

Source DB:  PubMed          Journal:  J Appl Crystallogr        ISSN: 0021-8898            Impact factor:   3.304


  64 in total

1.  Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions.

Authors:  D H Juers; B W Matthews
Journal:  J Mol Biol       Date:  2001-08-24       Impact factor: 5.469

2.  The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water.

Authors:  I V Kurinov; R W Harrison
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1995-01-01

3.  Quantifying instrument errors in macromolecular X-ray data sets.

Authors:  Kay Diederichs
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-05-15

4.  Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Authors:  P Therese Lang; Ho-Leung Ng; James S Fraser; Jacob E Corn; Nathaniel Echols; Mark Sales; James M Holton; Tom Alber
Journal:  Protein Sci       Date:  2010-07       Impact factor: 6.725

Review 5.  Cryocooling and radiation damage in macromolecular crystallography.

Authors:  Elspeth F Garman; Robin Leslie Owen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

6.  The PILATUS 1M detector.

Authors:  Ch Broennimann; E F Eikenberry; B Henrich; R Horisberger; G Huelsen; E Pohl; B Schmitt; C Schulze-Briese; M Suzuki; T Tomizaki; H Toyokawa; A Wagner
Journal:  J Synchrotron Radiat       Date:  2006-02-17       Impact factor: 2.616

7.  Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE.

Authors:  Karthik S Paithankar; Robin Leslie Owen; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2009-02-25       Impact factor: 2.616

Review 8.  The coming of age of de novo protein design.

Authors:  Po-Ssu Huang; Scott E Boyken; David Baker
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

9.  Radiation damage in macromolecular crystallography: what is it and why should we care?

Authors:  Elspeth F Garman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

10.  Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography.

Authors:  Robert J Southworth-Davies; Melissa A Medina; Ian Carmichael; Elspeth F Garman
Journal:  Structure       Date:  2007-12       Impact factor: 5.006

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  4 in total

Review 1.  High throughput and quantitative enzymology in the genomic era.

Authors:  D A Mokhtari; M J Appel; P M Fordyce; D Herschlag
Journal:  Curr Opin Struct Biol       Date:  2021-09-27       Impact factor: 6.809

2.  Native SAD phasing at room temperature.

Authors:  Jack B Greisman; Kevin M Dalton; Candice J Sheehan; Margaret A Klureza; Igor Kurinov; Doeke R Hekstra
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-27       Impact factor: 5.699

3.  Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.

Authors:  Filip Yabukarski; Tzanko Doukov; Daniel A Mokhtari; Siyuan Du; Daniel Herschlag
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-14       Impact factor: 5.699

4.  Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography.

Authors:  Chia Ying Huang; Sylvain Aumonier; Sylvain Engilberge; Deniz Eris; Kate Mary Louise Smith; Filip Leonarski; Justyna Aleksandra Wojdyla; John H Beale; Dominik Buntschu; Anuschka Pauluhn; May Elizabeth Sharpe; Alexander Metz; Vincent Olieric; Meitian Wang
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-27       Impact factor: 5.699

  4 in total

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