5kuz › Citations

Conformational variation of proteins at room temperature is not dominated by radiation damage.

Figure 1
Figure 2
Figure 3
Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H
OpenAccess logo J Synchrotron Radiat 24 73-82 (2017)

Cited: 27 times
EuropePMC logo PMID: 28009548

Abstract

Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 107 Gy at 100 K and 105 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

Articles - 5kuz mentioned but not cited (1)

  1. Proline/arginine dipeptide repeat polymers derail protein folding in amyotrophic lateral sclerosis. Babu M, Favretto F, de Opakua AI, Rankovic M, Becker S, Zweckstetter M. Nat Commun 12 3396 (2021)


Reviews citing this publication (2)

  1. Atomic displacement parameters in structural biology. Carugo O. Amino Acids 50 775-786 (2018)
  2. SARS-CoV-2 proteins structural studies using synchrotron radiation. Kosenko M, Onkhonova G, Susloparov I, Ryzhikov A. Biophys Rev 15 1185-1194 (2023)

Articles citing this publication (24)

  1. Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. de la Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I, Garman EF, Burghammer M, Colletier JP, Weik M. Proc Natl Acad Sci U S A 117 4142-4151 (2020)
  2. Specific radiation damage is a lesser concern at room temperature. Gotthard G, Aumonier S, De Sanctis D, Leonard G, von Stetten D, Royant A. IUCrJ 6 665-680 (2019)
  3. Foot-and-mouth disease virus nonstructural protein 2B interacts with cyclophilin A, modulating virus replication. Liu H, Xue Q, Cao W, Yang F, Ma L, Liu W, Zhang K, Liu X, Zhu Z, Zheng H. FASEB J fj201701351 (2018)
  4. X-ray radiation damage to biological macromolecules: further insights. Garman EF, Weik M. J Synchrotron Radiat 24 1-6 (2017)
  5. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. Protein Sci 30 270-285 (2021)
  6. FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II. Schneider DK, Shi W, Andi B, Jakoncic J, Gao Y, Bhogadi DK, Myers SF, Martins B, Skinner JM, Aishima J, Qian K, Bernstein HJ, Lazo EO, Langdon T, Lara J, Shea-McCarthy G, Idir M, Huang L, Chubar O, Sweet RM, Berman LE, McSweeney S, Fuchs MR. J Synchrotron Radiat 28 650-665 (2021)
  7. Temperature artifacts in protein structures bias ligand-binding predictions. Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Chem Sci 12 11275-11293 (2021)
  8. Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. Doukov T, Herschlag D, Yabukarski F. J Appl Crystallogr 53 1493-1501 (2020)
  9. Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. Yabukarski F, Doukov T, Mokhtari DA, Du S, Herschlag D. Acta Crystallogr D Struct Biol 78 945-963 (2022)
  10. Multimodal Non-Contact Luminescence Thermometry with Cr-Doped Oxides. Mykhaylyk VB, Kraus H, Zhydachevskyy Y, Tsiumra V, Luchechko A, Wagner A, Suchocki A. Sensors (Basel) 20 E5259 (2020)
  11. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. van den Bedem H, Wilson MA. J Synchrotron Radiat 26 958-966 (2019)
  12. Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Huang CY, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, Wojdyla JA, Beale JH, Buntschu D, Pauluhn A, Sharpe ME, Metz A, Olieric V, Wang M. Acta Crystallogr D Struct Biol 78 964-974 (2022)
  13. Quantifying and comparing radiation damage in the Protein Data Bank. Shelley KL, Garman EF. Nat Commun 13 1314 (2022)
  14. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. Stachowski TR, Snell ME, Snell EH. PLoS One 15 e0239702 (2020)
  15. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Šrajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA. IUCrJ 9 610-624 (2022)
  16. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. IUCrJ 9 756-767 (2022)
  17. Torsion angles to map and visualize the conformational space of a protein. Ginn HM. Protein Sci 32 e4608 (2023)
  18. An automated platform for structural analysis of membrane proteins through serial crystallography. Healey RD, Basu S, Humm AS, Leyrat C, Cong X, Golebiowski J, Dupeux F, Pica A, Granier S, Márquez JA. Cell Rep Methods 1 None (2021)
  19. FLEXR: automated multi-conformer model building using electron-density map sampling. Stachowski TR, Fischer M. Acta Crystallogr D Struct Biol 79 354-367 (2023)
  20. Megahertz non-contact luminescence decay time cryothermometry by means of ultrafast PbI2 scintillator. Mykhaylyk VB, Kraus H, Bobb L, Gamernyk R, Koronski K. Sci Rep 9 5274 (2019)
  21. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. Stachowski TR, Snell ME, Snell EH. J Synchrotron Radiat 28 1309-1320 (2021)
  22. Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations. Nagai T, Tama F, Miyashita O. Biophys J 116 395-405 (2019)
  23. Microfluidic rotating-target device capable of three-degrees-of-freedom motion for efficient in situ serial synchrotron crystallography. Zhao FZ, Wang ZJ, Xiao QJ, Yu L, Sun B, Hou Q, Chen LL, Liang H, Wu H, Guo WH, He JH, Wang QS, Yin DC. J Synchrotron Radiat 30 347-358 (2023)
  24. Protein structural changes on a CubeSat under rocket acceleration profile. Luna A, Meisel J, Hsu K, Russi S, Fernandez D. NPJ Microgravity 6 12 (2020)


Quick links