Uridine as a new scavenger for synchrotron-based structural biology techniques

Crosas, Eva; Castellví, Albert; Fullà, Daniel; Gil-Ortiz, F.; Fuertes, Gustavo; Kamma-Lorger, Christina S.; Malfois, Marc; Aranda, Miguel Á. G.; Juanhuix, Jordi

doi:10.1107/s1600577516018452

Cited by 20 publications

(27 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… summarize all the results on scavengers for MX up to 2013, and to the authors knowledge, there have been no additional studies since then apart from that of Ref. on uridine as a radical scavenger for both MX and SAXS.…”

Section: Introductionmentioning

confidence: 97%

Estimate your dose: RADDOSE‐3D

Bury¹,

Brooks-Bartlett²,

Walsh³

et al. 2017

Protein Science

112

100

View full text Add to dashboard Cite

We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal "x-axis" against which to plot various metrics.

show abstract

Section: Introductionmentioning

confidence: 97%

Estimate your dose: RADDOSE‐3D

Bury¹,

Brooks-Bartlett²,

Walsh³

et al. 2017

Protein Science

112

100

View full text Add to dashboard Cite

show abstract

“…The limiting factor in microcrystallography is that the total usable diffraction from each crystal is limited by the dose limit that can be tolerated by the crystal (Owen et al, 2006). Although laboratory techniques exist to slightly improve the dose tolerance (see, for example, Crosas et al, 2017;Allan et al, 2013), serial crystallography from microcrystals is usually the method of choice for overcoming the dose limit of small crystals.…”

Section: Discussionmentioning

confidence: 99%

Using sound pulses to solve the crystal-harvesting bottleneck

Samara

Brennan

McCarthy

et al. 2018

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

show abstract

“…In a seminal paper, Blake and Phillips observed that the structure factors of some reflections from myoglobin crystals increased, while others decreased, leading them to suggest that specific structural damage to certain amino acids must be occurring (Blake & Philips, 1962), a hypothesis confirmed later for RT crystals (Helliwell, 1988). The occurrence of specific damage at RT remains controversial, however, with some reports showing evidence for disulfide damage (Southworth-Davies et al, 2007;Coquelle et al, 2015), while others do not (Roedig et al, 2016), including Crosas et al in this issue (Crosas et al, 2017). Despite increased radiation sensitivity, RT data collection is desirable because the modification of conformational heterogeneity within the crystalline protein that may occur during cryocooling is avoided, potentially providing physiologically more meaningful structures (Fraser et al, 2011).…”

Section: Radiation Damagementioning

confidence: 98%

“…In the literature to date, there are conflicting results on the efficacy of the same compounds, and no consensus has yet emerged as to their effectiveness. Tests of uridine, a previously untried scavenger, for synchrotron-based structural biology techniques (MX and SAXS) are reported in this issue (Crosas et al, 2017). At 1 M concentration, uridine was found to be effective in increasing the dose-to-half-intensity, D 1/2 , by a factor of 1.7 for RT MX data collection on chicken egg-white lysozyme crystals, but was found to be ineffective at cryotemperatures (100 K).…”

Section: Radiation Damagementioning

confidence: 99%

“…Another method to increase the dose tolerance of the sample is to add compounds such as ethylene glycol, glycerol, sodium ascorbate or sucrose to the SAXS sample (Kuwamoto et al, 2004;Grishaev, 2012). As well as testing uridine as a scavenger for MX, Crosas et al (2017) tested it in SAXS experiments on lysozyme solutions. They found that it prevented radiation induced aggregation and, at 40 mM concentration, was as effective as 5% glycerol.…”

Section: Radiation Damagementioning

confidence: 99%

See 1 more Smart Citation

X-ray radiation damage to biological macromolecules: further insights

Garman

Weik

2017

J Synchrotron Rad

View full text Add to dashboard Cite

Despite significant progress made over more than 15 years of research, structural biologists are still grappling with the issue of radiation damage suffered by macromolecular crystals which is induced by the resultant radiation chemistry occurring during X-ray diffraction experiments. Further insights into these effects and the possible mitigation strategies for use in both diffraction and SAXS experiments are given in eight papers in this volume. In particular, damage during experimental phasing is addressed, scavengers for SAXS experiments are investigated, microcrystals are imaged, data collection strategies are optimized, specific damage to tyrosine residues is reexamined, and room temperature conformational heterogeneity as a function of dose is explored. The brief summary below puts these papers into perspective relative to other ongoing radiation damage research on macromolecules. ISSN 1600-5775Keywords: X-ray radiation damage; macromolecular crystallography; SAXS; dose; imaging; scavengers. # 2017 International Union of CrystallographyThere have been concerted efforts over the last 15 years to understand the manifestations and origins of radiation damage suffered by protein crystals during macromolecular crystallography (MX) experiments, and to establish mitigation strategies using various approaches. These have gradually resulted in a deeper understanding of the physical, chemical and structural factors affecting damage rates, and there is a growing literature which seeks to elucidate the pertinent parameters (see for example the special issues of the Journal of Synchrotron Radiation arising from talks and posters given at the 2nd to 8th International Workshops on Radiation Damage to Biological Crystalline Samples, published in 2002Samples, published in , 2005Samples, published in , 2007Samples, published in , 2009Samples, published in , 2011Samples, published in , 2013Samples, published in and 2015. As the range and scope of the investigations have broadened, so has our appreciation of the complexities of radiation damage phenomena, although a full knowledge of all the processes involved has not yet been achieved. However, the need for this has become more pressing, with the advent of X-ray free-electron lasers (XFEL) and new fourth-generation synchrotron sources such as MAX IV in Lund and NSLS II at Brookhaven now coming on-line with even higher flux densities than hitherto utilized. The high rate of damage inflicted by these X-ray beams has brought the issue of radiation damage during structural biology experiments into even sharper focus. Thus an awareness of the effects of radiation damage both on diffraction and small-angle X-ray scattering (SAXS) data, and on the macromolecular structures derived from them, will become increasingly important.There are eight papers on various aspects of radiation damage in this special issue of the Journal of Synchrotron Radiation. The studies reported here on MX and SAXS experiments were presented at the 9th International Workshop on Radiation Damag...

show abstract

Uridine as a new scavenger for synchrotron-based structural biology techniques

Cited by 20 publications

References 60 publications

Estimate your dose: RADDOSE‐3D

Estimate your dose: RADDOSE‐3D

Using sound pulses to solve the crystal-harvesting bottleneck

X-ray radiation damage to biological macromolecules: further insights

Contact Info

Product

Resources

About