Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs

Krueger, Susan

doi:10.1016/j.sbi.2022.102375

Cited by 24 publications

(11 citation statements)

References 60 publications

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“…Preliminary evaluations. While SANS has the unique advantage of using deuterium substitution to achieve contrast variation in studies of complex, multi-component systems (for recent reviews, see Mahieu & Gabel, 2018;Trewhella, 2022;Krueger, 2022), neutron sources are orders of magnitude less intense than synchrotron sources. For example, the flux on the sample for the high-intensity D22 SANS instrument at the ILL is comparable to that achieved with benchtop X-ray sources.…”

Section: Sans Resultsmentioning

confidence: 99%

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Trewhella¹,

Vachette²,

Bierma³

et al. 2022

Acta Cryst Sect D Struct Biol

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Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å−1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å−1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å−1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

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Section: Sans Resultsmentioning

confidence: 99%

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Trewhella¹,

Vachette²,

Bierma³

et al. 2022

Acta Cryst Sect D Struct Biol

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“…1A used to predict the decay profile of the pyrene excimer. The parameters a i and t i are employed to calculate the average lifetime hti of the part of the monomer fluorescence decay reflecting PEF, which is used to calculate the average rate constant hki for PEF according to eqn (2), where t M is the lifetime of the pyrene monomer.…”

Section: Models Used In the Study Of Pyrene-labeled Macromoleculesmentioning

confidence: 99%

“…Scattering techniques such as static light (SLS), small angle X-ray (SAXS), and small angle neutron (SANS) scattering are essential for the characterization of macromolecular conformations in solution. [1][2][3][4][5][6][7][8][9][10][11] Scattering techniques operate by sensing minute differences in density between the solvent and the dissolved macromolecule, which can be analysed to generate the scattering intensity profile of the macromolecule as a function of the scattering vector. The appeal of scattering techniques stems in part from their ability to provide a direct measure of the dimension of the macromolecule from its radius of gyration (R G ), which can be obtained for any, preferably monodisperse, macromolecule by applying Guinier's law to the analysis of its scattering intensity profile.…”

Section: Introductionmentioning

confidence: 99%

Probing the inner local density of complex macromolecules by pyrene excimer formation

Little,

Patel,

Duhamel

2023

Phys. Chem. Chem. Phys.

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“…These techniques have been widely adopted by structural biologists to understand the sizes and shapes of proteins, nucleic acids, lipids and plant biomass in solution as well as their complex molecular assemblies (Jacrot, 1976;Timmins & Zaccai, 1988;Engelman & Moore, 1975). For neutrons, the contrast-variation method is a unique and fundamental tool for highlighting individual components in multicomponent systems (Engelman & Moore, 1975;Krueger, 2022), effectively separating the scattering from a multicomponent complex into contributions from its components through the use of hydrogen-deuterium substitution in the solute and/or the solvent. By tuning the contrast, i.e.…”

Section: Introductionmentioning

confidence: 99%

SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology

Hicks

Abraham

Leite

et al. 2023

Acta Cryst Sect D Struct Biol

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The contrast-variation method in small-angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ. By altering the ρ of the target solute and the solvent through judicious incorporation of deuterium, the scattering of desired solute features can be highlighted. Most contrast-variation methods focus on highlighting specific bulk solute elements, but not on how the scattering at specific scattering vectors q, which are associated with specific structural distances, changes with contrast. Indeed, many systems exhibit q-dependent contrast effects. Here, a method is presented for calculating both bulk contrast-match points and q-dependent contrast using 3D models with explicit solute and solvent atoms and SASSENA, an explicit-atom SANS calculator. The method calculates the bulk contrast-match points within 2.4% solvent D2O accuracy for test protein–nucleic acid and lipid nanodisc systems. The method incorporates a general model for the incorporation of deuterium at non-exchangeable sites that was derived by performing mass spectrometry on green fluorescent protein. The method also decomposes the scattering profile into its component parts and identifies structural features that change with contrast. The method is readily applicable to a variety of systems, will expand the understanding of q-dependent contrast matching and will aid in the optimization of next-generation neutron scattering experiments.

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Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs

Cited by 24 publications

References 60 publications

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Probing the inner local density of complex macromolecules by pyrene excimer formation

SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology

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