Small-Angle Neutron Scattering from Biological Molecules

Krueger, Joanna K.; Wignall, G. D.

doi:10.1007/3-540-29111-3_8

Cited by 6 publications

(4 citation statements)

References 93 publications

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“…Interestingly, we do not observe any hint of Bessel-like oscillations in the form factor, a typical characteristic of hard sphere colloids. 30 Rather, the form factor (the scattered intensity I(q) at the lowest concentration) is a smoothly decreasing function of q and is well fit by the Debye model for Gaussian polymer chain (dashed line in Figure 2), with a form factor…”

Section: Sansmentioning

confidence: 74%

Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder

et al. 2022

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The in-cell environment is crowded with macromolecules, and the consequent reduction in free volume, based on the hard-sphere paradigm, is central to understanding macromolecular motions. A much-used model crowder, Ficoll, often assumed to be a compact, if not rigid, colloidal particle, is studied by rheology, small-angle neutron scattering, nuclear magnetic resonance diffusometry, and relaxometry. We find that the Ficoll suspension viscosity scales linearly with concentration c F in the dilute limit and as at high c F, i.e, consistent with the 15/4 (de Gennes) scaling for a reptating polymer. The form factor of Ficoll, obtained via small-angle neutron scattering (SANS), resembles either a Gaussian polymer or a soft polymer blob. From NMR diffusion measurements, we obtain an effective volume fraction for Ficoll that accounts for Ficoll-bound water in two ways and show that each results in a volume occupancy of 60% to 70% in the crowding limit, much larger than the traditionally reported values of around 30%. If we persist with the colloid paradigm and examine the dependence of the zero-q structure factor obtained via SANS in terms of this effective volume fraction, we find that only a combination of particle softness and interparticle attractions, quantified using a computational model, can replicate the experimental S(0). The stark difference between effective and traditional volume occupancies affects the interpretation of previous experiments on macromolecular crowding and might explain the intriguing non-monotonicity observed in the dependence of protein relaxation rates on crowder concentration.

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Section: Sansmentioning

confidence: 74%

Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder

et al. 2022

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“…As a result, neutrons scattered from 1 H are 180° out of phase with scattered neutrons from 2 H and the other biological elements. As the neutron contrast in a SANS experiment is simply the difference between the summed coherent scattering lengths per unit volume of a macromolecule compared to that of the solvent – i.e., the difference in average neutron scattering length density – and because the scattering length from 1 H is negative, the Δ ρ can be manipulated by simply substituting 1 H for 2 H in the solvent, macromolecule, or both47.…”

Section: Introductionmentioning

confidence: 99%

Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments

et al. 2016

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Small-angle X-ray and neutron scattering (SAXS and SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume including the solvent and buffer components as well as the macromolecules of interest. In order to obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis so it is essential that the samples are pure and monodisperse for the duration of the experiment. This Protocol outlines the basic physics of SAXS and SANS and reveals how the underlying conceptual principles of the techniques ultimately 'translate' into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size exclusion chromatography and light scattering. Also included are procedures specific to X-rays (in-line size exclusion chromatography SAXS) and neutrons, specifically preparing samples for contrast matching/variation experiments and deuterium labeling of proteins. * Primary corresponding author: cy.jeffries@embl-hamburg.de. Contributions.CMJ, MAG, CB, DBL, AEW and DIS helped develop SAXS and SANS sample preparation protocols and analytical tools. CMJ, MAG, CB, and DIS performed radiation damage studies and developed protocols for SEC-SAXS. CMJ, AEW and DBL contributed to 'in house' 2 H-labelling protocols. DBL, AEW, CMJ and DIS optimised protocols for preparing samples for SANS with contrast variation. AEW developed Contrast. CMJ, MAG, CB, DBL, AEW and DIS critically discussed and wrote the manuscript.

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“…This has If we were able to use a solvent with n ¼ 1.55, the plastic would have been matched out completely. Based upon the original demonstration by Don Engelman (Kreuger & Wignal 2006).…”

Section: Neutron Reflection In Biologymentioning

confidence: 99%

Neutrons for biologists: a beginner's guide, or why you should consider using neutrons

Lakey

2009

J. R. Soc. Interface.

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From the structures of isolated protein complexes to the molecular dynamics of whole cells, neutron methods can achieve a resolution in complex systems that is inaccessible to other techniques. Biology is fortunate in that it is rich in water and hydrogen, and this allows us to exploit the differential sensitivity of neutrons to this element and its major isotope, deuterium. Furthermore, neutrons exhibit wave properties that allow us to use them in similar ways to light, X-rays and electrons. This review aims to explain the basics of biological neutron science to encourage its greater use in solving difficult problems in the life sciences.

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Small-Angle Neutron Scattering from Biological Molecules

Cited by 6 publications

References 93 publications

Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder

Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder

Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments

Neutrons for biologists: a beginner's guide, or why you should consider using neutrons

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