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

Abstract

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.

Deconvoluting Structures of Component Plant Biopolymers Using Deuterium Labeled Brassica oleracea Stems

“…Based on the component biopolymers responsible for the structural features in the different Q -regions, the Q -resolved contrast matching solvents obtained were used to determine the extent of D/H substitution to the different component biopolymers. The concept of “ Q -dependence of scattering length density” has been reported in the literature on the structural study of E. coli , and a computational effort for a simpler system of protein in solution . A similar approach was applied in this study, and more details are provided in Supporting Information.…”

“…The concept of "Q-dependence of scattering length density" has been reported in the literature on the structural study of E. coli 50,51 and a computational effort for a simpler system of protein in solution. 52 A similar approach was applied in this study, and more details are provided in Supporting Information. With the scattering signal in the high-Q region (>0.07 Å −1 ) dominated by the cellulose microfibril structure, the contrast matched solvent for partially deuterated cellulose in the d-kale stem sample was measured to be ∼65.0 ± 2.5% D 2 O solvent (nSLD = (3.94 ± 0.17) × 10 −6 Å −2 ).…”