Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments.

Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced.

Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization.

Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.

Improved joint X-ray and neutron refinement procedure in Phenix.

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.

Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Šor higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.

Cellular dynamics as a marker of normal-to-cancer transition in human cells.

Normal-to-cancer (NTC) transition is known to be closely associated to cell´s biomechanical properties which are dependent on the dynamics of the intracellular medium. This study probes different human cancer cells (breast, prostate and lung), concomitantly to their healthy counterparts, aiming at characterising the dynamical profile of water in distinct cellular locations, for each type of cell, and how it changes between normal and cancer states. An increased plasticity of the cytomatrix is observed upon normal-to-malignant transformation, the lung carcinoma cells displaying the highest flexibility followed by prostate and breast cancers. Also, lung cells show a distinct behaviour relative to breast and prostate, with a higher influence from hydration water motions and localised fast rotations upon NTC transformation. Quasielastic neutron scattering techniques allowed to accurately distinguish the different dynamical processes taking place within these highly heterogeneous cellular systems. The results thus obtained suggest that intracellular water dynamics may be regarded as a specific reporter of the cellular conditions-either healthy or malignant.

Exploring the effects of high pressure on hydrogen bonding in pharmaceutical cocrystals: A systematic study of pyridine dicarboxylic acid systems using synchrotron and neutron diffraction.

Pharmaceutical cocrystals use common robust hydrogen bonding synthons to create novel materials with different physicochemical properties. In this systematic study of a series of cocrystals, we explore the effect of high pressure on one of these commonly used motifs, the acid-pyridine motif, to assess the commonality of behaviour under extreme conditions. We have surveyed five pyridine dicarboxylic acid systems using both synchrotron and neutron diffraction methods to elucidate the changes in structure. We observe that the hydrogen bonding in these systems compress at a similar rate despite the changes to the molecular make-up of the solids and that on compression the changes in structure are indicative that the layers move along the major slip planes in the structure. We have observed two phase transitions to new forms of the pyrazine:malonic acid system, one for each stoichiometric ratio. This study demonstrates that the combination of two complementary diffraction approaches is key to understanding polymorphic behaviour at high pressure.

Signature of functional enzyme dynamics in quasielastic neutron scattering spectra: The case of phosphoglycerate kinase.

We present an analysis of high-resolution quasi-elastic neutron scattering spectra of phosphoglycerate kinase which elucidates the influence of the enzymatic activity on the dynamics of the protein. We show that in the active state the inter-domain motions are amplified and the intra-domain asymptotic power-law relaxation ∝t-α is accelerated, with a reduced coefficient α. Employing an energy landscape picture of protein dynamics, this observation can be translated into a widening of the distribution of energy barriers separating conformational substates of the protein.

Site-specific relaxation of peptide bond planarity induced by electrically attracted proton/deuteron observed by neutron crystallography.

In structural biology, peptide bonds, fundamental linkages between hundreds of amino acids, of which a protein molecule is composed, have been commonly treated as a plane structure just as Linus Pauling et al. proposed. In this paper, a site-specific peptide bond relaxation mechanism by deuterons whose localization has been suggested by neutron crystallography is proposed. Such deuteron was observed as an arm of neutron scattering length density protruding from the carbonyl oxygen atoms in the main chain in the omit map drawn by neutron crystallography of human lysozyme. Our comprehensive study using x-ray and neutron diffraction and 15 N chemical shifts of individual amide nitrogen atoms within the same peptide bond strongly suggests the relaxation of the electronic resonance structure because of site-specific modulation by protons/deuterons localized on the electron orbital of the carbonyl oxygen. All experimental data used in this examination were obtained at room temperature, which is preferable for enzymatic activity. Such a close interaction between the electron resonance structure of a peptide bond and the exchangeable protons/deuterons well agreed with that observed in an intermediate state in an amide hydrolytic reaction simulated by the ab-initio calculation including water molecules.

Development of an automatic sample changer with variable temperature for small-angle neutron scattering at China Spallation Neutron Source.

A small-angle neutron scattering (SANS) instrument at the China Spallation Neutron Source (CSNS) is an operating instrument for studying structures and inhomogeneities with dimensions ranging from 1 to 100 nm. Preparing multiple samples at once and measuring them sequentially is a common approach in SANS experiments to reduce neutron beamline wastes and increase experimental efficiency. We present the development of an automatic sample changer for the SANS instrument, including system design, thermal simulation, optimization analysis, structure design details, and temperature control test results. It features a two-row construction that can hold 18 samples on each row. The controllable temperature range is -30 to 300 °C. Furthermore, neutron scattering experiments on SANS at CSNS proved that this instrument has good temperature control performance and low background. This automatic sample changer is optimized for usage at SANS and will be offered to other researchers through the user program.

Heterogeneous Aggregation of Humic Acids Studied by Small-Angle Neutron and X-ray Scattering.

Aggregation of humic acids (HAs) was studied by small-angle neutron and X-ray scattering techniques. The combination of these techniques enables us to examine the aggregation structures of HA particles. Two HAs with distinctive compositions were examined: a commercial HA (PAHA) and a HA extracted from deep sedimentary groundwater (HHA). While macroscopic coagulation tests showed that these HAs were stable in solutions except for HHA at pH < 6, small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) revealed that they formed aggregates with sizes exceeding the sub-micrometer length scale. The SAXS curves of PAHA remarkably varied with pD = log aD+, where aD+ stands for the activity of deuterium ions, whereas the SANS curves did not. With the help of theoretical fittings, it was revealed that PAHA aggregates consisted of two domains: poorly hydrated cores and well-hydrated proton-rich shells. The cores were (dis)aggregated with pD inside the aggregates of the shells. The SANS and SAXS curves of HHA resembled each other, and their intensities at low q, where q stands for the scattering vector, increased with a decrease of pD, indicating the formation of homogeneous aggregates within the spatial resolutions of SANS and SAXS. This study revealed that distinctive aggregation behaviors exist in humic substances with nm-scale heterogeneous structures like PAHA, which is important for their roles in the fate of contaminants or nutrients in aqueous environments.

Small Angle Neutron Scattering in Drug Discovery Research: A Novel Tool for Advanced Study of Structures of Biological Macromolecules.

Small Angle Neutron Scattering (SANS) is a powerful and novel tool for the study of soft condensed matter, including the microscopic and nanomaterials used for drug discovery and delivery. The sample is exposed to a neutron beam, and neutron scattering occurs, which is studied as a function of the scattering angle to deduce a variety of information about the dynamics and structure of the material. The technique is becoming very popular in biomedical research to investigate the various aspects of structural biology. The low-resolution information on large heterogeneous, solubilized biomacromolecular complexes in solution is obtained with the use of deuterium labelling and solvent contrast variation. The article reviews the basics of the SANS technique, its applications in drug delivery research, and its current status in biomedical research. The article covers and overviews the precise characterization of biological structures (membranes, vesicles, proteins in solution), mesoporous structures, colloids, and surfactants, as well as cyclodextrin complexes, lipid complexes, polymeric nanoparticles, etc., with the help of neutron scattering. SANS is continuously evolving as a medium for exploring the complex world of biomolecules, providing information regarding the structure, composition, and arrangement of various constituents. With improving modelling software automation in data reduction and the development of new neutron research facilities, SANS can be expected to remain mainstream for biomedical research.

Application of small angle scattering (SAS) in structural characterisation of casein and casein-based products during digestion.

In recent years, small and ultra-small angle scattering techniques, collectively known as small angle scattering (SAS) have been used to study various food structures during the digestion process. These techniques play an important role in structural characterisation due to the non-destructive nature (especially when using neutrons), various in situ capabilities and a large length scale (of 1 nm to ∼20 µm) they cover. The application of these techniques in the structural characterisation of dairy products has expanded significantly in recent years. Casein, a major dairy protein, forms the basis of a wide range of gel structures at different length scales. These gel structures have been extensively researched utilising scattering techniques to obtain structural information at the nano and micron scale that complements electron and confocal microscopy. Especially, neutrons have provided opportunity to study these gels in their natural environment by using various in situ options. One such example is understanding changes in casein gel structures during digestion in the gastrointestinal tract, which is essential for designing personalised food structures for a wide range of food-related diseases and improve health outcomes. In this review, we present an overview of casein gels investigated using small angle and ultra-small angle scattering techniques. We also reviewed their digestion using newly built setups recently employed in various research. To gain a greater understanding of micro and nano-scale structural changes during digestion, such as the effect of digestive juices and mechanical breakdown on structure, new setups for semi-solid food materials are needed to be optimised.

Role of Hydrogen Bond Defects for Cluster Formation and Distribution in Ionic Liquids by Means of Neutron Diffraction and Molecular Dynamics Simulations.

Defects fundamentally govern the properties of all real materials. Correlating molecular defects to macroscopic quantities remains a challenge, particularly in the liquid phase. Herein, we report the influence of hydrogen bonds (HB) acting as defects in mixtures of non-hydroxyl-functionalized ionic liquids (ILs) with an increasing concentration of hydroxyl-functionalized ILs. We observed two types of HB defects: The conventional HBs between cation and anion (c-a), and the elusive HBs between cations (c-c) despite the repulsive Coulomb forces. We use neutron diffraction with isotopic substitution in combination with molecular dynamics simulations for measuring the geometry, strength, and distribution of mobile OH defects in the IL mixtures. In principle, this procedure allows relating the number and stability of defects to macroscopic properties such as diffusion, viscosity, and conductivity, which are of utmost importance for the performance of electrolytes in batteries and other electrical devices.

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

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.

Data analysis and modeling of small-angle neutron scattering data with contrast variation from bio-macromolecular complexes.

Small-angle neutron scattering (SANS) with contrast variation (CV) is a valuable technique in the structural biology toolchest. Accurate structural parameters-e.g., radii of gyration, volumes, dimensions, and distance distribution(s)-can be derived from the SANS-CV data to yield the shape and disposition of the individual components within stable complexes. Contrast variation is achieved through the substitution of hydrogen isotopes (1H for 2H) in molecules and solvents to alter the neutron scattering properties of each component of a complex. While SANS-CV can be used a stand-alone technique for interrogating the overall structure of biomacromolecules in solution, it also complements other methods such as small-angle X-ray scattering, crystallography, nuclear magnetic resonance, and cryo-electron microscopy. Undertaking a SANS-CV experiment is challenging, due in part to the preparation of significant quantities of monodisperse samples that may require deuterium (2H) labeling. Nevertheless, SANS-CV can be used to study a diverse range biomacromolecular complexes including protein-protein and protein-nucleic acid systems, membrane proteins, and flexible systems resistant to crystallization. This chapter describes how to approach the data analysis and modeling of SANS data, including: (1) Analysis of the forward scattering (I(0)) and calculation of theoretical estimates of contrast; (2) Analysis of the contrast dependence of the radius of gyration using the Stuhrmann plot and parallel axis theorem; (3) Calculation of composite scattering functions to evaluate the size, shape, and dispositions of individual components within a complex, and; (4) Development of real-space models to fit the SANS-CV data using volume-element bead modeling or atomistic rigid body modeling.

Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS.

In the present book chapter we illustrate the state-of-the-art of time-resolved small-angle neutron scattering (TR-SANS) by a concrete example of a dynamic bio-macromolecular system, i.e., regulated protein degradation by the archaeal PAN-20S proteasome complex. We present the specific and unique structural information that can be obtained by this approach, in combination with bio-macromolecular deuteration and online spectrophotometric measurements of a fluorescent substrate (GFP). The complementarity with atomic-resolution structural biology techniques (SAXS, NMR, crystallography and cryo-EM) and with the advent of atomic structure prediction are discussed, as well as the respective limitations and future perspectives.

Incorporation and localisation of alkanes in a protomembrane model by neutron diffraction.

Protomembranes at the origin of life were likely composed of short-chain lipids, readily available on the early Earth. Membranes formed by such lipids are less stable and more permeable under extreme conditions, so a novel membrane architecture was suggested to validate the accuracy of this assumption. The model membrane includes the presence of a layer of alkanes in the mid-plane of the protomembrane in between the two monolayer leaflets and lying perpendicular to the lipid acyl chains. Here, we investigated such a possibility experimentally for membranes formed by the short-chain phospholipid 1,2-didecanoyl-sn-glycero-3-phophocholine, including or not the alkanes eicosane, squalane or triacontane by means of neutron membrane diffraction and contrast variation. We found strong indications for incorporation of two of the three alkanes in the membrane mid-plane through the determination of neutron scattering length density profiles with hydrogenated vs deuterated alkanes and membrane swelling at various relative humidities indicating a slightly increased bilayer thickness when the alkanes are incorporated into the bilayers. The selectivity of the incorporation points out the role of the length of the n-alkanes with respect to the capacity of the membrane to incorporate them.

In-Situ Anaerobic Heating of Human Bones Probed by Neutron Diffraction.

The first neutron diffraction study of in-situ anaerobic burning of human bones is reported, aiming at an interpretation of heat-induced changes in bone, which were previously detected by vibrational spectroscopy, including inelastic neutron scattering techniques. Structural and crystallinity variations were monitored in samples of the human femur and tibia, as well as a reference hydroxyapatite, upon heating under anaerobic conditions. Information on the structural reorganization of the bone matrix as a function of temperature, from room temperature to 1000 °C, was achieved. Noticeable crystallographic and domain size variations, together with O-H bond lengths and background variations, were detected. Above 700 °C, the inorganic bone matrix became highly symmetric, devoid of carbonates and organic constituents, while for the lower temperature range (<700 °C), a considerably lower crystallinity was observed. The present pilot study is expected to contribute to a better understanding of the heat-prompted changes in bone, which can be taken as biomarkers of the burning temperature. This information is paramount for bone analysis in forensic science as well as in archeology and may also have useful applications in other biomaterial studies.

A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin.

Collagen triple helices are critical in the function of mannan-binding lectin (MBL), an oligomeric recognition molecule in complement activation. The MBL collagen regions form complexes with the serine proteases MASP-1 and MASP-2 in order to activate complement, and mutations lead to common immunodeficiencies. To evaluate their structure-function properties, we studied the solution structures of four MBL-like collagen peptides. The thermal stability of the MBL collagen region was much reduced by the presence of a GQG interruption in the typical (X-Y-Gly)n repeat compared to controls. Experimental solution structural data were collected using analytical ultracentrifugation and small angle X-ray and neutron scattering. As controls, we included two standard Pro-Hyp-Gly collagen peptides (POG)10-13, as well as three more peptides with diverse (X-Y-Gly)n sequences that represented other collagen features. These data were quantitatively compared with atomistic linear collagen models derived from crystal structures and 12,000 conformations obtained from molecular dynamics simulations. All four MBL peptides were bent to varying degrees up to 85o in the best-fit molecular dynamics models. The best-fit benchmark peptides (POG)n were more linear but exhibited a degree of conformational flexibility. The remaining three peptides showed mostly linear solution structures. In conclusion, the collagen helix is not strictly linear, the degree of flexibility in the triple helix depends on its sequence, and the triple helix with the GQG interruption showed a pronounced bend. The bend in MBL GQG peptides resembles the bend in the collagen of complement C1q and may be key for lectin pathway activation.

Water Content in Nanoparticles Determined by Small-Angle Neutron Scattering and Light Scattering.

The amount of water in therapeutic nanoparticles (NPs) is of great importance to the pharmaceutical industry, as water content reflects the volume occupied by the solid components. For example, certain biomolecules, such as mRNA, can undergo conformational change or degradation when exposed to water. Using static light scattering (SLS) and dynamic light scattering (DLS), we estimated the water content of NPs, including extruded liposomes of two different sizes and polystyrene (PS) Latex NPs. In addition, we used small-angle neutron scattering (SANS) to independently access the water content of the samples. The water content of NPs estimated by SLS/DLS was systematically higher than that from SANS. The discrepancy is most likely attributed to the larger radius determined by DLS, in contrast to the SANS-derived radius observed by SANS. However, because of low accessibility to the neutron facilities, we validate the combined SLS/DLS to be a reasonable alternative to SANS for determining the water (or solvent) content of NPs.