Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering.

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

Histotoxic clostridia produce collagenases responsible for extensive tissue destruction in gas gangrene. The C-terminal collagen-binding domain (CBD) of these enzymes is the minimal segment required to bind to collagen fibril. Collagen binding efficiency of CBD is more pronounced in the presence of Ca(2+). We have shown that CBD can be functional to anchor growth factors in local tissue. A (1)H-(15)N HSQC NMR titration study with three different tropocollagen analogues ((POG)(10))(3), ((GPOG)(7)PRG)(3), and (GPRG(POG)(7)C-carbamidomethyl)(3), mapped a saddle-like binding cleft on CBD. NMR titrations with three nitroxide spin-labeled analogues of collagenous peptide, (PROXYL-G(POG)(7)PRG)(3), (PROXYL-G(POG)(7))(3), and (GPRG(POG)(7)C-PROXYL)(3) (where PROXYL represents 2,2,5,5-tetramethyl-l-pyrrolidinyloxy), unambiguously demonstrated unidirectional binding of CBD to the tropocollagen analogues. Small angle x-ray scattering data revealed that CBD binds closer to a terminus for each of the five different tropocollagen analogues, which in conjunction with NMR titration studies, implies a binding mode where CBD binds to the C terminus of the triple helix.

Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides alpha-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.

Small angle X-ray scattering (SAXS) is a powerful method for investigating macromolecular structure in solution. SAXS data provide information about the size and shape of a molecule with a resolution of ∼2 to 3 nm. SAXS is particularly useful for the investigation of nucleic acids, which scatter X-rays strongly due to the electron-rich phosphate backbone. Therefore, SAXS has become an increasingly popular method for modeling nucleic acid structures, an endeavor made tractable by the highly regular helical nature of nucleic acid secondary structures. Recently, SAXS was used in combination with NMR to filter and refine all-atom models of a U2/U6 small nuclear RNA complex. In this unit, general protocols for sample preparation, data acquisition, and data analysis and processing are given. Additionally, examples of correctly and incorrectly processed SAXS data and expected results are provided.

Structural Analysis of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Intracellular Domain Reveals a Conserved Interaction Epitope

Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS--an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.

To date, the sizes of the nanoscale ionic aggregates present in ionomers as determined by scanning transmission electron microscopy (STEM) experiments are inconsistent with small-angle X-ray scattering (SAXS) data interpreted by the Yarusso−Cooper model. To address this discrepancy, we have investigated a pair of model nanoparticles (11- and 55-atom Au clusters) with both STEM and SAXS. To mimic ionic aggregates, these nanoparticles were supported by amorphous PS films of predetermined thickness. While the size of the STEM probe was inconsequential to the resolution and measurement of the particles, the optimal specimen thickness was determined to be less than 50 nm. SAXS was performed on dilute solutions of the nanoparticles and fit using a monodisperse, noninteracting hard-sphere form factor model. For Au 11, STEM finds a diameter of 1.3 ± 0.14 nm and SAXS finds a diameter of 1.4 nm. Similarly, both STEM and SAXS determine a diameter of 1.7 nm for Au 55. For a combined system of Au 11 and Au 55, STEM data suggests a bimodal distribution of particle sizes consistent with those of the individual particles while SAXS data indicate hard spheres with diameter of 1.6 nm. Analysis of this model system has allowed us to optimize several experimental conditions of potential importance in reconciling STEM and SAXS data from ionomers.

The main objective of this study is to showcase the use of synergistic utilization of model‐independent and model‐dependent approaches for analyzing small angle X‐ray scattering (SAXS) data to determine the shape and size of different nanostructures viz. spherical, nanorod, and core‐shell. Herein, different gold nanostructures viz. spherical, nanorod, and core‐shell are synthesized and analyzed using SAXS. First, the SAXS data are analyzed using Guinier law, PDDF (pair–distance distribution function) plots, double logarithmic plots, and electron density curves to get primary information about the size and shape of nanostructures. This information is utilized for choosing an appropriate model and initial input parameters for fitting the SAXS data. The observations obtained from SAXS studies are compared with transmission electron microscopy and UV–vis spectroscopy. It is believed that this study will help in understanding the analysis of SAXS data using a systematic and synergistic approach of utilizing the two methods. It is believed that the study will further add to the understanding of the technique as an alternative approach for transmission electron microscopy.

Nanoparticle suspensions (also called nanofluids) are often polydisperse and tend to settle with time. Settling kinetics in these systems are known to be complex and hence challenging to understand. In this work, polydisperse spherical alumina (Al2O3) nanoparticles in the size range of ~10-100nm were dispersed in water and examined for aggregation and settling behaviour near its isoelectric point (IEP). A series of settling experiments were conducted and the results were analysed by photography and by Small Angle X-ray Scattering (SAXS). The settling curve obtained from standard bed height measurement experiments indicated two different types of behaviour, both of which were also seen in the SAXS data. But the SAXS data were remarkably able to pick out the rapid settling regime as a result of the high temporal resolution (10s) used. By monitoring the SAXS intensity, it was further possible to record the particle aggregation process for the first time. Optical microscopy images were produced on drying and dried droplets extracted from the suspension at various times. Dried deposits showed the rapid decrease in the number of very large particles with time which qualitatively validates the SAXS prediction, and therefore its suitability as a tool to study unstable polydisperse colloids. Keywords: Nanoparticles, nanofluids, polydisperse, aggregation, settling, alumina, microscopy, SAXS

Structural changes in non-isothermal crystallization process of melt-cooled polyoxymethylene[II] evolution of lamellar stacking structure derived from SAXS and WAXS data analysis

The structure of a diblock copolymer solution in the vicinity of the transition between micellar liquid and solid phases was investigated using small-angle x-ray scattering (SAXS). An amphiphilic poly(oxyethylene)–poly(oxybutylene) diblock was studied in water. Static and dynamic light scattering techniques were used to provide an independent measure of micelle dimensions and aggregation number. Dynamic shear rheometry and mobility measurements were used to locate phase transitions. A micellar liquid phase was identified at low concentration and a cubic micellar phase at higher concentration, the transition between the two occurring at higher temperature as the concentration increased. The cubic micellar phase behaves rheologically as a solid and SAXS confirmed a face-centered cubic structure. Intermediate between these two phases, a viscoelastic soft solid was observed, with a finite yield stress but with a much lower dynamic modulus than the crystalline solid. Several distinct suggestions have been put forward for the structure of the solution in this region. In a poly(oxyethylene)–poly(oxypropylene)–poly(oxyethylene) Pluronic triblock, small-angle neutron scattering and rheology provided evidence for a percolation transition between micellar liquid and solid phases [L. Lobry et al., Phys. Rev. E. 60, 7076 (1999)], indicating a fractal structure of micelles aggregated due to attractive interactions. Alternatively, a defective solid phase has been proposed. We analyzed the structure of solutions of our diblock copolymer via detailed model fits to the SAXS data for concentrations spanning the liquid–solid transition. The micellar form factor was modeled as a homogeneous micellar core with attached Gaussian chains; and the intermicellar structure factor could be described using the hard sphere model. Thus there is no evidence for percolation induced by effective attractive interactions between micelles in our system. In contrast SAXS data indicates there is a coexistence region between hard sphere fluid and solid crystal phases, in which small grains of close-packed crystal coexist with fluid. It is apparent that block copolymer micelles acts as model colloidal systems in which it is possible to investigate the influence of attractive and repulsive interactions between spherical particles by varying the copolymer composition.

SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes

Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification

Structural characteristics of various conformational states of porcine pepsin in solution under different pH conditions were investigated in terms of size and shape by small-angle X-ray scattering (SAXS). Low-resolution structural models of porcine pepsin were reconstructed from SAXS data, which were made inside the search volume of maximum dimension (Dmax), calculated from the pair distance distribution function p(r). The reconstructed structural models were obtained without imposing any restrictions on the symmetry or anisometry of the pepsin molecule. Under conditions emulating those for physiological activity of the enzyme, the reconstructed structural models exhibited a more extended C-terminal domain compared to the crystal structure. The differences between the solution and crystal structures of pepsin can be explained by inherent conformations of the flexible subdomain in the C-terminal domain under the solution pH conditions. Under mild acidic conditions where the enzyme is inactive, the reconstructed structural models revealed a compact globular conformation similar in overall shape to the crystal structure. These results indicate that the changes in fluorescence and circular dichroism curves observed under acidic conditions could also arise from the inherent conformation of the flexible subdomain, which has a tendency to roll into a sphere in the overall structure, but without affecting the stability of internal structure. Furthermore, the conformational changes in the subdomain might explain the inactivity of pepsin under mildly acidic conditions. Finally, compared to neutral denaturing conditions, pepsin under alkaline denaturing conditions had a larger expanded vertical conformation in the reconstructed model, as a consequence of alkaline denaturation of the N-terminal domain and a fully extended conformation of the C-terminal domain. The structural evidence presented here may have important implications for understanding the relationship between the structure of porcine pepsin and enzymatic function.