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Schematic small-angle X-ray scattering setup for beam line 12-ID at the Advanced Photon Source (APS). The SAXS intensity is typically recorded as a function of momentum transfer q , q = 4 π sin( θ ) /λ , where 2 θ is the total scattering angle and λ is the X-ray wavelength. Details of the measurement setup have been described in References 7, 61, and 83.
Source publication
Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D sc...
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Context 1
... X-ray scattering (SAXS) is a technique that allows the study of the structure and interactions of biological macromolecules in solution. SAXS can be used to probe proteins, nucleic acids, and their complexes under a variety of conditions, from (near-) physiological to highly denaturing, without the need to crystallize the sample and without the molecular weight limitations inherent in other methods such as NMR spec- troscopy. The increasing availability of high- flux, third-generation synchrotron sources, improvements in detector hardware, and al- gorithmic developments for data analysis have made SAXS a technique of choice for a range of biological applications. The grow- ing importance of SAXS as a tool in structural biology is reflected in the number of SAXS-related publications per year, which has tripled in the past decade (36). The basic principle of SAXS is to scatter X-ray photons elastically off molecules in solution and to record the scattering intensity as a function of the scattering angle. Figure 1 shows a schematic of a typical SAXS measurement. The recorded scattering profile provides information about the global structure and conformation of the studied molecules. Historically, SAXS has been used to obtain a few key parameters such as the molecular weight MW , radius of gyration R g , and maximum intramolecular distance D max (34, 37). Several excellent reviews on the physical principles and theory of SAXS describe in de- tail how the scattering data can be analyzed and how different parameters can be fit and interpreted (26, 34, 46, 93). In this review, we therefore focus on more recent developments and novel applications of SAXS and only briefly discuss the basic physical principles to highlight the challenges unique to different experimental targets. The past decade has seen the development of algorithms that allow ab initio reconstructions of low-resolution 3-D electron density maps from 1-D scattering profiles (18, 92, 94, 104), allowing one to obtain structural information beyond simple parameters such as the R g . Recently, Svergun and coworkers have created tools to model molecular complexes from SAXS data if the structures of the individual components are (partially) known from higher resolution experiments (49, 70, 72). We review these algorithms and recent applications to molecular complexes (see 3-D Reconstructions, below). Membrane proteins have received much attention for their importance in cell metabolism and as drug targets; however, they lead to significant challenges for most structural techniques (79, 105). One of the main obstacles is the need to solubilize membrane proteins, which is most often accomplished by micelle-forming detergents. Recent advances in the study of the resulting protein-detergent complexes (PDCs) by SAXS are reviewed (see Membrane Proteins and Protein-Detergent Complexes, below). The discovery in the early 1980s that RNA can act as an enzyme or ribozyme (32) and the more recent realization that RNA not only carries genetic information as mRNA, but is also highly involved in the regulation of that information (64, 87) have led to a surge in interest in RNA structural biology. We review the important contributions that SAXS has made to our understanding of RNA folding as well as the current trends in the field (see Nucleic Acids, below). SAXS has been an important technique for the investigation of the conformational ensembles populated by unfolded proteins under highly denaturing conditions (26, 67). The global structure of denatured proteins as measured by R g appears consistent with a simple Flory picture of a self-avoiding random walk. However, recent experiments have suggested residual structure even under highly denaturing conditions (66, 84) and have seen significant deviations from predictions of molecular dynamics simulations (111). These results bring up significant outstanding questions re- garding our current understanding of the unfolded state (see Unfolded Proteins and Pep- tides, below). The parameters most frequently extracted from a SAXS profile for a biomolecule in solution (which is sufficiently dilute to avoid the effects of interparticle interference) are R g and forward scattering intensity I (0). They are obtained from the Guinier formula I ( q ) ≈ I (0) exp( − q 2 R g 2 / 3), for small momentum transfer q ( q = 4 π sin( θ )/ λ , where 2 θ is the total scattering angle and λ the X-ray wavelength), by plotting ln( I ( q )) versus q 2 and fitting the slope and intercept (34, 37). R g is a model free characterization of the molecular size and I (0) can be related to the molecular weight with the relation I (0) = κ c ( ρ ) 2 ( MW ) 2 , 1. where κ is a proportionality constant that can be determined from a measurement of a molecular weight standard (e.g., a protein of known molecular weight and concentration), c is the concentration of the macromolecule, ρ is the average electron density contrast of the molecule, and MW is the molecular weight. More generally the scattering profile may be written in terms of the distribution function p ( r ) of intramolecular atomic distances ( D max being the maximum intramolecular distance): D max sin( qr ) ( ) = ( ) . 2. p ( r ) can be obtained from an indirect Fourier transform of the scattering profile, e.g., using the software GNOM by Svergun (91), which employs the regularization procedure of Tikhonov & Arsenin (101). However, in recent years the use of p ( r ) to help visualize the molecular shape has been superseded by algorithms that provide a low-resolution 3-D electron density map of the molecule from the 1-D SAXS profile. Owing to the physical constraint that a biomolecule in general has a rather uniform electron density, Stuhrmann proposed representing the scattering profile in terms of a spherical harmonic expansion of the molecular surface (88, 89, 95). Determination of the coefficients of the spherical harmonics by a nonlinear, least-squares fitting procedure to the data led to ...
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Citations
... Moreover, NAST predicts the 3D structures of the yeast phenylalanine tRNA (76 nt) and the P4-P6 domain of the Tetrahymena thermophile group I intron (158 nt) with~8 Å and~16 Å RMSDs from the native structures, respectively [26]. In addition, NAST can combine small-angle X-ray scattering data [85] and experimental solvent accessibility data as filters to rank the clusters of similar structures. The package of NAST can be downloaded at https://simtk.org/home/nast. ...
Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structure prediction has been paid much attention in the last two decades. Some computational models have been developed to predict RNA three-dimensional (3D) structures in silico, and these models are generally composed of predicting RNA 3D structure ensemble, evaluating near-native RNAs from the structure ensemble, and refining the identified RNAs. In this review, we will make a comprehensive overview of the recent advances in RNA 3D structure modeling, including structure ensemble prediction, evaluation, and refinement. Finally, we will emphasize some insights and perspectives in modeling RNA 3D structures.
... A fundamental requirement for the simulation of a biological pore is the presence of a reliable experimentally determined structure (i.e. the conformation of the folded proteins constituting the pore). Macromolecular structures can be determined from protein crystals using a variety of methods, including X-Ray Diffraction/X-ray crystallography [144], Cryogenic Electron Microscopy [145] (CryoEM), Small-angle X-ray scattering [146] and Neutron diffraction [147]. Those structures are typically accessible on the Protein Data Bank (PDB [148]), while dedicated databases, such as OPM [149] and MemProtMD [150], provide spatial arrangements of proteins with respect to the lipid bilayer membrane, largely facilitating the simulation setup. ...
Electroosmosis is a fascinating effect where liquid motion is induced by an applied electric field. Counter ions accumulate in the vicinity of charged surfaces, triggering a coupling between liquid mass transport and external electric field. In nanofluidic technologies, where surfaces play an exacerbated role, electroosmosis is thus of primary importance. Its consequences on transport properties in biological and synthetic nanopores are subtle and intricate. Thorough understanding is therefore challenging yet crucial to fully assess the mechanisms at play. Here, we review recent progress on computational techniques for the analysis of electroosmosis and discuss technological applications, in particular for nanopore sensing devices.
... X-ray crystallography exploits the diffraction lattice for collecting an electron density map of the crystal. The need for a solid crystalline sample and the ionizing properties of X-rays represent limitations in the study of proteins in the physiological environment [39][40][41][42]. ...
Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.
... 66 Except for size distribution, SAXS can provide detailed information on NMs, proteins, and their complex geometry, which are inaccessible for the conventional dynamic light scattering (DLS) technique. 67 In return, SR-SAXS can provide detailed information about size dynamics and structural configurations of a given sample, which is Under cryogenic conditions, TEM associated with crosscorrelation image processing and energy-filtered TEM allowed determination of PC morphology and thickness with imaging of its unstained hard and soft fractions. This strategy validates the applicability of TEM methodologies to decipher fundamental PC aspects and its behavior in simple and complex media, which can contribute to rational design of nanomedicines. ...
It is essential to study nano-bio interactions for nanosafety evaluation and nanomedicine development, but limited information is available on nano-bio interfacial interactions and their underlying mechanisms. The interaction of nanomaterials (NMs) with the biological system is complex and involves various physicochemical events at different levels. The conventional methods fail to study the in situ behavior and fate of NMs and cannot acquire enough physicochemical information. Advanced synchrotron radiation (SR)-based techniques can help systematically understand nano-bio interactions, i.e., a series of physical and chemical reactions at the biomolecular surface that dictate the fate of NMs in a biological system. It has been established that biomolecules rapidly adsorb on the surface of administered NMs and form a biomolecular corona. The adsorbed biomolecular corona changes the surface properties of NMs that may interfere with their intended functionalities. In this review, we incorporate SR-based methodologies to obtain insight into the detailed mechanism of nano-bio interactions. A deeper understanding of nano-bio interactions can help better investigate biological responses and promote the rational design of efficient nanomedicine. These techniques have broad applications in other fields of the life sciences and the environmental sciences.
... [6][7][8][9] By refining simulated structural models to the experimentally measured one-dimensional PDF patterns,o ne can directly visualize molecular structure. As ar esult, X-ray scattering has been extensively applied to awide variety of molecular materials including polymers, [10,11] metal oxides, [12][13][14][15][16][17][18] biomacromolecules, [19][20][21][22] aggregates of organic compounds [23][24][25] and supramolecular architectures. [26][27][28][29][30][31][32][33][34] Advancements at synchrotron X-ray sources have enabled high-energy X-ray scattering (HEXS) capabilities,which drastically expands the q range up to % 40 À1 and yields an achievable spatial resolution of % 0.1 . ...
High‐energy X‐ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long‐range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic CuI/RuII/OsII complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub‐Ångström conformational differences by direct comparison of solution phase and solid‐state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.
... A fundamental requirement for the simulation of a biological pore is the presence of a reliable experimentally-determined structure (i.e. the conformation of the folded proteins constituting the pore). Macromolecular structures can be determined from protein crystals using a variety of methods, including X-Ray Diffraction/X-ray crystallography [127], Cryogenic Electron Microscopy [128] (CryoEM), Small-angle X-ray scattering [129] and Neutron diffraction [130]. Those structures are typically accessible on the Protein Data Bank (PDB [131]), while dedicated databases, such as OPM [132] and MemProtMD [133], provide spatial arrangements of proteins with respect to the lipid bilayer membrane, largely facilitating the simulation setup. ...
Electroosmosis is a fascinating effect where liquid motion is induced by an applied electric field. Counter ions accumulate in the vicinity of charged surfaces, triggering a coupling between liquid mass transport and external electric field. In nanofluidic technologies, where surfaces play an exacerbated role, electroosmosis is thus of primary importance. Its consequences on the transport properties in biological and synthetic nanopores are subtle and intricate. Thorough understanding is therefore challenging yet crucial to fully assess the mechanisms at play. Here, we review recent progress on computational techniques for the analysis of electroosmosis and discuss technological applications, in particular for sensing devices.
... X-ray scattering is a well-established technique for the characterization of polymers, pharmaceuticals, nanoparticles, and biological materials [1][2][3]. WAXS provides structural information at the atomic scale down to 0.1 nm, similar to traditional XRD. SAXS provides information on complex molecules and materials such as polymers, colloids, and porous materials, up to 500 nm in size. ...
X-ray diffraction (XRD) is a fingerprint technique for the analysis of atomic and molecular structures of crystalline materials, from polymers and plastics, through to structural composites and biomaterials. These all have crystallographic phases in the nanostructure, which greatly influence the macro properties of the material—from insulin and hemoglobin to semiconductors and solar cells. Here, we look at how XRD analysis using a small- and wide-angle X-ray scattering (SAXS/WAXS) system under full vacuum brings the possibility of crystallographic sample characterization, with temperature and environmental control, direct to the laboratory, and how this improves the workflow for phase identification.
... Interactions between lncRNAs and proteins are ubiquitous. Only a few conventional methods such as X-ray diffraction [16], nuclear magnetic resonance [17], electron microscopy [18], neutron scattering [19], cross-linking immunoprecipitation [20] and miRNAs as mediators in a heterogeneous network [21] have been used to detect structural data of protein complexes. This is due to the shortcomings of experiments, like high cost, long time, and complicated test process. ...
Background
Plant long non-coding RNAs (lncRNAs) play vital roles in many biological processes mainly through interactions with RNA-binding protein (RBP). To understand the function of lncRNAs, a fundamental method is to identify which types of proteins interact with the lncRNAs. However, the models or rules of interactions are a major challenge when calculating and estimating the types of RBP.
Results
In this study, we propose an ensemble deep learning model to predict plant lncRNA-protein interactions using stacked denoising autoencoder and convolutional neural network based on sequence and structural information, named PRPI-SC. PRPI-SC predicts interactions between lncRNAs and proteins based on the k-mer features of RNAs and proteins. Experiments proved good results on Arabidopsis thaliana and Zea mays datasets (ATH948 and ZEA22133). The accuracy rates of ATH948 and ZEA22133 datasets were 88.9% and 82.6%, respectively. PRPI-SC also performed well on some public RNA protein interaction datasets.
Conclusions
PRPI-SC accurately predicts the interaction between plant lncRNA and protein, which plays a guiding role in studying the function and expression of plant lncRNA. At the same time, PRPI-SC has a strong generalization ability and good prediction effect for non-plant data.
... The authors considered that the co-crystallization would select for a subset of molecules that achieved complete folding like that of the natural ligand of the TPP riboswitch. To investigate this they applied small-angle X-ray scattering (SAXS), a lower resolution structure-determination method, [42] in order to determine the average global conformation of an RNA-fragment complex. Due to the sugar-phosphate backbone, RNA scatters X-ray more strongly than proteins, and it is considered easier to determine/predict RNA secondary structure, which makes SAXS a useful technique to determine the 3D topological structures of large RNAs without requiring crystallization. ...
... [59] More recently, the Disney group has presented additional potential privileged small-molecule scaffolds based on literature results, consisting of benzimidazoles (14), imidazoles (15), phenyl imidazolines (16), indoles (17), N-substituted carbazoles (18), alkyl pyridinium scaffolds (19), 2-amino-pyridines (20), 2amino-quinolines (21), 1,8-diamino-2,7-naphtyridines (22), and 2-aminopyrimidines (23). [4] In another study by Rizvi et al.,42 diverse RNA targets were screened against about 50,000 drug-like compounds and the results were analyzed to derive properties for RNA ligands. [56] This study suggests that most RNA ligands are in drug-like chemical space, and some privileged scaffolds could be identified among the hits ( Figure 12). ...
Rapid development within the fields of both fragment‐based drug discovery (FBDD) and medicinal targeting of RNA provides possibilities for combining technologies and methods in novel ways. This review provides an overview of fragment‐based screening (FBS) against RNA targets, including a discussion of the most recently used screening and hit validation methods such as NMR spectroscopy, X‐ray crystallography, and virtual screening methods. A discussion of fragment library design based on research from small‐molecule RNA binders provides an overview on both the currently limited guidelines within RNA‐targeting fragment library design, and future possibilities. Finally, future perspectives are provided on screening and hit validation methods not yet used in combination with both fragment screening and RNA targets.
... It was found that the morphological changes in the nanocomposites made of polypropylene (PP) and multiwall carbon nanotubes (MWCNT) and modified montmorillonite (m-MMT) can be also monitored by SAXS and WAXS [43]. The comprehensiveness of the SAXS analysis for structural investigation has also been appreciated in the research of biological macromolecules and advanced biological systems [44] represented by RNA and proteins [45,46]. The specific application of the SAXS includes also in situ studies for monitoring the structural changes of polymer nanocomposites upon heating in battery systems [47] and pore dynamics in ordered mesoporous electrode materials [48][49][50]. ...
The presented work follows the theme of applied chemistry toward nanomaterials and multiphase functional systems of practical importance. Structural studies of nanocomposite materials are important due to the correlation between physicochemical/structural properties and their application potential. In this work, we report the fabrication and structural characterization of nanocomposite materials constituting noble metal (plasmonic) nanoparticles (AgNP and AuNP) dispersed on selected types of nanostructured solid hosts (nonporous silica, microporous activated carbon, chitosan biopolymer, and ordered mesoporous silica). The ability to maintain a dispersed state of colloidal precursors throughout their deposition on solid hosts was assessed. The influence of the carrier role in the formation and stabilization of nanometallic phases was evaluated taking into account the physicochemical and textural properties of the support surfaces. The size and shape of nanoobjects, clustering effects, interfacial properties, and stability of the immobilized nanophase were implemented by analyzing relevant parameters of SAXS analysis. The dimensional characteristic of the scatterers was evaluated by volume-weighted particle size distribution Dv(R). The detailed overall shape and maximal particle dimension were described by the analysis of pair distance distribution functions (PDDFs). The radius of gyration (Rg) from PDDF and Guinier approximation was calculated for illustrating the dimension of scattered heterogeneities in the investigated solids. The asymptotic behavior of a scattering curve and Porod theory were applied for determining the diffusion and quality of the interfacial surfaces. The size and morphology of nanoparticles in colloidal precursor solutions have been defined as spherical and bimodal in size (~ 6 nm and 20 nm). It was observed that the spherical shape and dispersed state of nanoparticles were achieved for all systems after deposition. However, the morphology of their final form was conditioned by the solid matrices. The particle properties from SAXS were correlated with properties determined by TEM and low-temperature nitrogen sorption analysis. Obtained results suggest good compatibility and correctness of SAXS data reading of nanocomposite systems and can be successfully applied for quick, nondestructive, and effective evaluation of structural properties of complex systems.
Graphical abstract
