The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological ...macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems.
Assessing similarity between data sets with the reduced χ(2) test requires the estimation of experimental errors, which, if incorrect, may render statistical comparisons invalid. We report a ...goodness-of-fit test, Correlation Map (CorMap), for assessing differences between one-dimensional spectra independently of explicit error estimates, using only data point correlations. Using small-angle X-ray scattering data, we demonstrate that CorMap maintains the power of the reduced χ(2) test; moreover, CorMap is also applicable to other physical experiments.
Bright fluorophores in the near‐infrared and shortwave infrared (SWIR) regions of the electromagnetic spectrum are essential for optical imaging in vivo. In this work, we utilized a 7‐dimethylamino ...flavylium heterocycle to construct a panel of novel red‐shifted polymethine dyes, with emission wavelengths from 680 to 1045 nm. Photophysical characterization revealed that the 1‐ and 3‐methine dyes display enhanced photostability and the 5‐ and 7‐methine dyes exhibit exceptional brightness for their respective spectral regions. A micelle formulation of the 7‐methine facilitated SWIR imaging in mice. This report presents the first polymethine dye designed and synthesized for SWIR in vivo imaging.
Moving beyond the NIR: A series of polymethine dyes containing a 7‐dimethylamino flavylium heterocycle were designed and synthesized. These dyes display distinctly red‐shifted absorption and emission. The flavylium heptamethine dye is a bright shortwave infrared (SWIR) emitter and was employed for in vivo SWIR imaging.
With the emergence of applications based on short-wavelength infrared light, indium arsenide quantum dots are promising candidates to address existing shortcomings of other infrared-emissive ...nanomaterials. However, III-V quantum dots have historically struggled to match the high-quality optical properties of II-VI quantum dots. Here we present an extensive investigation of the kinetics that govern indium arsenide nanocrystal growth. Based on these insights, we design a synthesis of large indium arsenide quantum dots with narrow emission linewidths. We further synthesize indium arsenide-based core-shell-shell nanocrystals with quantum yields up to 82% and improved photo- and long-term storage stability. We then demonstrate non-invasive through-skull fluorescence imaging of the brain vasculature of murine models, and show that our probes exhibit 2-3 orders of magnitude higher quantum yields than commonly employed infrared emitters across the entire infrared camera sensitivity range. We anticipate that these probes will not only enable new biomedical imaging applications, but also improved infrared nanocrystal-LEDs and photon-upconversion technology.
Molecular mass (MM) is one of the key structural parameters obtained by small-angle X-ray scattering (SAXS) of proteins in solution and is used to assess the sample quality, oligomeric composition ...and to guide subsequent structural modelling. Concentration-dependent assessment of MM relies on a number of extra quantities (partial specific volume, calibrated intensity, accurate solute concentration) and often yields limited accuracy. Concentration-independent methods forgo these requirements being based on the relationship between structural parameters, scattering invariants and particle volume obtained directly from the data. Using a comparative analysis on 165,982 unique scattering profiles calculated from high-resolution protein structures, the performance of multiple concentration-independent MM determination methods was assessed. A Bayesian inference approach was developed affording an accuracy above that of the individual methods, and reports MM estimates together with a credibility interval. This Bayesian approach can be used in combination with concentration-dependent MM methods to further validate the MM of proteins in solution, or as a reliable stand-alone tool in instances where an accurate concentration estimate is not available.
Automated acquisition and analysis of small angle X-ray scattering data Franke, Daniel; Kikhney, Alexey G.; Svergun, Dmitri I.
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
10/2012, Volume:
689
Journal Article
Peer reviewed
Small Angle X-ray Scattering (SAXS) is a powerful tool in the study of biological macromolecules providing information about the shape, conformation, assembly and folding states in solution. Recent ...advances in robotic fluid handling make it possible to perform automated high throughput experiments including fast screening of solution conditions, measurement of structural responses to ligand binding, changes in temperature or chemical modifications. Here, an approach to full automation of SAXS data acquisition and data analysis is presented, which advances automated experiments to the level of a routine tool suitable for large scale structural studies. The approach links automated sample loading, primary data reduction and further processing, facilitating queuing of multiple samples for subsequent measurement and analysis and providing means of remote experiment control. The system was implemented and comprehensively tested in user operation at the BioSAXS beamlines X33 and P12 of EMBL at the DORIS and PETRA storage rings of DESY, Hamburg, respectively, but is also easily applicable to other SAXS stations due to its modular design.
A high‐brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small‐angle X‐ray scattering (SAXS) and has been designed and ...optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom‐designed miniature active beamstop ensures accurate data normalization and the photon‐counting PILATUS 2M detector enables the background‐free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in‐vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous‐flow in‐line sample purification and characterization, as well as an in‐air capillary time‐resolved stopped‐flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high‐throughput screening mode using sub‐microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real‐time assessments of overall parameters and the generation of low‐resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high‐throughput analysis, as well as time‐resolved and screening experiments for novice and expert biological SAXS users.
Recent technology developments have expanded the wavelength window for biological fluorescence imaging into the shortwave infrared. We show here a mechanistic understanding of how drastic changes in ...fluorescence imaging contrast can arise from slight changes of imaging wavelength in the shortwave infrared. We demonstrate, in 3D tissue phantoms and in vivo in mice, that light absorption by water within biological tissue increases image contrast due to attenuation of background and highly scattered light. Wavelengths of strong tissue absorption have conventionally been avoided in fluorescence imaging to maximize photon penetration depth and photon collection, yet we demonstrate that imaging at the peak absorbance of water (near 1,450 nm) results in the highest image contrast in the shortwave infrared. Furthermore, we show, through microscopy of highly labeled ex vivo biological tissue, that the contrast improvement from water absorption enables resolution of deeper structures, resulting in a higher imaging penetration depth. We then illustrate these findings in a theoretical model. Our results suggest that the wavelength-dependent absorptivity of water is the dominant optical property contributing to image contrast, and is therefore crucial for determining the optimal imaging window in the infrared.
Adipocytes possess remarkable adaptive capacity to respond to nutrient excess, fasting or cold exposure, and they are thus an important cell type for the maintenance of proper metabolic health. ...Although the endoplasmic reticulum (ER) is a critical organelle for cellular homeostasis, the mechanisms that mediate adaptation of the ER to metabolic challenges in adipocytes are unclear. Here we show that brown adipose tissue (BAT) thermogenic function requires an adaptive increase in proteasomal activity to secure cellular protein quality control, and we identify the ER-localized transcription factor nuclear factor erythroid 2-like 1 (Nfe2l1, also known as Nrf1) as a critical driver of this process. We show that cold adaptation induces Nrf1 in BAT to increase proteasomal activity and that this is crucial for maintaining ER homeostasis and cellular integrity, specifically when the cells are in a state of high thermogenic activity. In mice, under thermogenic conditions, brown-adipocyte-specific deletion of Nfe2l1 (Nrf1) resulted in ER stress, tissue inflammation, markedly diminished mitochondrial function and whitening of the BAT. In mouse models of both genetic and dietary obesity, stimulation of proteasomal activity by exogenously expressing Nrf1 or by treatment with the proteasome activator PA28α in BAT resulted in improved insulin sensitivity. In conclusion, Nrf1 emerges as a novel guardian of brown adipocyte function, providing increased proteometabolic quality control for adapting to cold or to obesity.
This article presents IMSIM, an application to simulate two‐dimensional small‐angle X‐ray scattering patterns and, further, one‐dimensional profiles from biological macromolecules in solution. IMSIM ...implements a statistical approach yielding two‐dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data‐analysis pipelines. Intensities and error estimates of one‐dimensional patterns obtained from the radial average of the two‐dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, cm−1/cmg ml−1, the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl‐hamburg.de/biosaxs/download.html).
An application is presented to simulate images on an area detector for isotropic small‐angle X‐ray scattering, explicitly accounting for the experimental geometry and yielding radially averaged 1D scattering patterns with statistically appropriate variations.
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