Pushing the Envelope

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Structural Information ◽  
Hydration Shell ◽  
Three Dimensional ◽  
Scattering Data ◽  
Saxs Data ◽  
Electron Density Function ◽  
Angle Scattering ◽  
Iterative Structure

Direct electron density determination from SAXS data opens up new opportunities. The ability to model density at high resolution and the implicit direct estimation of solvent terms such as the hydration shell may enable high-resolution wide angle scattering data to be used to calculate density when combined with additional structural information. Other diffraction methods that do not measure three-dimensional intensities, such as fiber diffraction, may also be able to take advantage of iterative structure factor retrieval. While the ability to reconstruct electron density ab initio is a major breakthrough in the field of solution scattering, the potential of the technique has yet to be fully uncovered. Additional structural information from techniques such as crystallography, NMR, and electron microscopy and density modification procedures can now be integrated to perform advanced modeling of the electron density function at high resolution, pushing the boundaries of solution scattering further than ever before.

Shape Reconstructions from Small Angle Scattering Data

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
Structural Information ◽  
Distinct Species ◽  
Singular Value ◽  
Scattering Data ◽  
Saxs Data ◽  
Hybrid Modelling ◽  
Complex Particle ◽  
Angle Scattering ◽  
Homogeneous Set ◽  
Value Decomposition

This chapter discusses recovering shape or structural information from SAXS data. Key to any such process is the ability to generate a calculated intensity from a model, and to compare this curve with the experimental one. Models for the particle scattering density can be approximated as pure homogenenous geometric shapes. More complex particle surfaces can be represented by spherical harmonics or by a set of close-packed beads. Sometimes structural information is known for components of a particle. Rigid body modeling attempts to rotate and translate structures relative to one another, such that the resulting scattering profile calculated from the model agrees with the experimental SAXS data. More advanced hybrid modelling procedures aim to incorporate as much structural information as is available, including modelling protein dynamics. Solutions may not always contain a homogeneous set of particles. A common case is the presence of two or more conformations of a single particle or a mixture of oligomeric species. The method of singular value decomposition can extract scattering for conformationally distinct species.

Three-Dimensional High Resolution Scaffold Fiber Architecture and Morphology in Tissue Engineered Heart Valve Tissue

2010 ◽  
Author(s):  
Chad E. Eckert ◽  
Brandon T. Mikulis ◽  
Dane Gerneke ◽  
Danielle Gottlieb ◽  
Bruce Smaill ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
High Resolution ◽  
Heart Valve ◽  
Structural Information ◽  
Three Dimensional ◽  
Tissue Scaffold ◽  
Valve Tissue ◽  
Sampling Protocols ◽  
Heart Valve Tissue

Engineered heart valve tissue (EHVT) has received much attention as a potential pediatric valve replacement therapy, offering prospective long-term functional improvements over current options. A significant gap in the literature exists, however, regarding estimating tissue mechanical properties from tissue-scaffold composites. Detailed three-dimensional structural information prior to implantation (in vitro) and after implantation in (in vivo) is needed for improved modeling of tissue properties. As such, a novel high-resolution imaging technique will be employed to obtain three-dimensional microstructural information. Analysis techniques will be used to fully quantify constituents of interest including scaffold, collagen, and cellular information and to develop appropriate two-dimensional sectioning sampling protocols. It is the intent of this work to guide modeling efforts to better elucidate EHVT tissue-specific mechanical properties.

scholarly journals New developments in theATSASprogram package for small-angle scattering data analysis

2012 ◽  
Vol 45 (2) ◽  
pp. 342-350 ◽  
Author(s):  
Maxim V. Petoukhov ◽  
Daniel Franke ◽  
Alexander V. Shkumatov ◽  
Giancarlo Tria ◽  
Alexey G. Kikhney ◽  
...  
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Scattering Data ◽  
New Developments ◽  
Angle Scattering ◽  
Automated Data Processing ◽  
Analyse Data ◽  
Three Dimensional Models ◽  
Structural Methods ◽  
New Algorithms

New developments in the program packageATSAS(version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The newATSASrelease includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to runATSASprograms, are also presented.

scholarly journals Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints

2015 ◽  
Vol 71 (1) ◽  
pp. 57-66 ◽  
Author(s):  
Henry S. Kim ◽  
Frank Gabel
Keyword(s):  
Small Angle ◽  
Hydration Shell ◽  
Small Angle Scattering ◽  
Conformational Space ◽  
Scattering Data ◽  
Body System ◽  
Angle Scattering ◽  
Recent Developments ◽  
The Impact ◽  
Nmr Restraints

Small-angle scattering (SAS) has witnessed a breathtaking renaissance and expansion over the past 15 years regarding the determination of biomacromolecular structures in solution. While important issues such as sample quality, good experimental practice and guidelines for data analysis, interpretation, presentation, publication and deposition are increasingly being recognized, crucial topics such as the uniqueness, precision and accuracy of the structural models obtained by SAS are still only poorly understood and addressed. The present article provides an overview of recent developments in these fields with a focus on the influence of complementary NMR restraints and of a hydration shell on the uniqueness of biomacromolecular models. As a first topic, the impact of incorporating NMR orientational restraints in addition to SAS distance restraints is discussed using a quantitative visual representation that illustrates how the possible conformational space of a two-body system is reduced as a function of the available data. As a second topic, the impact of a hydration shell on modelling parameters of a two-body system is illustrated, in particular on its inter-body distance. Finally, practical recommendations are provided to take both effects into account and promising future perspectives of SAS approaches are discussed.

Three-dimensional reconstruction of liquid phases in disordered mesopores usingin situsmall-angle scattering

2013 ◽  
Vol 46 (2) ◽  
pp. 493-504 ◽  
Author(s):  
Cedric J. Gommes
Keyword(s):  
Mesoporous Materials ◽  
Small Angle ◽  
Solid Phase ◽  
Gaussian Random Field ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Wetting Transition ◽  
X Rays ◽  
Angle Scattering

Small-angle scattering of X-rays (SAXS) or neutrons is one of the few experimental methods currently available for thein situanalysis of phenomena in mesoporous materials at the mesoscopic scale. In the case of disordered mesoporous materials, however, the main difficulty of the method lies in the data analysis. A stochastic model is presented, which enables one to reconstruct the three-dimensional nanostructure of liquids confined in disordered mesopores starting from small-angle scattering data. This so-called plurigaussian model is a multi-phase generalization of clipped Gaussian random field models. Its potential is illustrated through the synchrotron SAXS analysis of a gel permeated with a critical nitrobenzene/hexane solution that is progressively cooled below its consolute temperature. The reconstruction brings to light a wetting transition whereby the nanostructure of the pore-filling liquids passes from wetting layers that uniformly cover the solid phase of the gel to plugs that locally occlude the pores. Using the plurigaussian model, the dewetting phenomenon is analyzed quantitatively at the nanometre scale in terms of changing specific interface areas, contact angle and specific length of the triple line.

Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment

2014 ◽  
Vol 70 (2) ◽  
pp. 371-383 ◽  
Author(s):  
Søren A. R. Kynde ◽  
Nicholas Skar-Gislinge ◽  
Martin Cramer Pedersen ◽  
Søren Roi Midtgaard ◽  
Jens Baek Simonsen ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Small Angle ◽  
Structural Information ◽  
Protein Localization ◽  
Hybrid Approach ◽  
Small Angle Scattering ◽  
Phospholipid Bilayer ◽  
Scattering Data ◽  
Angle Scattering ◽  
Lipid Environment

Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein–lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.

Interactive visualization of electron density slices

2005 ◽  
Vol 38 (3) ◽  
pp. 563-565 ◽  
Author(s):  
Filipe R. N. C. Maia ◽  
Abraham Szöke ◽  
Warren DeLano ◽  
David van der Spoel
Keyword(s):  
High Resolution ◽  
Quantum Chemistry ◽  
Electron Density ◽  
Three Dimensional ◽  
Structure Model ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Molecular Visualization ◽  
Density Maps ◽  
Quantum Chemistry Calculations

A new tool has been developed to aid in the visualization of electron density in crystals or from quantum chemistry calculations. It displays the fine details of the electron density on a plane and the three-dimensional model of the molecule at the same time. The program enables the user to examine the details of weak or irregular features. Such features frequently occur in low-resolution maps, where they determine the correct tracing of a protein backbone. In high-resolution maps, solvent regions are difficult or impossible to observe using isosurfaces. The tool has been integrated into an existing molecular visualization package (PyMol) making it possible to observe and interact both with a structure model and the electron density slices freely, simultaneously and independently. This visualization model fills a gap in the visualization methods available to crystallographers and others who work with electron density maps.

scholarly journals Small-angle scattering and the protein crystallographer: A relationship of ever-increasing interest

2014 ◽  
Vol 36 (1) ◽  
pp. 44-48 ◽  
Author(s):  
David J. Scott
Keyword(s):  
High Resolution ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Structural Information ◽  
Crystallographic Analysis ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering ◽  
Relationship Of

Protein crystallography is one of the great intellectual achievements of the 20th Century, and it continues to open up new vistas of research as scientists are able to visualize in exquisite detail the molecules of Life. It has become increasingly apparent, however, that not all proteins are amenable to crystallographic analysis. These include (but are not confined to) proteins with functional flexible segments, glycoproteins and intrinsically disordered proteins. There are also proteins that, although rigid and folded, refuse to crystallize as an entire full-length construct, and hence high-resolution information has to be pieced together domain by domain. It is into this space that small-angle scattering is increasingly being used as the technique of choice with regard to attainable structural information.

scholarly journals Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

2014 ◽  
Vol 47 (2) ◽  
pp. 810-815 ◽  
Author(s):  
Andreas Hofmann ◽  
Andrew E. Whitten
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Ease Of Use ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Three Dimensional Models ◽  
Ray Scattering

Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described.MolScatis an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data.SAFIRis a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version ofMolScatis used to enable quick evaluation of the fit between the model and experimental scattering data.SAFIRalso provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach.

Combined scanning X-ray diffraction and holographic imaging of cardiomyocytes

2017 ◽  
Vol 50 (2) ◽  
pp. 612-620 ◽  
Author(s):  
Jan-David Nicolas ◽  
Marten Bernhardt ◽  
Martin Krenkel ◽  
Claudia Richter ◽  
Stefan Luther ◽  
...  
Keyword(s):  
Electron Density ◽  
Structural Changes ◽  
Structural Parameters ◽  
Scattering Data ◽  
Cardiac Muscle Cells ◽  
Saxs Data ◽  
Full Field ◽  
X Ray ◽  
Holographic Imaging ◽  
Freeze Dried

This article presents scanning small-angle X-ray scattering (SAXS) experiments on the actomyosin assemblies in freeze-dried neo-natal rat cardiac muscle cells. By scanning the cells through a sub-micrometre focused beam, the local structure and filament orientation can be probed and quantified. To this end, SAXS data were recorded and analyzed directly in reciprocal space to generate maps of different structural parameters (scanning SAXS). The scanning SAXS experiments were complemented by full-field holographic imaging of the projected electron density, following a slight rearrangement of the instrumental setup. It is shown that X-ray holography is ideally suited to complete missing scattering data at low momentum transfer in the structure factor, extending the covered range of spatial frequencies by two orders of magnitude. Regions of interest for scanning can be easily selected on the basis of the electron density maps. Finally, the combination of scanning SAXS and holography allows for a direct verification of possible radiation-induced structural changes in the cell.

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