Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles

Abstract

Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.

Figure 1

Screenshots of (top) the main welcome page and (bottom) the fit page on the Vesicle Viewer website. The fit page showcases the parameter selection panel (left), fit graph, including data points and the fit line (middle), and the scale and background adjustment panel (right). To see this figure in color, go online.

Figure 2

A flowchart describing the path taken as the user moves through Vesicle Viewer. The process begins with user authentication and proceeds as various inputs are requested. All data collected from a user are connected to their account and visible only to them. Users may move forward or backward through the program as they like; data are selectively displayed to them to help guide them through the process and keep things organized.

Figure 3

(a) Schematic of POPC bilayer indicating the EZ-SDP slabs. Slab colors correspond to the water (blue), headgroups (gold), the methylene (red), and the terminal methyl at the midplane (dashed line). These colors correspond to the volume probability distributions of (b). In (c) and (d), the SAXS and SANS, respectively, are shown. Open symbols indicate data generated from the MD simulations, and the solid lines represent the VV optimized models. The D₂O contrasts are indicated as 100%, 75%, and 50% D₂O. To see this figure in color, go online.

Figure 4

In (a) and (b), the SAXS and SANS curves, respectively, are shown. The open symbols are experimental data, and the solid line represent the optimized model. Note, the 50% D₂O SANS curve of (b) appears cut off because values must be >0 to be plotted on a logarithmic scale. In (c) and (d), the electron density (ED) profile and the neutron scattering length density profile from the optimized model, respectively, are shown. To see this figure in color, go online.