WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics.

Christopher J Knight,Jochen S Hub

doi:10.1093/nar/gkv309

Christopher J Knight, Jochen S Hub

Open Access

https://doi.org/10.1093/nar/gkv309

Copy DOI

Journal: Nucleic acids research	Publication Date: Apr 8, 2015
Citations: 149	License type: CC BY 4.0

Affiliation: University of Göttingen

Abstract

Small- and wide-angle X-ray scattering (SWAXS) has evolved into a powerful tool to study biological macromolecules in solution. The interpretation of SWAXS curves requires their accurate predictions from structural models. Such predictions are complicated by scattering contributions from the hydration layer and by effects from thermal fluctuations. Here, we describe the new web server WAXSiS (WAXS in solvent) that computes SWAXS curves based on explicit-solvent all-atom molecular dynamics (MD) simulations (http://waxsis.uni-goettingen.de/). The MD simulations provide a realistic model for both the hydration layer and the excluded solvent, thereby avoiding any solvent-related fitting parameters, while naturally accounting for thermal fluctuations.

Highlights

Small- and wide-angle X-ray scattering (SAXS/WAXS or SWAXS) has been gaining increased popularity as a structural probe for biomolecules in solution [1,2,3,4]
We describe the new web server WAXSiS (WAXS in solvent) that computes SWAXS curves based on explicit-solvent all-atom molecular dynamics (MD) simulations
The scattering contribution from the excluded solvent is computed from an MD trajectory of a pure-water simulation system, which is stored on the WAXSiS server

Summary

INTRODUCTION

Small- and wide-angle X-ray scattering (SAXS/WAXS or SWAXS) has been gaining increased popularity as a structural probe for biomolecules in solution [1,2,3,4]. The hydration layer has internal structure, which may contribute the scattering signal at wide angles. Apart from such complications with the solvent, thermal fluctuations have an effect on the scattering signal, in particular at wider angles [8,9]. A number of methods have been developed to predict SWAXS curves from structural models, and some of those are available as web servers ((6) and references therein). Net intensities computed by the two subtraction schemes differ slightly (yet significantly) at small angles, and they differ highly at wide angles where the water scattering becomes dominant.

WAXSIS METHOD

Findings

CONCLUSION