PSX: Protein-Solvent Exchange - Software for calculation of deuterium-exchange effects in SANS measurements from protein coordinates

Recent developments in neutron scatteringinstrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. To extract most information from such experiments it is thus desirable to determine accurate estimates of deuteration levels. We introduce and document software for exploring the effect of hydrogen-deuterium exchangefor proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effectsof both heterogenous exchange rates throughout the protein structure and by varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scatteringon biological macromoleculesin solution. We find that the common assumption of 90% exchange is in many cases a strong overestimate with the rapid sample handling systems currently available. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing license.