The function of proteins is closely linked to their three dimensional structure. Protein structure, however, is not static but constantly changing. The same is true for any chemical reaction, the structural dynamics of the reactants will determine the outcome of the reaction. In our research we use time-resolved X-ray scattering to characterize structural change in light sensitive proteins and photosensitive chemicals. To structurally interpret these data it is essential to use computational methods.
Over the last years we have made extensive use of molecular dynamics simulations to analyze the results of X-ray solution scattering experiments on different photoreceptor proteins belonging to the phytochrome [Takala et al., Nature 2014, doi: 10.1038/nature13310; Takala et al., Struct. Dyn. 2016, doi: 10.1063/1.4961911], LOV-domain containing [Berntsson et al., Structure 2017, doi: 10.1016/j.str.2017.04.006; Berntsson et al., Nat. Commun. 2017, doi: 10.1038/s41467-017-00300-5] and more recently cryptochrome [Berntsson et al., in preparation] protein families. We have also applied similar analysis schemes to study the bond fission in diiodomethane following the absorption of light [Panman et al., Submitted].
The simulations add atomic scale information to low resolution experimental data. The helps revealing the structural photocycle of different photoreceptor proteins and the structural events during fundamental chemical reactions.