Dipole Orientation of Gas Phase Ubiquitin Using Time Dependent Electric Fields

Sammanfattning: The method of dipole orientation of protein complexes using electric fields plays a key role in the development of single particle imaging, since it enables orientation of the protein in vacuum. In the orientation process the protein is exposed to an external electric field along which the dipole axis of the protein will eventually align. Earlier studies using molecular dynamics simulations have implemented a constant electric field to examine the dipole orientation process. However, when injected into the electric field the protein experiences a gradually increasing field strength converging to some terminal field strength rather than a constant electric field. In order to examine the effects of the time-dependant nature of the electric field, in comparison to a constant one, fields with different time dependances were implemented in molecular dynamics simulations in vacuum performed with GROMACS. Ubiquitin was chosen as a model protein. The results of the study show time-increasing fields tend to result in slower orientation, but preserve the structure of the protein better than for a constant field. It was also shown that after 10 ns electric field exposure, with terminal field strengths greater  or equal to 0.6Vnm^-1, there was no apparent difference of the average degree of orientation of proteins within the time-increasing fields and the constant one. However, for fields of greater or equal to 1.5Vnm^-1 the constant field tended to result in a larger change of the protein structure.