Sustaining Orientation of Ubiquitin for Single Particle Imaging Using Electric Fields

Sammanfattning: Single-particle imaging, or SPI, is a method used to obtain the three-dimensional structure of particles. Repeatedly aiming X-rays at samples of a particle produces diffraction patterns, which are combined to a best-fit three-dimensional model of the particle. SPI of proteins can be improved by orienting the protein before imaging. Protein dipole orientation makes use of a protein's dipole moment and an external electric field to generate torque, which can orient the protein. A protein subject to an electric field may however result in damage of the protein's geometrical structure, or insufficient protein orientation, depending on the magnitude of the electric field. Sufficient protein orientation without substantial protein damage is possible in an interval of electric field strengths. The results in this report reveal that the method of SPI can be further improved. With a protein being fully oriented in an electric field, it is possible to reduce the electric field strength and yet sustain sufficient orientation, with some constraints. Longer times for imaging and less structural damage to the protein are hence possible. This study implements Molecular Dynamics (MD) and the most extensively used open-source MD software, GROMACS, with ubiquitin as a sample protein.