Conformers of Ubiquitin 6+ for Different Charge Distributions: Atomistic Structures and Ion Mobility Cross Sections

In spite of the fact that protein chemistry occurs in solution, studying the structure of desolvated proteins in Mass Spectrometry vacuum conditions allows to study biological molecules in complete isolation. The Electro Spray Ionization process results in charged protein conformers for which the charge locations distribution and the corresponding structure are not known. In this paper we explore the influence of different charge distributions on the structure of conformers of Ubiquitin 6+ in the vacuum conditions of Mass Spectrometry. Using the Tinker implementation of the AMBER99FF force field the atomistic lowest energy structures for those charge distributions were calculated by the DEEPSAM algorithm. Differences among the calculated structures are analyzed and discussed in terms of the relation to experimentally observable Ion Mobility Mass Spectrometry cross sections. They also are compared to the neutral Ubiquitin's native structure, and to the nearly linear structure of the Ubiquitin 13+ ion. In g...