An atomistic structure of ubiquitin +13 relevant in mass spectrometry: Theoretical prediction and comparison with experimental cross sections

Abstract

The 3D structure of protein ions in the gas phase is presently not obtainable from experiment in atomic detail. Here we use a theoretical approach to determine the 3D structure of ubiquitin +13 (UBQ +13) in the absence of solvent. Global minimization of the UBQ +13 force field within the recently developed DEEPSAM algorithm yields a nearly linear overall geometry. Four helical segments are found in this full atomistic structure – three of them are 310-helices and one is an α-helix. The protein cross section computed for the predicted structure is in excellent accord with ion mobility experimental results of UBQ +13. This suggests that computational structure predictions together with (theoretical and experimental) cross section values can serve as a useful tool for determining the atomistic structures of charged proteins in the gas phase.