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

Citation:

Goldstein, M. ; Zmiri, L. ; Segev, E. ; Wyttenbach, T. ; Gerber, B. R. An atomistic structure of ubiquitin+13 relevant in mass spectrometry: Theoretical prediction and comparison with experimental cross sections. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014, 367, 10-15.

Date Published:

JUN 15

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 3(10)-helices and one is an a-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. (c) 2014 Elsevier B.V. All rights reserved.