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

Moshe Goldstein*, Liron Zmiri, Elad Segev, Thomas Wyttenbach, R. Benny Gerber

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

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.

Original languageEnglish
Pages (from-to)10-15
Number of pages6
JournalInternational Journal of Mass Spectrometry
Volume367
DOIs
StatePublished - 15 Jun 2014

Keywords

  • Highly charged protein
  • Mass spectrometry
  • Theoretical prediction

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