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. 2016 Aug 9;28(1):38–49. doi: 10.1007/s13361-016-1449-2

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© The Author(s) 2016

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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Computational strategy for modeling of chromophore-tagged ubiquitin structures in the gas phase. (a) Schematic overview of simulation conditions chosen for different stages (stars denote chromophores), see main text; (b) color-inverted graphical representation of the H₂O/CH₃OH simulation box (including ions) featuring a natively folded ubiquitin (compact, left) and a partially unfolded structure (elongated, right); (c) structural properties of chromophore-tagged ubiquitin in the gas phase in a low (6+) and a high (13+) charge state after equilibration in the gas phase and replica-exchange MD. Peptide backbone in ribbon representation color coded by residue index (blue N-terminus, red C-terminus)