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Issue 21, 2008
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Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures

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Abstract

Evidence from cross section data indicates that ubiquitin +13 ions lose their secondary and tertiary structure in mass spectrometric experiments. These transitions from the folded state into the near linear final structure occur at the experimental temperatures on time scales that are far too long for conventional molecular dynamics simulations. In this study, an approach to mass spectrometric unfolding processes is developed and a detailed application to an ubiquitin +13 ion system is presented. The approach involves a sequence of molecular dynamics simulations at gradually increasing temperatures leading to identification of major intermediate states, and the unfolding pathway. The unfolding rate at any temperature can then be calculated by a Rice–Ramsperger–Kassel (RRK) approach. For ubiquitin +13, three interesting intermediate states were found and the final near linear geometry was computed. The several relevant energy barriers calculated for the process are in the range of 7 to 15 kcal mol−1. The unfolding time scale at 300 K was computed to be 2 ms. Cross section calculations using a hard sphere scattering model were carried out for the final structure and found to be in good accord with the results of electrospray experiments supporting the theoretical model used. The approach employed here should be applicable to any other solvent-free protein system.

Graphical abstract: Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures

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Publication details

The article was received on 03 Dec 2007, accepted on 13 Mar 2008 and first published on 08 Apr 2008


Article type: Paper
DOI: 10.1039/B718610J
Citation: Phys. Chem. Chem. Phys., 2008,10, 3077-3082
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    Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures

    E. Segev, T. Wyttenbach, M. T. Bowers and R. B. Gerber, Phys. Chem. Chem. Phys., 2008, 10, 3077
    DOI: 10.1039/B718610J

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