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Effcient Dynamic Proton Transfer in Classical Molecular Dynamics: Instantaneous Charge Exchange
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. (David van der Spoel)
Max Planck Institute for Biophysical Chemistry.
Theoretical & Computational Membrane Biology, Universität des Saarlandes.
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(English)Manuscript (preprint) (Other academic)
URN: urn:nbn:se:uu:diva-150760OAI: oai:DiVA.org:uu-150760DiVA: diva2:409643
Available from: 2011-04-10 Created: 2011-04-05 Last updated: 2011-07-01
In thesis
1. Gas-Phase Protein Structure Under the Computational Microscope: Hydration, Titration, and Temperature
Open this publication in new window or tab >>Gas-Phase Protein Structure Under the Computational Microscope: Hydration, Titration, and Temperature
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Although the native environment of the vast majority of proteins is a complex aqueous solution, like the interior of a cell, many analysis methods for assessing chemical and physical properties of biomolecules require the sample to be aerosolized; that is, transferred to the gas-phase. An important example is electrospray-ionization mass spectrometry, which can provide a wide range of information about e.g. biomolecules. That includes structural features, charged sites, and gas-phase equilibrium constants of reactions. To date much of the microscopic detail about the aerosolization process remains beyond the limits of experimental observation. How is the gas-phase structure of a protein related to the solution-phase structure? How transferable are observations done in the gas phase to solution? On the basis of classical molecular-dynamics simulations this thesis reveals important features of gas-phase biomolecular structure near the end of the the aerosolization process, the relation between gas-phase structure and native structure, microscopic detail about the de-wetting of gas-phase biomolecules, and the impact of temperature and residual solvent on structure preservation. Residual solvent on proteins is shown to have a stabilizing effect on proteins, in part because it allows the scarcely hydrated protein to cool through solvent evaporation, but also because part of the solvent provides structural support by hydrogen bonding to the protein. The gas-phase structure of micellar aggregates is seen to depend on composition, where some types of lipids cause rapid micelle inversion, whereas others maintain much of their collective structure when transferred to the gas phase. The thesis also addresses proton-transfer reactions, which have an impact on the biophysical aspects of proteins, both in the gas phase and in solution. The thesis presents a computationally efficient method for including proton-transfer reactions in classical molecular-dynamics simulations, which expands the range of scientific problems that can be addressed with molecular dynamics.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2011. 65 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 826
Molecular dynamics, gas phase, proteins, micelles, proton transfer, Grothuss mechanism, kinetics
National Category
Physical Sciences
Research subject
Physics with specialization in Biophysics
urn:nbn:se:uu:diva-151006 (URN)978-91-554-8080-6 (ISBN)
Public defence
2011-05-25, BMC B22, Husargatan 3, Uppsala, 09:00 (English)
Available from: 2011-05-04 Created: 2011-04-10 Last updated: 2011-07-01Bibliographically approved

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