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Proteins structures under electrospray conditions
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.ORCID iD: 0000-0002-9804-5009
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2007 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 46, no 4, 933-945 p.Article in journal (Refereed) Published
Abstract [en]

During electrospray ionization (ESI), proteins are transferred from solution into vacuum, a process that influences the conformation of the protein. Exactly how much the conformation changes due to the dehydration process, and in what way, is difficult to determine experimentally. The aim of this study is therefore to monitor what happens to protein structures as the surrounding waters gradually evaporate, using computer simulations of the transition of proteins from water to vacuum. Five different proteins have been simulated with water shells of varying thickness, enabling us to mimic the entire dehydration process. We find that all protein structures are affected, at least to some extent, by the transfer but that the major features are preserved. A water shell with a thickness of roughly two molecules is enough to emulate bulk water and to largely maintain the solution phase structure. The conformations obtained in vacuum are quite similar and make up an ensemble which differs from the structure obtained by experimental means, and from the solution phase structure as found in simulations. Dehydration forces the protein to make more intramolecular hydrogen bonds, at the expense of exposing more hydrophobic area (to vacuum). Native hydrogen bonds usually persist in vacuum, yielding an easy route to refolding upon rehydration. The findings presented here are promising for future bio-imaging experiments with X-ray free electron lasers, and they strongly support the validity of mass spectrometry experiments for studies of intra- and intermolecular interactions.

Place, publisher, year, edition, pages
2007. Vol. 46, no 4, 933-945 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-96401DOI: 10.1021/bi061182yISI: 000243682700001OAI: oai:DiVA.org:uu-96401DiVA: diva2:170965
Available from: 2007-11-09 Created: 2007-11-09 Last updated: 2016-09-09Bibliographically approved
In thesis
1. From Solution into Vacuum - Structural Transitions in Proteins
Open this publication in new window or tab >>From Solution into Vacuum - Structural Transitions in Proteins
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure.

Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure.

Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure.

Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions.

The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket, 2007. viii, 44 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 360
Keyword
molecular dynamics, computer simulations, mass spectrometry, electrospray ionization, free-electron laser, vacuum structure of proteins, solvation, desolvation, single molecule imaging
National Category
Other Basic Medicine
Identifiers
urn:nbn:se:uu:diva-8300 (URN)978-91-554-7014-2 (ISBN)
Public defence
2007-12-01, B7:113a, BMC, Husargatan 3, Uppsala, 13:00
Opponent
Supervisors
Available from: 2007-11-09 Created: 2007-11-09 Last updated: 2016-08-24Bibliographically approved
2. 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.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 826
Keyword
Molecular dynamics, gas phase, proteins, micelles, proton transfer, Grothuss mechanism, kinetics
National Category
Physical Sciences
Research subject
Physics with specialization in Biophysics
Identifiers
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)
Opponent
Supervisors
Available from: 2011-05-04 Created: 2011-04-10 Last updated: 2011-07-01Bibliographically approved

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