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Gas-Phase Protein Structure Under the Computational Microscope: Hydration, Titration, and Temperature
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. (David van der Spoel)
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 [en]
Molecular dynamics, gas phase, proteins, micelles, proton transfer, Grothuss mechanism, kinetics
National Category
Physical Sciences
Research subject
Physics with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-151006ISBN: 978-91-554-8080-6OAI: oai:DiVA.org:uu-151006DiVA: diva2:409651
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
List of papers
1. Proteins structures under electrospray conditions
Open this publication in new window or tab >>Proteins structures under electrospray conditions
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.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96401 (URN)10.1021/bi061182y (DOI)000243682700001 ()
External cooperation:
Available from: 2007-11-09 Created: 2007-11-09 Last updated: 2016-09-09Bibliographically approved
2. Structural stability of electrosprayed proteins: temperature and hydration effects
Open this publication in new window or tab >>Structural stability of electrosprayed proteins: temperature and hydration effects
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2009 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 36, 8069-8078 p.Article in journal (Refereed) Published
Abstract [en]

Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 angstrom preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-142196 (URN)10.1039/b903846a (DOI)000269548300033 ()
External cooperation:
Available from: 2011-01-13 Created: 2011-01-13 Last updated: 2016-09-09Bibliographically approved
3. Proteins, Lipids, and Water in the Gas Phase
Open this publication in new window or tab >>Proteins, Lipids, and Water in the Gas Phase
2011 (English)In: Macromolecular Bioscience, ISSN 1616-5187, E-ISSN 1616-5195, Vol. 11, no 1, 50-59 p.Article in journal (Refereed) Published
Abstract [en]

Evidence from mass-spectrometry experiments and molecular dynamics simulations suggests that it is possible to transfer proteins, or in general biomolecular aggregates, from solution to the gas-phase without grave impact on the structure. If correct, this allows interpretation of such experiments as a probe of physiological behavior. Here, we survey recent experimental results from mass spectrometry and ion-mobility spectroscopy and combine this with observations based on molecular dynamics simulation, in order to give a comprehensive overview of the state of the art in gas-phase studies. We introduce a new concept in protein structure analysis by determining the fraction of the theoretical possible numbers of hydrogen bonds that are formed in solution and in the gas-phase. In solution on average 43% of the hydrogen bonds is realized, while in vacuo this fraction increases to 56%. The hydrogen bonds stabilizing the secondary structure (alpha-helices, beta-sheets) are maintained to a large degree, with additional hydrogen bonds occurring when side chains make new hydrogen bonds to rest of the protein rather than to solvent. This indicates that proteins that are transported to the gas phase in a native-like manner in many cases will be kinetically trapped in near-physiological structures. Simulation results for lipid-and detergent-aggregates and lipid-coated (membrane) proteins in the gas phase are discussed, which in general point to the conclusion that encapsulating proteins in "something'' aids in the conservation of native-like structure. Isolated solvated micelles of cetyl-tetraammonium bromide quickly turn into reverse micelles whereas dodecyl phosphocholine micelles undergo much slower conversions, and do not quite reach a reverse micelle conformation within 100 ns.

Keyword
GROMACS, insulin, lysozyme, myoglobin, OmpA, structures, Trp-Cage, ubiquitin, X-ray
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-145221 (URN)10.1002/mabi.201000291 (DOI)000285932600006 ()21136535 (PubMedID)
External cooperation:
Available from: 2011-02-08 Created: 2011-02-07 Last updated: 2016-09-09Bibliographically approved
4. Effcient Dynamic Proton Transfer in Classical Molecular Dynamics: Instantaneous Charge Exchange
Open this publication in new window or tab >>Effcient Dynamic Proton Transfer in Classical Molecular Dynamics: Instantaneous Charge Exchange
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(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:uu:diva-150760 (URN)
Available from: 2011-04-10 Created: 2011-04-05 Last updated: 2011-07-01

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