uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Exploring the Molecular Dynamics of Proteins and Viruses
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Knowledge about structure and dynamics of the important biological macromolecules — proteins, nucleic acids, lipids and sugars — helps to understand their function. Atomic-resolution structures of macromolecules are routinely captured with X-ray crystallography and other techniques. In this thesis, simulations are used to explore the dynamics of the molecules beyond the static structures.

Viruses are machines constructed from macromolecules. Crystal structures of them reveal little to no information about their genomes. In simulations of empty capsids, we observed a correlation between the spatial distribution of chloride ions in the solution and the position of RNA in crystals of satellite tobacco necrosis virus (STNV) and satellite tobacco mosaic virus (STMV). In this manner, structural features of the non-symmetric RNA could also be inferred.

The capsid of STNV binds calcium ions on the icosahedral symmetry axes. The release of these ions controls the activation of the virus particle upon infection. Our simulations reproduced the swelling of the capsid upon removal of the ions and we quantified the water permeability of the capsid. The structure and dynamics of the expanded capsid suggest that the disassembly is initiated at the 3-fold symmetry axis.

Several experimental methods require biomolecular samples to be injected into vacuum, such as mass-spectrometry and diffractive imaging of single particles. It is therefore important to understand how proteins and molecule-complexes respond to being aerosolized. In simulations we mimicked the dehydration process upon going from solution into the gas phase. We find that two important factors for structural stability of proteins are the temperature and the level of residual hydration. The simulations support experimental claims that membrane proteins can be protected by a lipid micelle and that a non-membrane protein could be stabilized in a reverse micelle in the gas phase. A water-layer around virus particles would impede the signal in diffractive experiments, but our calculations estimate that it should be possible to determine the orientation of the particle in individual images, which is a prerequisite for three-dimensional reconstruction.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. , 45 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 919
Keyword [en]
molecular dynamics, virus dynamics, capsid dissolution, satellite tobacco necrosis virus, satellite tobacco mosaic virus, virus genome structure, gas phase protein structure, water layer, micelle embedded protein, membrane protein
National Category
Biological Sciences Biochemistry and Molecular Biology Biophysics Structural Biology
Research subject
Chemistry with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-172284ISBN: 978-91-554-8335-7 (print)OAI: oai:DiVA.org:uu-172284DiVA: diva2:513912
Public defence
2012-05-25, B41, Uppsala Biomedicinska Centrum, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Note
BMC B41, 25/5, 9:15Available from: 2012-05-04 Created: 2012-04-03 Last updated: 2012-08-01Bibliographically approved
List of papers
1. Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
Open this publication in new window or tab >>Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
2012 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 8, no 5, e1002502- p.Article in journal (Refereed) Published
Abstract [en]

Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

National Category
Biophysics Structural Biology
Identifiers
urn:nbn:se:uu:diva-171701 (URN)10.1371/journal.pcbi.1002502 (DOI)000305964600012 ()
Available from: 2012-03-26 Created: 2012-03-26 Last updated: 2013-07-04Bibliographically approved
2. Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids
Open this publication in new window or tab >>Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids
2012 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 7, 2474-2483 p.Article in journal (Refereed) Published
Abstract [en]

The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the S-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of genome packaging might be exploited for both antiviral therapy and technological applications.

National Category
Structural Biology Biophysics
Identifiers
urn:nbn:se:uu:diva-172285 (URN)10.1021/ct3002128 (DOI)000306245900032 ()
Available from: 2012-04-03 Created: 2012-04-03 Last updated: 2012-08-06Bibliographically approved
3. Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study
Open this publication in new window or tab >>Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study
2009 (English)In: Biochemistry, ISSN 1520-4995, E-ISSN 0006-2960, Vol. 48, no 5, 1006-1015 p.Article in journal (Refereed) Published
Abstract [en]

A recently published paper describes encapsulation of myoglobin into cetyl trimethylammonium bromide (CTAB) micelles by electrospray ionization followed by detection using mass spectrometry [Sharon, M., et al. (2007) J. Am. Chem. Soc. 129, 8740-8746]. Here we present molecular dynamics simulations aimed at elucidating the structural transitions that accompany the encapsulation and dehydration processes. Myoglobin associates with CTAB surfactants in solution, but no complete reverse micelle is formed. Upon removal of most of the water and exposure of the system to vacuum, a stable protein-surfactant reverse micelle forms. The surfactants shield the protein to a large extent from dehydration-related conformational changes, in the same manner that a water shell does, as previously described by Patriksson et al. [(2007) Biochemistry 46, 933-945]. Solvated CTAB micelles undergo a rapid inversion when transported to the gas phase and form very stable reverse micelles, independent of the amount of water present.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-104076 (URN)10.1021/bi801952f (DOI)000263047900022 ()19154126 (PubMedID)
Available from: 2009-05-27 Created: 2009-05-27 Last updated: 2014-11-05Bibliographically approved
4. 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
Show others...
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
5. Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo
Open this publication in new window or tab >>Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo
2009 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 46, 16606-16607 p.Article in journal (Refereed) Published
Abstract [en]

We report the first molecular dynamics simulations of an integral membrane protein in a detergent micelle under vacuum conditions. To mimic the dehydration process in electrospray ionization, the N-terminal outer membrane protein A transmembrane domain (OmpA171) from Escherichia coli embedded in a dodecylphosphocholine (DPC) detergent micelle has been simulated with water shells of varying thickness. Removal of the water molecules leaves the membrane protein relatively unaffected by the vacuum conditions. The major structural change occurs in the surrounding micelle, where the DPC molecules structurally rearrange from a normal-phase micelle with DPC detergents radiating spherically from OmpA171 to a structure where the DPC molecules form a layered onion structure in which the head groups, which strive to interact with each other, form an intermediate layer between the inner layer of tail groups that are expelled to the surface, protruding into the void.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-127396 (URN)10.1021/ja902962y (DOI)000272185400002 ()
Available from: 2010-07-14 Created: 2010-07-13 Last updated: 2014-11-05Bibliographically approved
6. 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
7. Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information
Open this publication in new window or tab >>Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information
Show others...
2011 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, 031907-1-031907-5 p.Article in journal (Refereed) Published
Abstract [en]

Coherent diffractive imaging using x-ray free-electron lasers (XFELs) may provide a unique opportunity for high-resolution structural analysis of single particles sprayed from an aqueous solution into the laser beam. As a result, diffraction images are measured from randomly oriented objects covered by a water layer. We analyze theoretically how the thickness of the covering water layer influences the structural and orientational information contained in the recorded diffraction images. This study has implications for planned experiments on single-particle imaging with XFELs.

National Category
Condensed Matter Physics
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-166440 (URN)10.1103/PhysRevE.83.031907 (DOI)000288699900004 ()
Available from: 2012-01-12 Created: 2012-01-12 Last updated: 2015-07-22Bibliographically approved

Open Access in DiVA

fulltext(8428 kB)1131 downloads
File information
File name FULLTEXT01.pdfFile size 8428 kBChecksum SHA-512
979732b8aebe7eb42f8c9d202f57f20ab9ad03a5ae78401dd5d59213b5dad86972aa8f08b956525fe8a5b48751c6cd89709fc8cb4909f832c23289b94ef7d5e9
Type fulltextMimetype application/pdf
Buy this publication >>

Search in DiVA

By author/editor
Larsson, Daniel
By organisation
Computational and Systems Biology
Biological SciencesBiochemistry and Molecular BiologyBiophysicsStructural Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 1131 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 591 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf