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Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2009 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, 031905- p.Article in journal (Refereed) Published
Abstract [en]

X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7 angstrom and 7.6 angstrom, respectively. These are significantly worse than the root-mean-square deviation of the hydrated (2.7 angstrom for all atoms and 1.45 angstrom for C-alpha positions) or dehydrated (3.7 angstrom for all atoms and 2.5 angstrom for C-alpha positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.

Place, publisher, year, edition, pages
2009. Vol. 80, no 3, 031905- p.
Keyword [en]
x-ray-diffraction, electron cascades, proteins, crystallography, resolution, pulses
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-111993DOI: 10.1103/PhysRevE.80.031905ISI: 000270383400104ISBN: 1539-3755 (print)OAI: oai:DiVA.org:uu-111993DiVA: diva2:284252
Note

Part 1 501LM Times Cited:0 Cited References Count:32

Available from: 2010-01-05 Created: 2010-01-05 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Ultrafast Coherent X-ray Diffractive Nanoimaging
Open this publication in new window or tab >>Ultrafast Coherent X-ray Diffractive Nanoimaging
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 49 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 731
Keyword
XFEL, Phasing, Image Reconstruction, Single Particle Imaging, Ultrafast Diffraction, X-ray diffraction, Coherent Diffractive Imaging, CXDI
Identifiers
urn:nbn:se:uu:diva-122002 (URN)978-91-554-7776-9 (ISBN)
Public defence
2010-05-14, B41, BMC, Husargatan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2010-04-22 Created: 2010-04-05 Last updated: 2010-05-11Bibliographically approved
2. Flash Diffractive Imaging in Three Dimensions
Open this publication in new window or tab >>Flash Diffractive Imaging in Three Dimensions
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers.

These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus.

We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient.

Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 68 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 960
Keyword
X-ray, diffraction, mimivirus, three dimensional, phase retrieval, EMC, manifold embedding, CXI, FEL, free-electron laser, single particle
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-179643 (URN)978-91-554-8439-2 (ISBN)
Public defence
2012-10-05, B22, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2012-09-14 Created: 2012-08-21 Last updated: 2013-01-22Bibliographically approved

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Maia, Filipe R. N. C.Ekeberg, TomasTimneanu, Nicusorvan der Spoel, DavidHajdu, Janos

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