Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session W5: Crystallography Without Crystals |
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Sponsoring Units: FIAP Chair: Abbas Ourmazd, University of Wisconsin-Milwaukee Room: Colorado Convention Center Korbel 1A-1B |
Thursday, March 8, 2007 2:30PM - 3:06PM |
W5.00001: Crystallography without Crystals: An Overview Invited Speaker: Protein X-ray crystallography, an ``outgrowth of physics,'' is now the mainstay of biology, biochemistry, and the pharmaceutical industry. However, roughly 40{\%} of biological molecules do not crystallize. And although more than half a million proteins have been sequenced, the structure of less than 40,000 has been determined. By obviating the need for purification and crystallization, the ability to determine the structure of individual biological molecules would constitute a fundamental breakthrough. The confluence of four developments has generated intense interest in achieving this by short-pulse X-ray scattering: \begin{enumerate} \item The advent of algorithms capable of ``solving the phase problem'' with practical demonstrations in astronomy, high-energy electron diffraction, and protein crystallography [1,2,3]. \item Development of sophisticated techniques for determining the relative orientation of electron microscope \textit{images} of biological entities such as cells and large macromolecules [4]. \item Development of techniques for producing beams of hydrated proteins [3,5]. \item The promise of ultra-bright, short pulses of X-rays from X-ray Free Electron Lasers (XFELs) under construction in the US, Europe, and Japan. \end{enumerate} I will describe how these and other key developments have brought the prospect of single-molecule structure determination ``tantalizingly close,'' perhaps even closer than generally realized in the literature. \newline [1] J. R. Fienup, Appl. Opt. \textbf{21}, 2758 (1982). \newline [2] J. Miao et al. PNAS \textbf{98}, 6641 (2001). \newline [3] J.C.H. Spence et al. Acta Cryst. \textbf{A61}, 237 (2005) \newline [4] J. Frank, \textit{Three-Dimensional Electron Microscopy of Macromolecular Assemblies} (OUP Press, 2006) \newline [5] J.B. Fenn, J. Biomolecular Techniques \textbf{13}, 101 (2002). [Preview Abstract] |
Thursday, March 8, 2007 3:06PM - 3:42PM |
W5.00002: New X-Ray Optics and Sources for Single-particle Crystallography Invited Speaker: With the continued development of extremely bright x-ray sources, the minimum size of objects suitable for detailed study with x-ray scattering now approaches that of single molecules and other nanoparticles. To date, x-ray scattering is a tool which explores the statistical structural properties of an ensemble of particles. While this has been an extremely powerful approach to understanding the structural properties of materials and structure/property relationships, important details are often difficult to extract because of averaging. In particular, when looking at collections of nanoparticles, the only information available is small angle x-ray scattering which yields the general shape of the particles. Combining the current statistical information with detailed scattering from individual particles would greatly reduce the difficulty of extracting the important structural information. This talk will discuss the status of x-ray sources and optics, and explore the feasiblity and challenges of applying them to real-world crystallographic studies of single nanoparticles. [Preview Abstract] |
Thursday, March 8, 2007 3:42PM - 4:18PM |
W5.00003: Serial Crystallography Invited Speaker: To solve proteins which cannot be crystallized we have devised an aerodynamic focussing, monodispered droplet beam, which runs in single file across a synchrotron X-ray beam (LBNL Advanced Light Source) as it freezes in vacuum. The aim is to obtain a charge-density map of the protein at 0.7nm resolution , sufficient to locate alpha-helices. Water is removed before the proteins, coated by a thin ice-jacket, are aligned by the dipole moment induced by a 100 W NIR polarized fiber laser. All three orthogonal beams (proteins, X-rays, laser) intersect in a 10 micron diameter volume, and run continuously without sychronization. Elliptical polarization aligns molecular axes in direction but not sense. Data is collected continuously until adequate statistics are achieved before rotating the polarization to a new orientation. Details of the adiabatic laser-alignment and damping processes will be given. Misalignment is shown to be proportional to temperature and inversely to laser power and molecular volume. Polarizability tensor calculations for proteins will be discussed. Preliminary X-ray results (without laser) will be shown. Iterative methods for solving the phase problem will be demonstrated using experimental soft X-ray diffraction patterns from non-crystalline particles. Detailed simulations of the continuous diffraction patterns from a moving stream of partially aligned large hydrated molecules will be shown, and inverted to density maps using the Fienup-Gerchberg-Saxton algorithm. From this the exposure time and resolution may be estimated for tomographic reconstruction. Experimental comparisons of Rayleigh, electrospray and aerodynamic focussing droplet beam sources will also be described. The research team includes B.Doak, U. Weierstall, D. Shapiro (LBNL), D. Deponte, P. Fromme, D. Starodub, G. Hembree and H. Chapman (LLNL). [Preview Abstract] |
Thursday, March 8, 2007 4:18PM - 4:54PM |
W5.00004: Electron Densities from Diffraction Patterns of Randomly Oriented Molecules Invited Speaker: A diffraction pattern from a single biological molecule would consist of a more or less continuous intensity distribution rather than Bragg spots. Successive diffraction patterns from molecules of the same protein in a molecular beam would each represent the intensity diffracted by a single molecule in a random orientation. Each diffraction pattern may in fact be regarded as an Ewald sphere passing through a random part of the molecular reciprocal space containing the origin. In principle, these portions can be ``patched together'' to extract the 3-dimensional diffracted intensity distribution of the molecule. The problem is to identify each measured pixel of a 2-dimensional diffraction pattern produced by a molecule of unknown orientation with a unique position in the 3D reciprocal space representing the Fourier Transform of the molecule's electron density. Methods for identifying relative molecular orientations from a set of projected images have been developed for 3D electron microscopy [1]. However, the absence of phase information in diffraction patterns causes additional difficulties, including ``Friedel pair'' ambiguities. Nevertheless, inspired by 3D electron microscopy, we have explored two different approaches to this problem: the method of common lines [2]; and a projection matching method [3]. We will describe the extent to which such approaches, combined with an iterative phase recovery algorithm [4] may be expected to yield the electron density distribution, and hence the structure of individual biological molecules. \newline \newline [1] J. Frank, Three-Dimensional Electron Microscopy of Macromolecular Assemblies, Oxford University Press, 2006. \newline [2] A. B. Goncharov \textit{et al.}, Sov. Phys. Crystallogr. \textbf{32}, 504 (1987). \newline [3] P. Penczek \textit{et al.}, Ultramicroscopy \textbf{40}, 33 (1994). [4] e.g. J. R. Fienup, Appl. Optics \textbf{21}, 2758 (1982) [Preview Abstract] |
Thursday, March 8, 2007 4:54PM - 5:30PM |
W5.00005: Crypto-tomography: the data assembly challenge in single-molecule diffraction Invited Speaker: In the absence of a molecular alignment mechanism, the diffraction patterns collected in single-molecule XFEL experiments will sample randomly oriented, 2D slices of a 3D data set. The signal to noise ratio in the individual slices will be so low that the relative orientations of any two will be poorly determined. This talk describes a new strategy for data assembly, where the relationships among multiple slices are determined collectively. [Preview Abstract] |
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