Electric Field X-ray Scattering Measurements on Tobacco Mosaic Virus

Koch, Michel H. J.; Dorrington, E.; Kläring, R.; Michon, Anne-Marie; Sayers, Zehra; Marquet, Roland; Houssier, Claude

doi:10.1126/science.3353716

Cited by 13 publications

(7 citation statements)

References 16 publications

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“…In the dilute regime the position of its first maximum, determined by the centre to centre separation between rigid segments, varies like the square root of the concentration. The length distribution has, however, a strong influence on the relaxation times observed in electric field scattering [107,108] and on the slow mode observed in dynamic light scattering [109].…”

Section: Interacting Systems and Structure Factormentioning

confidence: 99%

Small-angle scattering studies of biological macromolecules in solution

2003

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Small-angle scattering (SAS) of x-rays and neutrons is a fundamental tool in the study of biological macromolecules. The major advantage of the method lies in its ability to provide structural information about partially or completely disordered systems. SAS allows one to study the structure of native particles in near physiological environments and to analyse structural changes in response to variations in external conditions. In this review we concentrate on SAS studies of isotropic systems, in particular, solutions of biological macromolecules, an area where major progress has been achieved during the last decade. Solution scattering studies are especially important, given the challenge of the 'post-genomic' era with vast numbers of protein sequences becoming available. Numerous structural initiatives aim at large-scale expression and purification of proteins for subsequent structure determination using x-ray crystallography and NMR spectroscopy. Because of the requirement of good crystals for crystallography and the low molecular mass requirement of NMR, a significant fraction of proteins cannot be analysed using these two high-resolution methods. Progress in SAS instrumentation and novel analysis methods, which substantially improve the resolution and reliability of the structural models, makes the method an important complementary tool for these initiatives. The review covers the basics of x-ray and neutron SAS, instrumentation, mathematical methods used in data analysis and major modelling techniques. Examples of applications of SAS to different types of biomolecules (proteins, nucleic acids, macromolecular complexes, polyelectrolytes) are presented. A brief account of the new opportunities offered by third and fourth generation synchrotron radiation sources (time-resolved studies, coherent scattering and single molecule scattering) is also given.

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Section: Interacting Systems and Structure Factormentioning

confidence: 99%

Small-angle scattering studies of biological macromolecules in solution

2003

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“…At higher concentrations other effects also play a role as shown by extensive theoretical calculations (Weyerich et al 1990). The length distribution has, however, a strong influence on the relaxation times observed in electric field scattering (Koch et al 1988(Koch et al , 1995 and on the slow mode observed in dynamic light scattering (Skibinska et al 1999).…”

Section: Linearizing the Problem For Moderate Interactions : The Secomentioning

confidence: 99%

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

Koch

Vachette

Svergun

2003

Quart. Rev. Biophys.

500

481

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A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies--on ribosomes and on the allosteric protein aspartate transcarbamoylase--illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

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“…By rotating the polarization of an elliptically polarized laser, this process may then be repeated for many orientations to fill the 3D volume in reciprocal space with diffraction data. Other alignment methods, such as static electric or magnetic fields, or flow alignment have been considered and demonstrated (Bras et al, 1998;Koch et al, 1988), as well as employed in the field of birefringence measurements (Fredericq and Houssier, 1973). These alignment techniques may also be helpful to avoid the problem of orientation classification of diffraction patterns from single molecules in random orientations, which is the main difficulty arising for single molecule imaging using pulsed X-ray free-electron lasers (Chapman et al, 2006a;Huldt et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Dose, exposure time and resolution in serial X-ray crystallography

Starodub

Rez

Hembree

et al. 2007

J Synchrotron Radiat

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The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent Xray imaging. We find that multiple single-file protein beams will be needed for subnanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 7 Å should be possible with short (below 100 s) exposures.

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Electric Field X-ray Scattering Measurements on Tobacco Mosaic Virus

Cited by 13 publications

References 16 publications

Small-angle scattering studies of biological macromolecules in solution

Small-angle scattering studies of biological macromolecules in solution

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

Dose, exposure time and resolution in serial X-ray crystallography

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