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Talk: "SAXS/WAXS from molecular dynamics simulations: Towards atomic-resolution structures from solution scattering experiments"

Location: Oct. 22nd, 05:00 p.m. Seminarraum SR 45.31 (ZMB, Humboldtstr. 50, 3. Stock, Graz)

Date: 2012-10-22 - 0000-00-00

Jürgen Köfinger
National Institutes of Health, Bethesda, MD, USA

Montag, 22. 10. 2012, 17 Uhr (s.t.)
Seminarraum SR 45.31 (ZMB, Humboldtstr. 50, 3. Stock, Graz)

SAXS/WAXS from molecular dynamics simulations: Towards atomic-resolution structures from solution scattering experiments



Abstract
X-ray and neutron scattering experiments on macromolecules in solution (e.g., proteins, DNA and RNA molecules) provide signatures of their atomistic three-dimensional structure. Combining this information with molecular dynamics simulations, we aim to obtain atomistically detailed insight into structure, dynamics, and ultimately the biological function of these molecules.

Traditionally, scattering intensities are measured at small angles (SAXS and SANS for X-ray and neutron scattering, respectively), which provides information about size and shape of macromolecules. With advances in the generation of high-flux, monochromatic, X-rays, i.e., third generation synchrotron sources and X-ray free electron lasers, the wide-angle regime (WAXS) can now be probed with great precision, providing additional information about intra-molecular distances. These scattering intensities, which are Fourier transforms of pair-distance distribution functions, do not provide sufficient structural information for model-free reconstruction of the atomistic three-dimensional structures. However, the measured intensities have high discriminatory power and are used to distinguish between structural models. These models have to account for contributions to the intensity not only from the macromolecule itself, but also from its solvation layer and its excluded volume. Such models are readily provided by molecular dynamics simulations.

In my talk, I will first introduce solution scattering experiments, where the size disparity between sample volume and molecular structure allows us to probe the internal structure of the sample. This is contrast to molecular dynamics simulations, where a single macromolecule is solvated in a relatively tight fitting box. We therefore developed a simple and efficient method to calculate scattering intensities, in excellent agreement with experiment, by accounting properly for the finite system size. Moreover, in simulations we can directly asses the real-space information and calculate electron pair-distance distribution functions, which contain the maximum amount of information that can be probed in solution X-ray scattering experiments. We show that pair-distance distribution functions of a selection of proteins exhibit rich structural features, which are not probed in traditional SAXS experiments. Finally, I will briefly discuss the implications of our findings for the design of future scattering experiments their analysis.



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