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Deciphering solution scattering data with experimentally guided molecular dynamics simulations.

ABSTRACT: Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.

SUBMITTER: Bjorling A

PROVIDER: S-EPMC4325560 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Deciphering solution scattering data with experimentally guided molecular dynamics simulations.

Björling Alexander A Niebling Stephan S Marcellini Moreno M van der Spoel David D Westenhoff Sebastian S

Journal of chemical theory and computation 20150201 2

Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. The ...[more]

PMID: 25688181

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