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Lipid Bilayer Structure Refinement with SAXS/SANS Based Restrained Ensemble Molecular Dynamics

preprint
revised on 19.03.2021, 17:38 and posted on 22.03.2021, 05:19 by Yevhen Cherniavskyi, Svetlana Baoukina, Bryan W. Holland, D. Peter Tieleman
Small-angle scattering is a powerful technique that can probe the structure of lipid bilayers on the nanometer scale. Retrieving the real space structure of lipid bilayers from the scattering intensity can be a challenging task, as their fluid nature results in a liquid-like scattering pattern which is hard to interpret. The standard approach to this problem is to describe the bilayer structure as a sum of density distributions of separate components of the lipid molecule and then to fit the parameters of the distributions against experimental data. The accuracy of the density-based analysis is partially limited by the choice of the functions used to describe component distributions, especially in the case of multi-component bilayers. The number of parameters in the model is balanced by the need for an accurate description of the underlying bilayer structure and the risk of overfitting the data. Here, we present an alternative method for the interpretation of small-angle scattering intensity data for lipid bilayers. The method is based on restrained ensemble molecular dynamics simulations that allow direct incorporation of the scattering data into the simulations in the form of a restraining potential. This approach combines the information implicitly contained in the simulation force field with structural data from the scattering intensity and is free from prior assumptions regarding the bilayer structure.

Funding

Natural Science and Engineering Research Council of Canada

Canada Research Chairs Program

Compute Canada

History

Email Address of Submitting Author

yevhen.chernivaskyi@ucalgary.ca

Institution

University of Calgary

Country

Canada

ORCID For Submitting Author

0000-0002-2671-1949

Declaration of Conflict of Interest

no conflict of interest

Version Notes

Equals sign was missing in eq.8 and 9. Now it is displayed properly. A new note is added that states that the abstract of the current paper was previously published in a Supplement of Biophysical Journal among all other abstracts of the research presented at the 63rd Annual Meeting of Biophysical Society.

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