Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data
Author(s)
Latham, Andrew P; Zhang, Bin
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Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for biomolecules in solution. We develop a highly efficient maximum entropy approach to fit SAXS data by introducing minimal biases to a coarse-grained protein force field, the associative memory, water mediated, structure, and energy model (AWSEM). We demonstrate that the resulting force field, AWSEM-SAXS, succeeds in reproducing scattering profiles and models protein structures with shapes that are in much better agreement with experimental results. Quantitative metrics further reveal a modest, but consistent, improvement in the accuracy of modeled structures when SAXS data are incorporated into the force field. Additionally, when applied to a multiconformational protein, we find that AWSEM-SAXS is able to recover the population of different protein conformations from SAXS data alone. We, therefore, conclude that the maximum entropy approach is effective in fine-tuning the force field to better characterize both protein structure and conformational fluctuation.
Date issued
2019-02Department
Massachusetts Institute of Technology. Department of ChemistryJournal
Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Citation
Latham, Andrew P., and Bin Zhang. "Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data." Journal of Physical Chemistry B 123, 5 (February 2019): 957-1214 doi 10.1021/ACS.JPCB.8B10336 ©2019 Author(s)
Version: Author's final manuscript
ISSN
1520-6106